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author | Norbert Preining <norbert@preining.info> | 2019-09-02 13:46:59 +0900 |
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committer | Norbert Preining <norbert@preining.info> | 2019-09-02 13:46:59 +0900 |
commit | e0c6872cf40896c7be36b11dcc744620f10adf1d (patch) | |
tree | 60335e10d2f4354b0674ec22d7b53f0f8abee672 /macros/latex/contrib/texshade |
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-rw-r--r-- | macros/latex/contrib/texshade/texshade.dtx | 24180 | ||||
-rw-r--r-- | macros/latex/contrib/texshade/texshade.ins | 73 | ||||
-rw-r--r-- | macros/latex/contrib/texshade/texshade.pdf | bin | 0 -> 625524 bytes | |||
-rw-r--r-- | macros/latex/contrib/texshade/tsfaq.pdf | bin | 0 -> 77546 bytes | |||
-rw-r--r-- | macros/latex/contrib/texshade/tsfaq.tex | 432 |
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diff --git a/macros/latex/contrib/texshade/README b/macros/latex/contrib/texshade/README new file mode 100644 index 0000000000..71e52fa0c2 --- /dev/null +++ b/macros/latex/contrib/texshade/README @@ -0,0 +1,153 @@ + TeXshade v1.25 + >> + >> A LaTeX package for setting nucleotide and peptide alignments, + >> fingerprints, as well as sequence and subfamily logos. + >> + >> Setting alignments of nucleotides and peptides for publication + >> or presentation purposes is usually a time consuming two-step + >> process. First, a scientific software is used for the calcula- + >> tion of the alignment. This is done in a few minutes. Then, in + >> order to highlight special sequence relationships and to label + >> positions and regions of interest a second software with high + >> output capability is needed. + >> + >> Manipulating sequence alignments with standard word processing + >> or graphics programs takes its time--often several hours--and + >> simple layout changes such as re-breaking lines, say from 50 + >> to 40 residues per line, elongate the working time considerab- + >> ly. + >> + >> TeXshade is an alignment shading software completely written + >> in TeX/LaTeX which can process multiple sequence alignments in + >> the MSF, ALN and FASTA file format. It provides in addition to + >> common shading algorithms special shading modes featuring + >> functional aspects, e.g. charge or hydropathy, and a plenitude + >> of commands for handling shading colors, text styles, labels, + >> legends and even allows the user to define completely new sha- + >> ding modes. TeXshade combines highest flexibility and the + >> habitual TeX output quality--with reasonable time expenditure. + >> + Copyright (C) 1999 - 2018 Eric Beitz + + + + FOR THE HASTY READER + + Be sure to use a docstrip version 2.4 or later! + Otherwise you will not be able to tex the documentation! + + + +1 - FILES DISTRIBUTED WITH THIS PACKAGE + + texshade.ins Batch file, run through LaTeX + texshade.dtx Docstrip archive, run twice through LaTeX + tsfaq.tex Frequently asked questions about TeXshade + texshade.txt This file + + + (a) FILES THAT WILL BE GENERATED FROM TEXSHADE.INS + + texshade.sty LaTeX package + texshade.def Standard definitions + AQPDNA.MSF Example nucleotide alignment file (MSF-format) + AQPpro.MSF Example protein alignment file (MSF-format) + AQP_TC.asc Example T-Coffee shading file + AQP2spec.ALN Example protein alignment file (ALN-format) + AQP1.top Example topology data file generated from PHD + AQP1.phd Example PHD secondary structure file + AQP1_HMM.sgl Example HMMTOP topology data (single line format) + AQP1_HMM.ext Example HMMTOP topology data (extended format) + Standard.cod Standard genetic code definitions + Ciliate.cod Ciliate macronuclear genetic code definitions + + + (b) FILE THAT WILL BE GENERATED FROM TEXSHADE.DTX + + texshade.dvi Package documentation + + + +2 - INSTALLATION + + (a) EXTRACTING FILES FROM THE DOCSTRIP ARCHIVE + + All files provided by TeXshade are compacted to one single file, + namely "texshade.dtx". To extract the archive run "texshade.ins" + - which contains the corresponding instructions - through LaTeX. + A list of the generated files is given above, see 1(a). + + AGAIN: Be sure to use a docstrip version 2.4 or later! Otherwise + you will not be able to tex the documentation! + + + (b) THE DOCUMENTATION + + The file "texshade.dtx" further contains the package documentation. + Therefore, run this file through LaTeX now. As you will recognize + two runs are needed to make proper references within the document. + + TeXshade needs lots of TeX's memory, so adjust your parameter set- + tings to make TeXshade feel comfortable. The documentation is a + good test for this. (If you encounter problems texing the doc, you + should tex and read section A of the FAQ-list (see d below) or + download an on-line version [PDF-, DVI-, or PostScript format] at + http://homepages.uni-tuebingen.de/beitz/) + + The resulting file "texshade.dvi" can be viewed and printed using a + DVI-viewer which is able to display embedded PostScript. Another + possibility is to run "texshade.dvi" through DVIPS, a DVI to Post- + Script converter, and finally view and print the converted file + which will be most likely "texshade.ps" with GhostView from the GNU + free software foundation. + + TeXshade makes use of "color.sty" by David Carlisle. This style is + part of the Standard LaTeX Graphics Bundle. Usually, the bundle is + present in a comprehensive LaTeX installation. If this is not the + case for your system you have to download the package from a CTAN- + server, e.g. ftp.dante.de. + + + (c) MAKING TEXSHADE.STY AVAILABLE FOR YOUR LATEX SYSTEM + + In the final step, copy at least the files "texshade.sty" and + "ciliate.cod" to a directory searched by TeX in order to make these + files available for all documents you'll produce in the future. The + remaining files are example files which are not necessary for run- + ning TeXshade. Nevertheless, it would be a good idea to keep all + the files together. + + + (d) THE FAQ LIST + + The FAQ list contains frequently asked questions about the package. + Use it as a helpful source for solving problems with TeXshade. You + get the list by simply running "tsfaq.tex" through LaTeX once. + + + +3 - CONTACT + + E-Mail: ebeitz@pharmazie.uni-kiel.de + WWW: http://www.pharmazie.uni-kiel.de/chem/ + (On-line documentation and updates) + Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry, + Gutenbergstrasse 76, D-24118 Kiel (Germany) + + + +4 - AGREEMENT + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + In order to receive a copy of the GNU General Public License write to + the Free Software Foundation, Inc., 59 Temple Place - Suite 330, + Boston, MA 02111-1307, USA. diff --git a/macros/latex/contrib/texshade/texshade.dtx b/macros/latex/contrib/texshade/texshade.dtx new file mode 100644 index 0000000000..adf4e661c3 --- /dev/null +++ b/macros/latex/contrib/texshade/texshade.dtx @@ -0,0 +1,24180 @@ +% \iffalse +% +% texshade.dtx +% Docstrip archive, to extract documentation run twice through +% LaTeX. +% To successfully extract the documentation it is necessary to +% first run the file `texshade.ins' through LaTeX. This produces +% the needed style file `texshade.sty' and the parameter file +% `texshade.def' as well as several example files. See the file +% `README.txt' for further information! +% +% +% Copyright (C) 1999-2018 Eric Beitz +% See the file texshade.txt +% +% \fi +% +% \changes{1.0}{1999-5-12}{First release} +% \changes{1.1}{1999-5-26}{% +% Corrections: `emphregion' is not extending to the next +% alignment any more; +% `namecolor' & `numbercolor' are now correctly +% reordered; +% sequence gaps at the beginning or the end are +% now treated correctly, i.e. no symbols are shown. +% Introduction: `seqlength' +% `gapcolors' +% `rulersteps' +% `hideresidues' +% `showresidues' +% `fingerprint'.} +% \changes{1.2}{1999-6-12}{% +% Corrections: functional shading error in funcgroup no. 8. +% Introduction: `includeDSSP' +% `includeSTRIDE' +% `includePHDsec' +% `includePHDtopo' +% `appearance' +% `numcount' +% `alphacount' +% `Alphacount' +% `showonDSSP' +% `hideonDSSP' +% `showonSTRIDE' +% `hideonSTRIDE' +% `showonPHDsec' +% `hideonPHDsec' +% `showonPHDtopo' +% `hideonPHDtopo'.} +% \changes{1.2a}{1999-6-24}{% +% Corrections: `namecolor' & `numbercolor' are now really +% correctly reordered; +% in sequence names ( and ) are now allowed; +% option `case' in `funcshadingstyle' works now.} +% \changes{1.3}{2000-3-3}{% +% Corrections: features in the ttop row do not produce line +% scrambling any more; +% `language' replaced by `germanlanguage' +% and `englishlanguage' due to +% incompatibilities with babel; +% incompatibility with amsmath's text command fixed. +% Introduction: new feature option `translate' +% `codon' +% `geneticcode' +% `backtranslabel' +% `backtranstext' +% `romancount' +% `Romancount' +% TeXtopo compatibility.} +% \changes{1.3a}{2000-7-28}{% +% Introduction: `showleadinggaps' +% `hideleadinggaps' to hide or show gap symbols +% before the actual seq start.} +% \changes{1.3b}{2000-7-30}{% +% Corrections: `showleadinggaps' +% `hideleadinggaps' were extended to `ending' gaps; +% sequence names input routine now accepts special +% characters.} +% +% \changes{1.4}{2000-9-12}{% +% Introduction: `movelegend' allows one to move the legend; +% series of sequence numbers, e.g. in `orderseqs', +% can now be written with a dash, e.g. {1-3,6-4,7} instead +% of {1,2,3,6,5,4,7}.} +% +% \changes{1.4a}{2000-10-3}{Documentation and FAQ additions} +% +% \changes{1.5}{2001-02-22}{% +% Corrections: `X's in the alignment lead to a run-time error; +% Introduction: `ttopspace' +% `topspace' +% `bottomspace' +% `bbottomspace' for controlling vertical space +% between feature lines. +% `showcaption' for adding a caption to the alignment. +% the sequence lengths are now stored in the .aux +% in order to have correct gap breaks after the seqs.} +% +% \changes{1.5a}{2001-03-08}{% +% Corrections: Eckhart Guth\"orlein noticed a sorting problem +% when in addition some sequences where `killed' and +% the consensus was set to a particular sequence. +% This update fixes this problem.} +% +% \changes{1.6}{2002-03-26}{% +% Corrections: There is no restriction to `dvips' anymore. One +% can add an option to the \usepackage{texshade} +% call which is passed to color.sty, e.g. `dvipdf'; +% `noblockskip' led to over-printing of lines; +% `namecolor' and `numbercolor' did not support +% sequence lists - fixed (thanks to Denys Bashtovyy). +% Introduction: The FASTA file format is now supported; +% references to sequences can be made by name in +% addition to number; +% sequences can be refered to by their name in +% addition to their number in the input file +% (suggested by Christoph Gille); +% `flexblockspace' optimizes the space between +% sequence blocks to be minimal (is +% default as before); +% `fixblockspace' leads to an equal separation of +% sequence blocks independent of +% feature lines; +% `firstcolumnDSSP' lets you choose the first numbering +% column in DSSP input files and +% `secondcolumnDSSP' the second column.} +% +% \changes{1.7}{2004-01-05}{% +% Corrections: Several bugs were fixed. +% In gaps the wrong character was plotted in `donotshade' +% mode. Gaps were colored incorrectly when a single +% sequence was set as consensus. (thanks to Jeferson J. +% Arenzon). Another `donotshade' problem was solved +% which led to a halt of the LaTeX run (thanks go to +% Naomi Siew). The gap and match labels in diverse +% mode were switched (`-' in gaps; `.' at matching +% positions) in order to follow convention. +% Introduction: Spanish labels (contributed by Mikel Egana Aranguren); +% New feature label `helix'.} +% +% \changes{1.8}{2004-08-26}{% +% Corrections: Minor bugs were fixed. +% Introduction: Definition of "light" versions of all colors; +% Definition of three color ramps: +% Red-Blue, Green-Red and Cold-Hot; +% New feature labels `bar' and `color'.} +% +% \changes{1.9}{2005-02-08}{% +% Corrections: Fixed TeXtopo incompatibility introduced with v1.8. +% (Thanks to Meike Schmedt) +% Introduction: Implementation of HMMTOP topology prediction. +% `includeHMMTOP' +% `showonHMMTOP' +% `hideonHMMTOP' +% new `appearance' option {HMMTOP} with {internal} +% {external} +% {TM}; +% new arrow look with scalable line thickness; +% new arrow option `ball'; +% `frameblock' colored frame around sequence block; +% `shortcaption' allows one to define short caption +% versions for the List of Figures.} +% +% \changes{1.10}{2005-03-29}{% +% Corrections: Sped up drawing of color scales and bar graphs by +% by more than 10fold! +% (Thanks, Christoph Gille, for asking for it) +% Introduction: Definition of even lighter versions of all colors; +% implementation of a new labeling mode 'tint': +% `tintregion' +% `tintblock' +% `tintdefault'; +% new `feature' option {restriction} for putting a +% triangle label pointing between two residues; +% data files for color scales and bar graphs can +% now contain 'NaN' (not a number) values +% (Also requested by Christoph Gille.)} +% +% \changes{1.11}{2005-04-13}{% +% Corrections: Frames were drawn with the wrong height when +% separation lines were used. Fixed. +% Spacing between bar graph feature line and +% sequence block was wrong after `bargraphstretch'. +% Introduction: Additional optional parameter for feature rule +% thickness; +% additional optional parameters for feature box +% frame color and frame thickness; +% definition of three more color scales: +% {RedBlue}, {RedGreen}, and {HotCold}; +% plotting of amino acid features as bar graphs +% or color scales: +% `hydrophobicity' +% `molweight' +% `charge'; +% plotting of protein sequence conservation as +% bar graph or color scale: +% `conservation'; +% separate command for stretching color scales: +% `colorscalestretch'; +% color scales on consensus sequence according +% to sequence conservation. +% } +% +% \changes{1.12}{2005-09-20}{% +% Corrections: Combination of 'setends' with regional labeling +% using 'shaderegion', 'frameblock', 'emphregion' +% or 'tintregion' produced incorrect output +% (thanks to Chris Page). Fixed. +% Introduction: Optional colors for `showconsensus' foreground +% and background. +% } +% +% \changes{1.13}{2006-02-23}{% +% Corrections: Helix symbols in feature lines were not drawn +% correctly if the standard Computer Modern Font +% was changed to another one, e.g. Palatino (thanks +% to Markus Heller). Fixed. +% Unintended gaps occurred due to numbers at the +% end of lines in Clustal W alignment files. Fixed. +% Frames were too tall when sequences were hidden +% or killed. Fixed. +% The limitations in the number of sequences per +% alignment have finally been overcome by a more +% restrictive use of counter variables. +% Introduction: The numbering can now be displayed on both sides +% of the alignment with the optional parameter +% {leftright}; +% TeXshade tries to guess the sequence type (protein +% or nucleotide) if not defined by the user; +% Implementation of sequence logos: +% `showsequencelogo', `hidesequencelogo', +% `namesequencelogo', `logostretch', +% `logocolor', `clearlogocolors', +% `showlogoscale', `hidelogoscale' +% `dofrequencycorrection', `undofrequencycorrection'; +% The ruler numbering can now be rotated with +% `rotateruler' and back with `unrotateruler', +% this way every position can be numbered which is +% often wanted when e.g. sequence logos are plotted; +% the font family (sf, rm, tt) can be set for the +% ruler, e.g. `rulertt' or `setfamily{ruler}{tt}'; +% `hideseqs' and `showseqs' in order to hide/show +% all sequences, esp. useful with sequence logos; +% `allowzero' and `disallowzero' - use (or do not +% use) the number `0' in the sequence numbering as +% sometimes wanted in sequence logos; +% Implementation of a new way to visualize residues +% which are characteristic for protein subfamilies, +% i.e. subfamily logos: +% `showsubfamilylogo', `hidesubfamilylogo', +% `namesubfamilylogo', +% `setsubfamily', +% `shownegatives', `hidenegatives'. +% } +% +% \changes{1.14}{2006-05-11}{% +% Introduction: `showrelevance', `hiderelevance', +% `relevance': commands to set a bit-value above +% which subfamily deviations are considered relevant +% and to label such positions in the subfamily logo. +% } +% +% \changes{1.15}{2006-06-27}{% +% Correction: Logos can now be plotted with pdflatex; pstricks is +% not needed anymore. +% } +% +% \changes{1.16}{2007-02-18}{% +% Corrections: TeXshade crashed when doing conservation +% calculations with sequences containing untypical +% residues symbols, such as X. Fixed. +% Shading of the reference sequence in diverse mode +% is now achieved with `conservedresidues' and +% `allmatchresidues' instead of `nomatchresidues'. +% Introduction: `exportconsensus' produces a pymol script for +% coloring according to the TeXshade conservation +% calculation; +% `namerulerpos' allows one to change labels of +% the ruler individually; +% `hideblock' allows one to hide parts of the +% alignment (still in experimental stage!). +% New home: TeXshade, TeXtopo, and BioTeX have a new home: +% `www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html' +% } +% +% \changes{1.17}{2007-06-19}{% +% Corrections: . +% Introduction: `allmatchspecial' now accepts an optional threshold +% percentage allowing one to set two levels off +% conservation; +% the same effect can be achieved by using a +% number as an optional parameter in +% `shadingmode', +% or by setting an additional parameter in +% `threshold'; +% names can be displayed left or right of feature +% lines using: +% `showfeaturename', `showfeaturestylename'; +% `hidefeaturename', `hidefeaturestylename'; +% `hidefeaturenames', `hidefeaturestylenames'; +% the color of such names can be changed with +% `featurenamescolor' +% `featurestylenamescolor' +% font styles can be set as usual, e.g. +% `setsize{featurenames}{large}' or +% `featurestylenamesrm' etc. +% } +% +% +% \changes{1.18}{2008-04-15}{% +% Corrections: bug fixes (featurenames, ordering, numbering). +% Introduction: T-Coffee shading in alignment, consensus and +% feature color scales and bar graphs +% `shadingmode[ASCII-file]{T-Coffee}' +% `includeTCoffee'; +% two more feature lines on top and at bottom: +% `ttttop', `tttop', `bbbottom', and `bbbbottom'; +% fusion of the `startnumber' and `setends' commands +% via optional parameters. +% } +% +% \changes{1.19}{2009-03-09}{% +% Corrections: horizontal scaling of logo characters with `charstretch'; +% further bug fixes. +% Introduction: selection of residues depending on PDB file coordinates; +% works with `feature', `shaderegion', `shadeblock', +% `tintregion', `tintblock', `emphregion', +% `emphblock', `frameblock'; +% 3D selection possible around a point, along a line, or +% within a plane; +% list of selected residues printable with `printPDBlist', +% or viewable during the TeX run with `messagePDBlist'; +% show only selected residues in alignment with `setdomain', +% `domaingaprule' sets thickness of a domain separator rule, +% `domaingapcolors' sets fg/bg colors for the separator rule, +% these commands replace the unstable `hideblock' command. +% } +% +% \changes{1.19a}{2009-06-11}{% +% Corrections: gaps are now treated correctly when setting domains. +% Introduction: a special character can be displayed for stop-positions +% in protein sequences indicated by `*' in the input file; +% the stop character can be set using `stopchar'. +% } +% +% \changes{1.20}{2009-10-05}{% +% Corrections: landscape mode works now correctly; +% annoying `Overfull \hbox ...' signals appearing after +% `residuesperline*' commands are ignored; +% domains work now with frequency corrected sequence logos. +% Introduction: new commands for setting residue weight tables: +% `weighttable' (with parameters: identity, structural, +% PAM250, PAM100, and BLOSUM62), +% `gappenalty', and `setweight'; +% similarity/identity percentage tables can be printed with +% `similaritytable' and values for specific sequence pairs +% can be utilized with `percentsimilarity{seq1}{seq2}' and +% `percentidentity{seq1}{seq2}'. +% } +% +% \changes{1.20a}{2009-11-30}{% +% Corrections: identity/similarity tables work now without the need to +% set a conservation plot in the feature line. +% } +% +% \changes{1.21}{2010-03-01}{% +% Corrections: `setdomain' ignored a changed `startnumber', corrected; +% further bug fixes. +% Introduction: in several commands sequence motifs can be given instead +% of numeral sequence stretch definitions; +% new type of sequence emphasis by lowercase characters: +% `lowerregion' and `lowerblock'. +% } +% +% \changes{1.22}{2010-10-11}{% +% Corrections: minor bug fixes. +% Introduction: `defshadingcolors' defines and names sets of shading +% colors for later re-use within the alignment; +% `changeshadingcolors' allows one to use different sets +% of shading colors in different sequence blocks. +% } +% +% \changes{1.23}{2011-05-13}{% +% Introduction: `hideallmatchpositions' removes all positions in the +% alignment where all residues match, i.e. a handy feature for +% diverse mode to condense the output to the relevant sites. +% } +% +% \changes{1.24}{2011-12-01}{% +% Introduction: `rulerspace' allows one to adjust the space between the +% ruler and the top or bottom sequence row; +% the textsize of the ruler numbering can now be set; +% Postscript color samples are shown in the manual. +% } +% +% \changes{1.25}{2011-12-01}{% +% Corrections: aligments with many seqs produced wrong calculation +% of threshold shading, corrected. +% Introduction: new feature style |S-S| for disulfide bridges; +% hooks in top feature lines can be drawn down to alignment. +% } +% +% +% +% +% \CharacterTable +% {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z +% Lower-case \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z +% Digits \0\1\2\3\4\5\6\7\8\9 +% Exclamation \! Double quote \" Hash (number) \# +% Dollar \$ Percent \% Ampersand \& +% Acute accent \' Left paren \( Right paren \) +% Asterisk \* Plus \+ Comma \, +% Minus \- Point \. Solidus \/ +% Colon \: Semicolon \; Less than \< +% Equals \= Greater than \> Question mark \? +% Commercial at \@ Left bracket \[ Backslash \\ +% Right bracket \] Circumflex \^ Underscore \_ +% Grave accent \` Left brace \{ Vertical bar \| +% Right brace \} Tilde \~} +% +% +% \newsavebox{\mybox} +% \newenvironment{fmpage}[1][0.975\textwidth]{% +% \begin{lrbox}{\mybox}\begin{minipage}{#1}} +% {\end{minipage}\end{lrbox}\fbox{\usebox{\mybox}}} +% +% \parindent0mm +% +% +% \title{The \TeXshade{} package\footnote{Please cite: Eric Beitz (2000), +% \TeX{}shade: +% shading and labeling multiple sequence alignments using \LaTeXe. +% \textit{Bioinformatics}: \textbf{16}, 135--139.}\\[2mm] \large +% Typesetting \\ nucleotide and peptide alignments} +% \author{Eric Beitz\footnote{University of Kiel, +% Pharmaceutical Chemistry, Gutenbergstrasse 8, +% D-24118 Kiel, Germany; +% send electronic mail to \texttt{ebeitz@pharmazie.uni-kiel.de}; +% for further information, updates and on-line documentation +% see my homepage at +% \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }} +% \date{\small v1.25; 2018/01/17\\[2pt]} +% \maketitle +% \begin{abstract} +% Setting alignments of nucleotides and peptides for publication +% or presentation purposes is usually a time consuming two-step process. +% First, a scientific software is used for the calculation of the +% alignment. This +% is done in a few minutes. Then, in order to highlight special sequence +% relationships and to label positions and regions of interest a +% second software with high quality output capability is needed. +% Manipulating sequence alignments with standard word processing +% or graphics programs takes its time---often several hours---and +% simple layout changes such as +% re-breaking lines, say from 50 to 40 residues per line, +% elongate the working time considerably. +% +% \TeXshade{} is an alignment shading software +% written in \TeX/\LaTeX{} which can process +% multiple sequence alignments in the MSF, ALN +% and FASTA file format. +% It provides in addition to common shading algorithms special +% shading modes featuring functional aspects, e.\,g.\ charge or +% hydropathy, and a plenitude of commands for handling +% shading colors, text styles, labels, legends and even allows +% the user to define completely new shading modes. \TeXshade{} +% combines highest flexibility and the habitual \TeX{} output +% quality---with reasonable time expenditure. +% +% \end{abstract} +% +% \thispagestyle{empty} +% +% \tableofcontents +% \newpage +% +% \section{Package Overview} +% +% \label{over} +% +% After |texshade.ins| is run through \TeX{} the following files +% should appear in the directory: +% +% \begin{tabbing} +% \quad|texshade.sty|\quad\= the style file with all \TeXshade{} +% commands\\ +% \quad|texshade.def|\> an example parameter file with the +% standard \\ +% \> parameter settings\\ +% \quad|AQPDNA.MSF| \> an example nucleotide alignment +% (MSF-format)\\ +% \quad|AQPpro.MSF| \> an example protein alignment +% (MSF-format)\\ +% \quad|AQP_TC.asc| \> an example T-Coffee shading file +% (|score_ascii|-format)\\ +% \quad|AQP2spec.ALN|\> a further protein alignment +% (minimal ALN-file)\\ +% \quad|AQP1.phd|\> secondary structure information +% (PHD-format)\\ +% \quad|AQP1.top|\> topology data extracted +% from |AQP1.phd|\\ +% \quad|AQP1_HMM.sgl|\> topology information (single line, +% HMMTOP-format)\\ +% \quad|AQP1_HMM.ext|\> topology information (extended, +% HMMTOP-format)\\ +% \quad|standard.cod|\> standard genetic code definitions\\ +% \quad|ciliate.cod|\> ciliate macronuclear genetic code\\ +% \end{tabbing} +% The alignment file examples as well as the topology data file are +% needed for \TeX{}ing this documentation +% and can serve as illustrations for the MSF and ALN +% file format. +% +% The following subsections give an overview on the capabilities of +% the \TeXshade{} package. All commands are described in detail +% later on. +% +% +% \subsection{Version History} +% +% \textbf{v1.25 2018/01/17} +% \medskip +% +% \emph{Corrections}: Aligments with many seqs produced wrong calculation +% of threshold shading,\footnote{Noted by Kathryn Parker.} corrected; minor bug fixes. +% +% \emph{Introduction}: A new feature style |S-S| for disulfide bridges is +% implemented; hooks in top feature lines can be drawn down to alignment. +% \medskip +% +% \textbf{v1.24 2011/12/01} +% \medskip +% +% \emph{Introductions:} +% The space between the ruler and the top or bottom sequence row +% can now be adjusted using |\rulerspace| and the textsize of the +% ruler numbering can be set with |\setsize| or |\rulerLarge| etc. +% Postscript color samples are shown in the manual next to the +% color names list. +% \medskip +% +% \textbf{v1.23 2011/05/13} +% \medskip +% +% \emph{Introductions:} +% In diverse mode sequence positions where all residues match do not +% contain much information. A new command, +% |\hideallmatchpositions|,\footnote{Requested by Matt Russell.} +% will remove all such positions from the alignment and hence condense +% the output considerably. +% \medskip +% +% \textbf{v1.22 2010/10/11} +% \medskip +% +% \emph{Introductions:} +% Sets of shading colors can be defined and named using +% |\defshadingcolors| (p.\ \pageref{Ldefshadingcolors}) and different +% sets of colors can be selected for different sequence blocks by +% |\changeshadingcolors| (\ref{Lchangeshadingcolors}). +% \medskip +% +% +% \textbf{v1.21 2010/03/01} +% \medskip +% +% \emph{Corrections:} |\setdomain| now recognizes a changed |\startnumber|. +% +% \emph{Introductions:} +% (a) Sequence motifs (\ref{Lshaderegion}) can be given as a selection pattern +% in sequence stretch labeling commands, such as |\shaderegion|, +% |\emphregion| or |\frameblock|, instead of numeral stretch definitions. +% +% (b) A new type of sequence emphasis by lowercase letters was implemented: +% |\lowerregion| and |\lowerblock| (\ref{Llowerregion}). +% \medskip +% +% \textbf{v1.20a 2009/11/30} +% \medskip +% +% \emph{Corrections:} Identity/similarity tables +% work now without having to set a conservation plot in the feature +% line. +% \medskip +% +% +% \textbf{v1.20 2009/10/05} +% \medskip +% +% \emph{Corrections:} Landscape mode works now correctly. +% Annoying |Overfull \hbox ...| signals appearing after +% |\residuesperline*| commands are ignored; +% domains work now with frequency corrected sequence logos. +% +% \emph{Introductions:} +% (a) New commands for setting residue weight tables were introduced +% |\weighttable| (with parameters: |identity|, |structural|, +% |PAM250|, |PAM100|, and |BLOSUM62|), +% |\gappenalty|, and |\setweight|. +% (b) Similarity/identity percentage tables can be printed with +% |\similaritytable|\footnote{Asked for by Giovanni M.\ Lesa.} and +% values for specific sequence pairs can be utilized with +% |\percentsimilarity{|\meta{seqref1}|}{|\meta{seqref2}|}| and +% |\percentidentity{|\meta{seqref1}|}{|\meta{seqref2}|}|. +% \medskip +% +% \textbf{v1.19a 2009/06/11} +% \medskip +% +% \emph{Correction:} Gaps are now treated correctly when setting +% domains. +% +% \emph{Introduction:} +% Stop-positions in protein sequences (|*| in the input file) can be +% indicated by a special character (|\stopchar|) in the alignment +% output.\footnote{Suggestion by Yun He.} +% \medskip +% +% +% \textbf{v1.19 2009/03/09} +% \medskip +% +% \emph{Correction:} Logo characters are now horizontally +% scalable using |\charstretch|. Minor bugs were fixed. +% +% \emph{Introduction:} +% (a) Selection of residue positions was enhanced (\ref{Lshaderegion}) +% \TeXshade{} can +% now select residues based on their 3D coordinates provided in a +% PDB structure file. 3D selection can be due to a certain distance +% around a point, along a line, or above and below a plane. It +% works with |\feature|, |\shaderegion|, |\shadeblock|, |\tintregion|, +% |\tintblock|, |\emphregion|, |\emphblock|, |\frameblock|. +% (b) The list of selected residues is printable with |\printPDBlist| or +% viewable during the \TeX{} run with |\messagePDBlist|. +% (c) |\hideblock| and related commands were replaced by |\setdomain| +% (\ref{Lsetdomain}). +% This command will display only selected residues in the alignment. +% Thickness and colors of a domain separator rule can be set using +% |\domaingaprule| and |\domaingapcolors|. +% \bigskip +% +% \textbf{v1.18 2008/04/15} +% \medskip +% +% \emph{Correction:} several bug fixed concerning featurename +% display, sequence ordering and numbering. +% +% \emph{Introduction:} +% (a) T-Coffee shading information can be loaded and put on the +% alignment.\footnote{Suggestion by Florian Mertes.} +% The conservation data can also be displayed in the +% consensus as well as feature color scales and bar plots. +% (b) Two more feature lines were added on the top and at the +% bottom (|ttttop|, |tttop|, |bbbottom|, |bbbbottom|). +% (c) The |startnumber| and |setends| commands have been fused; +% either command can set both, a new start number as well as +% end definitions of the sequence section to be displayed. +% \bigskip +% +% \textbf{v1.17 2007/06/19} +% \medskip +% +% \emph{Introduction:}\footnote{Asked for by Marat Kazanov.} +% (a) A second threshold percentage was introduced in order to label +% two levels of conservation in `identical' and `similar' mode. This is +% achieved by setting an optional parameter in |\threshold| or in +% |\allmatchspecial|, or by using a number as an optional parameter in +% |\shadingmode|. (b) The feature lines can be additionally labeled with +% a name left or right of the feature. This is handled using +% |\showfeaturename|, |\showfeaturestylename|, +% |\hidefeaturename|, |\hidefeaturestylename|, +% |\hidefeaturenames|, |\hidefeaturestylenames|. +% The color of such names can be changed with +% |\featurenamecolor|, |\featurestylenamecolor|, +% |\featurenamescolor|, |\featurestylenamescolor|, +% Font styles in feature names can be set as usual, e.g. +% |\setsize{featurenames}{large}| or +% |\featurestylenamesrm|. +% \bigskip +% +% +% \textbf{v1.16 2007/02/18} +% \medskip +% +% \emph{Correction:} \TeXshade{} crashed when calculating conservation +% using sequences with untypical residue characters, such as "X". +% Fixed. The reference sequence in diverse mode can now be shaded with +% |\conservedresidues| and, if active, |\allmatchresidues|.\footnote{For this +% and suggesting |namerulerpos| credit to Marco Pasi.} +% +% \emph{Introduction:}\footnote{Both extensions were suggested by Phillip Hahn.} +% (a) A command was introduced, i.e. |\exportconsensus| +% which produces a pymol script file for coloring a 3D model according to +% \TeXshade's conservation calculation. (b) With |namerulerpos| labels of the +% ruler can be exchanged by a string. (c) Various parts of the alignment +% can now be hidden by |\hideblock|. +% +% \emph{New home:} \TeXshade, \TeXtopo, and \BioTeX{} have a new home: +% |www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html|. +% \bigskip +% +% +% \textbf{v1.15 2006/06/27} +% \medskip +% +% \emph{Correction:} Sequence and subfamily logos can now be plotted +% with pdflatex; pstricks is not needed anymore. +% \bigskip +% +% +% \textbf{v1.14 2006/05/11} +% \medskip +% +% \emph{Introduction:} In order to better recognize relevant positions +% in a subfamily logo [14], a bit-value can now be set by |\relevance| +% above which a deviation is considered relevant. Such positions +% can be labeled with a symbol by |\showrelevance| and hidden +% by |\hiderelevance|. +% \bigskip +% +% +% \textbf{v1.13 2006/02/23} +% \medskip +% +% \emph{Corrections:} Helix symbols in feature lines were not drawn +% correctly if the standard Computer Modern Font was changed to +% another one, e.g. Palatino.\footnote{Thanks to Markus Heller} +% Fixed. Unintended gaps occurred due to numbers at the +% end of lines in Clustal W alignment files. Fixed. The limitations +% in the number of sequences per alignment have finally been overcome +% by a more restrictive use of counter variables. +% +% \emph{Introductions:} (a) The numbering can now be displayed---in +% addition to left or right---on both sides of the alignment with +% the optional parameter |{leftright}| in the |\shownumbering| +% command (p.\pageref{Lshownumbering}). (b) TeXshade tries to guess +% the sequence type, i.\,e.\ protein or nucleotide, if not defined +% by the user. (c) Plotting of sequence logos has been implemented +% (p.\pageref{Lshowsequencelogo}). +% Logos can be shown in addition to or together with the consensus, +% or alone without any alignment sequences. (d) The ruler numbering +% can be rotated in order to make labeling of every position possible. +% (e) A new way to visualize subfamily characteristics has been +% implemented, i.e. subfamily logos (p.\pageref{Lshowsubfamilylogo}) [14]. +% \bigskip +% +% +% \textbf{v1.12 2005/09/20} +% \medskip +% +% \emph{Corrections:} When regional labeling with |\shaderegion|, +% |\emphregion|, |\tintregion|, or |\frameblock| was combined with +% |\setends| incorrect output was produced lacking the +% labeling.\footnote{Discovered by Chris Page.} Other minor fixes. +% +% \emph{Introductions:} An additional optional parameter for setting +% consensus colors was implemented in the |\showconsensus| command +% (p.\pageref{Lshowconsensus}). This even allows one to use color +% scales illustrating sequence conservation in the consensus line. +% \bigskip +% +% \textbf{v1.11 2005/04/13} +% \medskip +% +% \emph{Corrections:} Bounding boxes with |\frameblock| had a wrong +% height when |\separationline|s were used. Other minor fixes. +% +% \emph{Introductions:} (a) An additional parameter for setting +% individual bar and arrow thicknesses in feature lines has been +% introduced. (b) Additional parameters for setting the frame color +% and thickness of boxes in feature lines have been implemented. (c) +% Three more color scales have been defined: |RedBlue|, |RedGreen|, +% and |HotCold|. (d) Plotting of amino acid features (|hydrophobicity|, +% |molweight|, |charge|) as bar graphs or color scales. (e) Plotting +% of protein sequence |conservation| as bar graph or color +% scale\footnote{Ahmad Mirza asked for (e) and (f), great suggestion!}. +% (f) Color scales can be used for shading the consensus sequence +% according to protein sequence conservation. +% (g) Separate command for stretching color scales |\colorscalestretch|. +% \bigskip +% +% \textbf{v1.10 2005/03/29} +% \medskip +% +% \emph{Corrections:} Plotting of color scales and bar graphs has +% been sped up by more than a factor of 10.\footnote{This and (d) +% I owe again to Christoph Gille.} +% +% \emph{Introductions:} (a) More colors have been introduced, i.e. +% even lighter versions of the existing PostScript colors +% `LightLight' plus color name and `LightLightLight' plus color +% name. (b) Sequence stretches and blocks can be tinted for +% labeling purposes |\tintreqion|, |\tintblock| and |\tintdefault|. +% (c) A new feature label style |{restriction}| has been introduced. +% (d) Java-typical `NaN' values are now allowed in data files for +% bar graphs and color scales. +% \bigskip +% +% +% +% \textbf{v1.9 2005/02/08} +% \medskip +% +% \emph{Corrections:} \TeXshade{} version 1.8 introduced an +% incompatibility with \TeXtopo{}. This problem was identified +% by Meike Schmedt and has been fixed. +% +% \emph{Introductions:} (a) A short version of the figure caption +% can now be defined for display in the list of figures\footnote{% +% Meike, here you go \dots} |\shortcaption{|\meta{text}|}|. (b) A +% colored frame can be drawn around a sequence block for labeling +% purposes with the command |\frameblock|.\footnote{Alan Robinson, +% this is for you.} (c) A new look for feature arrows has been +% implemented with scalable line thickness and a new end style +% `ball'. (d) HMMTOP topology predictions can +% now be included for plotting feature lines with information on +% the location of the transmembrane domains.\footnote{Implemented +% after a request by Steffen Moeller.} +% \bigskip +% +% \textbf{v1.8 2004/08/26} +% \medskip +% +% \emph{Corrections:} Only minor bugs were fixed. +% +% \emph{Introductions:} (a) More colors have been designed, i.e. +% `light' versions of the existing PostScript colors. (b) +% Three color ramps in 5\% steps have been introduced: +% i) Blue-Red, ii) Green-Red and iii) Cold-Hot. +% (c) Two new feature label styles |bar| and |color| have been +% introduced which allow one to display number +% values as bar graphs or color scales along the +% alignment\footnote{Inspired by Christoph Gille's {\tt STRAP}}. +% \bigskip +% +% +% \textbf{v1.7 2004/01/05} +% \medskip +% +% \emph{Corrections:} Several bugs were fixed. +% In gaps the wrong character was plotted in `donotshade' +% mode. Gaps were colored incorrectly when a single +% sequence was set as consensus. Another `donotshade' problem was +% solved which led to a halt of the LaTeX +% run\footnote{Thanks to Jeferson J.\ Arenzon and Naomi Siew}. +% Due to several requests, the gap and match labels in |diverse| +% mode were switched (`|-|' in gaps; `|.|' at matching +% positions) in order to follow convention. +% +% \emph{Introduction:} \TeXshade{} speaks spanish (|\spanishlanguage|). +% Necessary translations were contributed by Mikel Ega\~na Aranguren. +% A new feature label style |helix| has been introduced. +% \bigskip +% +% +% \textbf{v1.6 2002/03/26} +% \medskip +% +% \emph{Corrections:} The unnecessary restriction to the DVIPS +% driver for |color.sty| has been removed\footnote{As suggested by +% Eckhart Guth\"ohrlein.}. Any color.sty compatible +% driver option can be given with the |\usepackage{texshade}| call +% and is then passed to the |color| package. The `|\namecolor|' and +% `|\numbercolor|' commands do now support sequence +% lists.\footnote{Thanks to Denys Bashtovyy.} +% +% \emph{Introductions:} (a) The FASTA file format is supported by +% \TeXshade{} as alignment inputs. (b) Two commands set the space +% between sequence blocks either to be flexible (as so far) +% `|\flexblockspace|' or the be fixed `|\fixblockspace|'. (c) One +% can now refer to sequences by their name in addition to the number +% in the input file. (d) Using +% `|\firstcolumnDSSP|' and `|\secondcolumnDSSP|' one can choose +% which of the first to columns should refer to the sequence numbering +% (the second column remains default setting)\footnote{c and d were +% suggested by Christoph Gille.}. +% \bigskip +% +% \textbf{v1.5a 2001/03/08} +% \medskip +% +% \emph{Corrections:} `X's in the alignment file caused a run-time +% error. Fixed. +% +% \emph{Introductions:} (a) The vertical space between feature +% lines can be controlled by four new commands: |\ttopspace|, +% |\topspace|, |\bottomspace| and +% |\bbottomspace|\footnote{Suggested by Ulrike Folkers.}. (b) It is +% now easily possible to add a caption to the alignment with +% the |\showcaption| command. (c) \TeXshade{} stores the +% sequence lengths in the |.aux| file in order to have correct +% breaks of the gaps after the sequences. +% \bigskip +% +% +% \textbf{v1.4\&4a 2000/9/12 \& 2000/10/3} +% \medskip +% +% \emph{Introductions:} (a) The alignment legend can now be moved +% by the command `|\movelegend|'. (b) In commands with parameters +% that contain series of sequence numbers, e.\,g. |\orderseqs|, a +% dash can be used, e.\,g. |{1-3,6-4,7}| instead of +% |{1,2,3,6,5,4,7}|. +% \bigskip +% +% +% \textbf{v1.3a\&b 2000/7/28 \& 2000/7/30} +% \medskip +% +% \emph{Introductions:} (a) It is now possible to force \TeXshade{} to +% display gap symbols before and after the actual sequence +% by the commands `|\showleadinggaps|' and `|\hideleadinggaps|' +% (\ref{Lshowleadinggaps}). +% (b) The sequence names input routine is now more tolerant concerning +% special characters. +% \bigskip +% +% \textbf{v1.3 2000/3/3} +% \medskip +% +% \emph{Corrections:} Line scrambling occured when features where +% set in the |ttop| row without a feature in the |top| row. Fixed. +% The incompatible command `|\language|' with the |babel| package has been +% replaced by `|\germanlanguage|' and `|\englishlanguage|'\footnote% +% {Thanks to Eckhart Guth\"ohrlein.}. +% +% \emph{Introductions:} (a) Now, translations of sequence stretches +% are possible. Either nucleotide or amino acid sources can be +% translated. This is done by the new |{translate}| option for the +% feature command. (b) The codons are defined by the new command +% `|\codon|'. Complete codon sets can be loaded by `|\geneticcode|'. +% (c) Further, the size and style of the nucleotide triplets of +% backtranslations can be set by `|\backtranslabel|' and +% `|\backtranstext|'. (d) Two more feature counter styles were introduced: +% `|\Romancount|' and `|\romancount|'. (e) \TeXshade{} is now +% compatible with \TeXtopo, a new \TeX{} software +% for drawing and shading topology plots of membrane proteins. +% \bigskip +% +% \textbf{v1.2a 1999/6/24 (not released)} +% \medskip +% +% \emph{Minor corrections:} `|\namecolor|' and `|\numbercolor|' are +% now really correctly reordered. Brackets ( and ) are now allowed +% in sequence names. The option |{case}| in `|\funcshadingstyle|' +% works now. +% \bigskip +% +% +% \textbf{v1.2 1999/6/12} +% \medskip +% +% \emph{Corrections:} (a) Functional group definitions of more than +% seven groups produced an error when displaying group number +% eight. These residues where skipped in the alignment. Fixed. +% +% \emph{Introductions:} (a) Protein secondary structure files in the DSSP, +% STRIDE and PHD format can be included and displayed auto\-matically +% within the alignment by `|\includeDSSP|' (and similar commands for +% STRIDE, PHDsec and PHDtopo, \ref{structure}). +% (b) Which types of secondary structures are to be included or +% skipped in the alignment is chosen by `|\showonDSSP|' and +% `|\hideonDSSP|' (and respective commands for STRIDE, PHDsec and PHDtopo). +% (c) The appearance of the labels is defined by `|\appearance|'. +% (d) Internal counters for repeatedly occuring structure types +% can be activated by `|\numcount|', `|\alphacount|' and +% `|\Alphacount|'. All commands are described in \ref{structure}. +% \bigskip +% +% +% \textbf{v1.1 1999/5/26} +% \medskip +% +% \emph{Corrections:} (a) The activation of `|emphregion|' lead to +% an em\-pha\-sized following alignment. This has been +% corrected. (b) `|\namecolor|' and `|\numbercolor|' were not +% reordered with the command `|orderseqs|'. Fixed. (c) Sequence +% gaps at the beginning or the end of a sequence, i.\,e. before +% the first and after the last residue where labeled with the +% gap symbol. Now these positions are left blank. +% +% \emph{Introductions:} (a) In order to treat the preceeding and +% sequence following gaps correctly, \TeXshade{} needs to know the +% length of the sequences. Therefore, the command `|\seqlength|' was +% introduced (\ref{seqlines}). (b) With `|\gapcolors|' (also +% \ref{seqlines}) the +% color selection for gap symbols is independent from non-conserved +% residues. (c) The divisions of the ruler where so far fixed to +% 10. Now, this value is changeable by `|\rulersteps|' (again +% \ref{seqlines}). (d) `|\hideresidues|' and `|\showresidues|' turn +% off or on the residue names, i.\,e. one can choose between a +% display of shaded boxes only or with letters in the boxes +% (\ref{kill}). (e) The changes (c) through (d) were necessary +% for the introduction of `|\fingerprint|'. This command allows one to +% display the complete sequence in one line for an easy survey of +% the alignment (\ref{fingerprint}). +% \bigskip +% +% \textbf{v1.0 1999/5/12} +% \medskip +% +% First release. +% \bigskip +% +% +% \subsection{\LaTeX{} basics} +% +% \subsubsection{Typesetting documents using \LaTeX} +% +% In order to use any of the macros provided by the +% \BioTeX-project +% (\TeXshade/\TeXtopo) efficiently a basic understanding of the \TeX{} +% typesetting system and its usage is required. Several books are +% available on this topic, but a rather quick and easy introduction +% is the \emph{Not so short introduction to \LaTeX}. This document +% is available from all Comprehensive \TeX{} Archive Network +% (CTAN) servers, +% e.\,g. from |ftp://ftp.dante.de/pub/tex/documentation/lshort/|, +% in many different languages and formats besides \LaTeX{}, such +% as \textsc{PostScript} and on-line viewable PDF. +% I also put a link from the \BioTeX{} (\TeXshade/\TeXtopo) homepage +% to the document collection +% (|http://pharmazie.uni-kiel.de/chem/Prof_Beitz/BioTeX|). +% +% +% \subsubsection{Memory shortness when using \TeX{}shade} +% +% If you are using \TeXshade{} to align several large sequences (about 1000 +% residues/sequence), LaTeX will probably stop compiling and quit with one +% of the following messages: +% +% |!\ TeX capacity exceeded, sorry [main memory size=384000]| +% +% or +% +% |!\ TeX capacity exceeded, sorry [stack size=300]|. +% +% \TeX{} allocates space for different kinds of internal variables. +% Setting alignments needs lots of memory, +% usually more than for typesetting plain text. +% Thus, the parameter settings of a standard \TeX{} installation might not +% be sufficient for certain projects. This manifests +% in \TeX{} error messages about insufficient memory +% and the setting process is interrupted. There is no reason to be +% concerned. The parameters can be set by hand. Unfortunately, +% each \TeX{} system hides its default parameter file in a different +% place in the system. +% +% +% +% +% +% \subsection{System requirements} \label{require} +% +% \TeXshade{} requires \LaTeXe{} with |color.sty| and |graphics.sty| +% for shading. For arrows in the feature line (p.\pageref{Lfeature}) +% the AMS Math style is needed. +% David Carlisle's |color.sty| is part of the Standard \LaTeX{} +% `Graphics Bundle' [1]. This and the other packages can be downloaded +% from any \TeX{} archive, e.g.\ |ftp.dante.de|; usually they are +% included in a comprehensive \TeX{} installation. +% +% The |color| style allows one to use several |[|\meta{options}|]|, e.\,g. +% |dvips|, |pdftex| or |dviwin|. These provide the commands which +% different devices/programs need to display colored output. It is +% advisable to make yourself familiar with the |color.sty| manual. +% You should define a default driver in the file |color.cfg|. +% Since there is no direct call of |color.sty| by the user, the +% option can be stated when \TeXshade{} is loaded, see next +% subsection. If no option is stated the |DVIPS| driver will be +% loaded. +% +% With the |[dvips]| option the output DVI-file +% can be converted to \textsc{PostScript} using the |DVIPS| program +% and can later be viewed or printed with the public domain +% {\sc GhostView} program which is +% available for almost all computer platforms. Further, more and more +% standard \TeX{} viewers are to a certain extent \textsc{PostScript} +% compatible. +% \bigskip +% +% \subsection{The \texttt{texshade} environment} +% +% \label{tsenvironment} +% +% The commands provided by the \TeXshade{} package are enabled by +% the following command in the document header section: +% \medskip +% +% \quad |\usepackage[|\meta{option}|]{texshade}| +% +% \medskip +% Make sure that the file `|texshade.sty|' is present in a directory +% searched by \TeX{} (see the installation notes in the file +% `|texshade.txt|'). +% +% The \meta{option} given here is passed to |color.sty| which +% handles the color commands for a particular output device, see +% previous subsection and the |color.sty| manual. +% +% The \TeXshade{} package provides only one single new environment: +% |texshade|. This environment has one mandatory and +% one optional argument, both of them designating file names which +% must be present in a directory searched by \TeX. The +% required file \meta{alignmentfile} contains the aligned nucleotide +% or peptide sequences +% (see section~\ref{alignfilestruc}). This file is needed, because +% \TeXshade{} does no alignment by +% itself, it has to take a preprocessed alignment as input. +% The optional file is a parameter file (section~\ref{paramfilestruc}) +% with definitions for the +% customized calculation of the consensus, special sequence features +% or labels etc. In this parameter file all \TeXshade{} commands +% which are allowed in the |texshade| environment can be used and are +% fully functional. +% Within the environment further \TeXshade{} commands can be given +% to replace or complete settings from the parameter file. +% +% Thus, setting an alignment with \TeXshade{} is as simple as +% this: +% +% \begin{quote} +% |\begin{texshade}[|\meta{parameterfile}|]| +% |{|\meta{alignmentfile}|}| +% +% \quad\emph{further \emph{\TeXshade} commands, if needed} +% +% |\end{texshade}| +% \end{quote} +% +% \subsection{Shading modes predefined in this package} +% +% \subsubsection{Identity mode} +% +% \label{ident} +% +% This basic type of shading is provided by almost any alignment +% program. All identical residues at a position are shaded if the +% number of matching residues is higher than a given threshold +% (default is 50\%).\medskip +% +% \begin{texshade}{AQPpro.MSF} +% \setends{1}{80..112} +% \hideconsensus +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \setends{1}{80..112} +% \hideconsensus +% \end{texshade} +% \end{verbatim} +% } +% +% Quite uncommon for an alignment shading program is the possibility +% to display only selected sequence domains, e.\,g.\ to eliminate uninteresting +% positions from the output: +% \medskip +% +% \begin{texshade}{AQPpro.MSF} +% \setdomain{1}{80..90,100..110,120..130} +% \showruler{1}{top} +% \hidenumbering +% \hideconsensus +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \setdomain{1}{80..90,100..110,120..130} +% \showruler{1}{top} +% \hidenumbering +% \hideconsensus +% \end{texshade} +% \end{verbatim} +% } +% +% This goes even further. You can have \TeXshade{} select positions +% based on the 3D coordinates provided by a PDB file, e.\,g.\ show +% all residues that are within an 8 \AA{} radius around the +% $\alpha$-carbon of the residue at position 81: +% \bigskip +% +% \begin{texshade}{AQPpro.MSF} +% \setdomain{1}{75..86,103..103,148..148,151..153,155..156,193..195,218..219,222..222} +% \showruler{top}{1} \rulersteps{1} +% \hidenumbering +% \hideconsensus +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \setdomain{1}{point[8]:1J4N.pdb,81[CA]} +% \showruler{top}{1} \rulersteps{1} +% \hidenumbering +% \hideconsensus +% \end{texshade} +% \end{verbatim} +% } +% +% If you like, positions where conservation is very high (here $\ge$ 80\%) can +% be shaded in a special color and the consensus can be shown with +% or without shading according to the degree of conservation: +% \medskip\label{shadecons} +% +% \begin{texshade}{AQPpro.MSF} +% \threshold[80]{50} +% \setends{1}{80..112} +% \showconsensus[ColdHot]{bottom} +% \defconsensus{.}{lower}{upper} +% \showlegend +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \threshold[80]{50} +% \setends{1}{80..112} +% \showconsensus[ColdHot]{bottom} +% \defconsensus{.}{lower}{upper} +% \showlegend +% \end{texshade} +% \end{verbatim}} +% +% \subsubsection{Similarity mode} +% +% \label{similar} +% +% In many cases it is expedient---mostly when comparing protein +% sequences---to shade also residues +% which are not identical but similar to the consensus sequence. +% Consider a position where three out of five residues are basic +% arginines and two more residues are also basic but lysines. +% In similarity mode \TeXshade{} shades similar residues in a different +% color to distinguish them from the consensus residue. Even when +% none of the residues alone reaches the +% threshold but a group of similar residues does these are shaded +% in the `similarity' color. This case is given for instance +% when at a position in a five sequence alignment two aliphatic +% valines and two also aliphatic isoleucins are present and the +% threshold is set to 50\%. Neither residue exceeds this percentage +% but as a group of similars they do. +% +% In grayscale printouts some colors of the following alignment may appear +% undistinguishable. Don't worry if you usually use grayscale---all +% colors/grays can be selected freely (see \ref{colors}). +% \medskip +% +% \begin{texshade}{AQPpro.MSF} +% \shadingmode{similar} +% \threshold[80]{50} +% \setends{1}{80..112} +% \hideconsensus +% \feature{top}{1}{93..93}{fill:$\downarrow$}{first case (see text)} +% \feature{bottom}{1}{98..98}{fill:$\uparrow$}{second case (see text)} +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode{similar} +% \threshold[80]{50} +% \setends{1}{80..112} +% \hideconsensus +% \feature{top}{1}{93..93}{fill:$\downarrow$}{first case (see text)} +% \feature{bottom}{1}{98..98}{fill:$\uparrow$}{second case (see text)} +% \end{texshade} +% \end{verbatim}} +% +% Probably you know +% this kind of shading from the public domain program +% |BoxShade| +% by \textsc{Kay Hofmann} or from the Macintosh version +% |MacBoxShade| by \textsc{Michael D. Barron}. \TeXshade{} +% provides the same functionality---and goes truly beyond---for the +% \TeX{} community. +% +% +% \subsubsection{T-Coffee shading} +% +% \label{TCoffee} +% +% \TeXshade{}'s capabilities of calculating alignment shadings are +% limited. |T-Coffee| (|www.tcoffee.org|) is a sophisticated alignment/shading +% software. You can apply shading from |T-Coffee| in \TeXshade{} +% by loading the shading information file (|score_ascii|) generated by +% |T-Coffee|. +% \medskip +% +% +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[AQP_TC.asc]{T-Coffee} +% \setends{1}{30..63} +% \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{} +% \showfeaturestylename{top}{feat-cons} +% \showconsensus{bottom} +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[AQP_TC.asc]{T-Coffee} +% \setends{1}{30..63} +% \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{} +% \showfeaturestylename{top}{feat-cons} +% \showconsensus{bottom} +% \end{texshade} +% \end{verbatim}} +% +% +% +% +% +% +% +% \subsubsection{Diversity mode} +% +% \label{diverse} +% +% Contrary to the above described modes this shading style displays +% sequence differences. Thus, it is most suitable for comparing very +% similar sequences, e.\,g.\ species variants of a protein. +% +% One sequence is used as consensus. +% Matching residues in other sequences are blanked out, +% mismatches are shown in lowercase. +% \medskip +% +% \begin{texshade}{AQP2spec.ALN} +% \shadingmode{diverse} +% \setends{1}{77..109} \residuesperline*{33} +% \featureslarge +% \feature{top}{1}{77..109}{}{AQP2 species variants} +% \namesrm\namessl +% \hidenumbering +% \showruler{top}{1} +% \shownames{left} +% \nameseq{1}{Bos taurus} +% \nameseq{2}{Canis familiaris} +% \nameseq{3}{Dugong dugong} +% \nameseq{4}{Equus caballus} +% \nameseq{5}{Elephas maximus} +% \frameblock{1}{82..82,106..106}{Red[1pt]} +% \end{texshade}\label{frame} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQP2spec.ALN} +% \shadingmode{diverse} +% \setends{1}{77..109} +% \featureslarge +% \feature{top}{1}{77..109}{}{AQP2 species variants} +% \namesrm\namessl +% \hidenumbering\showruler{top}{1} +% \shownames{left} +% \nameseq{1}{Bos taurus} +% \nameseq{2}{Canis familiaris} +% \nameseq{3}{Dugong dugong} +% \nameseq{4}{Equus caballus} +% \nameseq{5}{Elephas maximus} +% \frameblock{1}{82..82,106..106}{Red[1pt]} +% \end{texshade}\label{frame} +% \end{verbatim}} +% +% +% \subsubsection{Functionality modes} +% +% \label{func} +% +% Displaying functional peptide similarities is one of \TeXshade's +% strong capabilities. Six functional shading modes are predefined; +% further user specific modes can easily be created. The examples +% may not look very impressive when printed in grayscale. Enjoy +% them on your screen or use color printouts. As mentioned before, +% all colors can be changed to others or to grays without restrictions +% (see chapter \ref{colors}). +% +% \begin{itemize} +% \item [\textbf{charge}:] residues which are charged at physiological pH +% (7.4) are shaded if their number at a position +% is higher than the threshold \label{charge} +% +% \begin{texshade}{AQPpro.MSF} +% \residuesperline*{34} +% \shadingmode[charge]{functional} +% \setends{1}{138..170} +% \feature{top}{3}{153..165}{bar[-50,50]:-50,-45,% +% -40,-30,-20,-10,0,10,20,30,40,45,50}{} +% \feature{top}{3}{167..186}{color:5,10,15,20,25,30,35,% +% 40,45,50,55,60,65,70,75,80,85,90,95,100[ColdHot]}{} +% \showlegend +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[charge]{functional} +% \setends{1}{138..170} +% \feature{top}{3}{153..165}{bar[-50,50]:-50,-45,% +% -40,-30,-20,-10,0,10,20,30,40,45,50}{} +% \feature{top}{3}{167..186}{color:5,10,15,20,25,30,35,% +% 40,45,50,55,60,65,70,75,80,85,90,95,100[ColdHot]}{} +% \showlegend +% \end{texshade} +% \end{verbatim}} +% +% \item [\textbf{hydropathy}:] discrimination between acidic and +% basic, polar uncharged and hydrophobic nonpolar residues +% \label{hydro} +% \bigskip +% +% \begin{texshade}{AQPpro.MSF} +% \residuesperline*{34} +% \shadingmode[hydropathy]{functional} +% \feature{top}{1}{158..163}{brace}{tinted} +% \tintblock{1}{158..163} +% \feature{top}{1}{QLVLC}{brace}{lowercased} +% \lowerblock{1}{QLVLC} +% \setends{1}{138..170} +% \showlegend +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[hydropathy]{functional} +% \feature{top}{1}{158..163}{brace}{tinted} +% \tintblock{1}{158..163} +% \feature{top}{1}{QLVLC}{brace}{lowercased} +% \lowerblock{1}{QLVLC} +% \setends{1}{138..170} +% \showlegend +% \end{texshade} +% \end{verbatim}} +% +% +% \item [\textbf{structure}:] displays the potential +% localization within the tertiary structure of +% the protein \label{struc} +% \bigskip +% +% \begin{texshade}{AQPpro.MSF} +% \residuesperline*{34} +% \shadingmode[structure]{functional} +% \setends{1}{138..170} +% \feature{top}{1}{138..157}{box[Blue,Red][0.5pt]: % +% $\alpha$-helix[Yellow]}{transmembrane domain 4} +% \feature{top}{1}{158..163}{translate[Blue]}{} +% \backtranslabel{oblique} +% \feature{bottom}{1}{[DE]RXXR[DE]}{brace[Blue]}{loop D [Blue]} +% \feature{top}{1}{164..170}{o->[Red]}{trans. dom. 5} +% \showlegend +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[structure]{functional} +% \setends{1}{138..170} +% \feature{top}{1}{138..157}{box[Blue,Red][0.5pt]: % +% $\alpha$-helix[Yellow]}{transmembrane domain 4} +% \feature{top}{1}{158..163}{translate[Blue]}{} +% \backtranslabel{oblique} +% \feature{bottom}{1}{[DE]RXXR[DE]}{brace[Blue]}{loop D [Blue]} +% \feature{top}{1}{164..170}{o->[Red]}{trans. dom. 5} +% \showlegend +% \end{texshade} +% \end{verbatim}} +% +% +% \item [\textbf{chemical}:] residues are shaded due to chemical +% properties of +% their functional groups \label{chem} +% \bigskip +% +% \begin{texshade}{AQPpro.MSF} +% \residuesperline*{34} +% \shadingmode[chemical]{functional} +% \setends{1}{138..170} +% \showlegend +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[chemical]{functional} +% \setends{1}{138..170} +% \showlegend +% \end{texshade} +% \end{verbatim}} +% +% With |\shadeallresidues| the threshold is ignored and +% all residues are shaded due to their group assignment. +% This is \emph{not} identical to a threshold of 0\% +% where only the majority group would be shaded. See the +% difference: +% \bigskip +% +% \begin{texshade}{AQPpro.MSF} +% \residuesperline*{34} +% \shadingmode[chemical]{functional} +% \setends{1}{138..170} +% \shadeallresidues +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[chemical]{functional} +% \setends{1}{138..170} +% \shadeallresidues +% \end{texshade} +% \end{verbatim}} +% +% +% \item [\textbf{rasmol}:] similar to |[chemical]| but with +% shading following the rasmol +% color scheme \label{ras} +% \bigskip +% \bigskip +% \bigskip +% +% \begin{texshade}{AQPpro.MSF} +% \residuesperline*{34} +% \shadingmode[rasmol]{functional} +% \setends{1}{138..170} +% \showruler{top}{1} +% \rulersteps{1} +% \namerulerpos{150}{site A[Red]} +% \namerulerpos{155}{site B[Green]} +% \shadeallresidues +% \showlegend +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[rasmol]{functional} +% \setends{1}{138..170} +% \showruler{bottom}{1} +% \rulersteps{1} +% \namerulerpos{150}{site A[Red]} +% \namerulerpos{155}{site B[Green]} +% \shadeallresidues +% \showlegend +% \end{texshade} +% \end{verbatim}} +% +% +% +% \item [\textbf{standard area}:] this shading displays the +% differences in the surface +% area \label{starea} +% of the different amino acid's sidechains +% \bigskip +% +% \begin{texshade}{AQPpro.MSF} +% \residuesperline*{34} +% \shadingmode[standard area]{functional} +% \setends{1}{138..170} +% \showlegend +% \shadeallresidues +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[standard area]{functional} +% \setends{1}{138..170} +% \showlegend +% \shadeallresidues +% \end{texshade} +% \end{verbatim}} +% +% \item [\textbf{accessible area}:] \label{accarea} +% here, the surface area which can +% be accessed by solvent molecules is used as a +% basis for shading; low accessibility means +% hydrophobic (i.\,e.\ strongly buried +% residues), whereas highly accessible +% sidechains are hydrophilic (compare to +% \textbf{hydropathy} and \textbf{structure}) +% \bigskip +% +% \begin{texshade}{AQPpro.MSF} +% \residuesperline*{34} +% \shadingmode[accessible area]{functional} +% \setends{1}{138..170} +% \showlegend +% \feature{top}{1}{138..157,164..170}{helix}{membr.} +% \feature{top}{1}{158..163}{---}{loop} +% \featurerule{1mm} +% \shadeallresidues +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[accessible area]{functional} +% \setends{1}{138..170} +% \showlegend +% \feature{top}{1}{138..157,164..170}{helix}{membr.} +% \feature{top}{1}{158..163}{---}{loop} +% \featurerule{1mm} +% \shadeallresidues +% \end{texshade} +% \end{verbatim}} +% +% \end{itemize} +% +% +% +% \subsection{Bar graphs and color scales} +% +% \label{graphs} +% +% Amino acid properties, such as hydrophobicity, molecular weight, +% or charge can be shown as bar graphs or color scales along the +% alignment. Further, the degree of protein sequence conservation +% can be indicated. As an example, in the following +% aquaporin alignment plots of residue conservation (bars, top), +% are shown as well as properties of the AQP1 sequence: charge (scale, top), +% molecular weight are shown (scale, bottom), and hydrophobicity (bars, bottom). +% +% +% \begin{texshade}{AQPpro.MSF} +% \residuesperline*{34} +% \setends{1}{138..170} +% \feature{ttop}{1}{138..170}{bar:conservation}{} +% \showfeaturestylename{ttop}{conserv.} +% \ttopspace{-\baselineskip} +% \feature{top}{1}{138..170}{color:charge}{} +% \showfeaturestylename{top}{charge} +% \feature{bottom}{1}{138..170}{color:molweight[ColdHot]}{} +% \showfeaturestylename{bottom}{weight} +% \bbottomspace{-\baselineskip} +% \feature{bbottom}{1}{138..170}{bar:hydrophobicity[Red,Gray10]}{} +% \showfeaturestylename{bbottom}{hydrophob.} +% \bargraphstretch{3} +% \featurestylenamescolor{Red} +% \featurestylenamesrm \featurestylenamesit +% \hideconsensus +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \setends{1}{138..170} +% \feature{ttop}{1}{138..170}{bar:conservation}{} +% \showfeaturestylename{ttop}{conserv.} +% \ttopspace{-\baselineskip} +% \feature{top}{1}{138..170}{color:charge}{} +% \showfeaturestylename{top}{charge} +% \feature{bottom}{1}{138..170}{color:molweight[ColdHot]}{} +% \showfeaturestylename{bottom}{weight} +% \bbottomspace{-\baselineskip} +% \feature{bbottom}{1}{138..170}{bar:hydrophobicity[Red,Gray10]}{} +% \showfeaturestylename{bbottom}{hydrophob.} +% \bargraphstretch{3} +% \featurestylenamescolor{Red} +% \featurestylenamesrm \featurestylenamesit +% \hideconsensus +% \end{texshade} +% \end{verbatim}} +% \medskip +% +% The degree of similarity and identity between all sequences in the alignment +% can be shown in a table using |\similaritytable| (\ref{simtable}) outside the |texshade| +% environment: \label{simtableEx} +% +% \DeleteShortVerb{\|} +% \begin{center}\similaritytable\end{center} +% \MakeShortVerb{\|} +% +% +% \subsection{Secondary structures} +% +% \label{sec} +% +% Predicted protein secondary structures in the DSSP, STRIDE +% PHD or HMMTOP file format can be included and displayed in the +% alignment. As an example, the following few commands show an +% aquaporin alignment with the PHD topology data for aquaporin +% type 1 (top sequence). +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[allmatchspecial]{similar} +% \includePHDtopo{1}{AQP1.phd} +% \end{texshade} +% \end{verbatim} +% } +% +% Abbr.: \emph{int.} -- internal; \emph{ext.} -- external; \emph{TM} -- +% transmembrane domain +% +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[allmatchspecial]{similar} +% \includePHDtopo{1}{AQP1.phd} +% \end{texshade} +% +% \subsection{Sequence fingerprints} +% +% \label{finger} +% +% To gain a quick overview of sequence similarities or properties +% the |\fingerprint| command has been implemented. It can depict the +% complete sequence in one single line. The residues are presented +% as colored vertical lines. The implementation of this kind of output +% was inspired by a publication by \textsc{Kai-Uwe Fr\"ohlich} [6]. +% \medskip +% +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[allmatchspecial]{similar} +% \shadingcolors{grays} +% \fingerprint{360} +% \showlegend +% \feature{top}{1}{13..36,51..68,94..112,138..156,% +% 165..185,211..232}{,-,}{TM} +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[allmatchspecial]{similar} +% \shadingcolors{grays} +% \fingerprint{360} +% \showlegend +% \feature{top}{1}{13..36,51..68,94..112,138..156,% +% 165..185,211..232}{,-,}{TM} +% \end{texshade} +% \end{verbatim}} +% +% The higher the similarity the darker the vertical lines. In this +% overview it becomes obvious that the transmembrane regions of the +% aquaporin isoforms are most conserved. +% \medskip +% +% A fingerprint of charge distribution on different aquaporins is shown. +% below. Sequence gaps can be left blank (example above) or drawn as lines +% between the sequence blocks. +% +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[charge]{functional} +% \shadeallresidues +% \fingerprint{360} +% \gapchar{rule} +% \showlegend +% \end{texshade} +% +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[charge]{functional} +% \shadeallresidues +% \fingerprint{360} +% \gapchar{rule} +% \showlegend +% \end{texshade} +% \end{verbatim}} +% +% +% \subsection{Sequence logos} +% +% \label{logo} +% +% Sequence logos represent the information content of the aligned +% sequences at a position in bit (max.\ 2 bit for DNA, i.\,e. +% log$_2$4, and 4.322 bit for proteins, i.\,e. log$_2$20) and the +% relative frequency of a base or amino acid at this +% position [7]. Thus, more information is contained in logos than in +% a standard consensus sequence. +% The example below shows a DNA sequence alignment with the logo on the +% top. +% +% It must be remarked that a logo from only five sequences does not +% produce meaningful results - it rather illustrates the technique. +% +% \medskip +% +% \begin{texshade}{AQPDNA.MSF} +% \setends{1}{414..443} +% \showsequencelogo{top} +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPDNA.MSF} +% \setends{1}{414..443} +% \showsequencelogo{top} +% \end{texshade} +% \end{verbatim}} +% +% +% Next, only the logo of a protein alignment is displayed plus the +% degree of sequence conservation as a color scale in the consensus +% line. Note, that the full functionality of the feature lines remains. +% \medskip +% +% \begin{texshade}{AQPpro.MSF} +% \setends{AQP3.PRO}{203..235} +% \showsequencelogo{top} \showlogoscale{leftright} +% \hideseqs +% \residuesperline*{33} +% \defconsensus{{$\bullet$}}{{$\bullet$}}{{$\bullet$}} +% \showconsensus[ColdHot]{bottom} +% \nameconsensus{conservation} \namessf\namessl +% \showruler{bottom}{AQP3.PRO} \rulersteps{1} +% \feature{top}{AQP3.PRO}{208..210}{---}{NPA} +% \feature{top}{AQP3.PRO}{211..219}{helix}{} +% \feature{top}{AQP3.PRO}{220..232}{brace}{loop E} +% \feature{top}{AQP3.PRO}{233..235}{helix}{TM6} +% \feature{bottom}{AQP3.PRO}{203..235}{brace}{1-step numbering} +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \setends{AQP3.PRO}{203..235} +% \showsequencelogo{top} \showlogoscale{leftright} +% \hideseqs +% \residuesperline*{33} +% \defconsensus{{$\bullet$}}{{$\bullet$}}{{$\bullet$}} +% \showconsensus[ColdHot]{bottom} +% \nameconsensus{conservation} \namessf\namessl +% \showruler{bottom}{AQP3.PRO} \rulersteps{1} +% \feature{top}{AQP3.PRO}{208..210}{---}{NPA} +% \feature{top}{AQP3.PRO}{211..219}{helix}{} +% \feature{top}{AQP3.PRO}{220..232}{brace}{loop E} +% \feature{top}{AQP3.PRO}{233..235}{helix}{TM6} +% \feature{bottom}{AQP3.PRO}{203..235}{brace}{1-step numbering} +% \end{texshade} +% \end{verbatim}} +% +% The same logo is shown below but with frequency correction turned +% on (|\dofrequencycorrection|), see p.\pageref{Lshowsequencelogo}. +% This takes into account the difference between the amino acid +% distribution in the alignment and the equal distribution of +% 5\% for each residue. +% \medskip +% +% \begin{texshade}{AQPpro.MSF} +% \setends{AQP3.PRO}{203..235} +% \showsequencelogo{top} \showlogoscale{leftright} +% \hideseqs +% \residuesperline*{33} +% \defconsensus{{$\bullet$}}{{$\bullet$}}{{$\bullet$}} +% \showconsensus[ColdHot]{bottom} +% \nameconsensus{conservation} \namessf\namessl +% \showruler{bottom}{AQP3.PRO} \rulersteps{1} +% \feature{top}{AQP3.PRO}{208..210}{---}{NPA} +% \feature{top}{AQP3.PRO}{211..219}{helix}{} +% \feature{top}{AQP3.PRO}{220..232}{brace}{loop E} +% \feature{top}{AQP3.PRO}{233..235}{helix}{TM6} +% \feature{bottom}{AQP3.PRO}{203..235}{brace}{1-step numbering} +% \dofrequencycorrection +% \end{texshade} +% +% +% \subsection{Subfamily logos} +% +% \label{sublogo} +% +% The following output is derived from the calculation of a +% subfamily logo [14]. Such logos display relevant deviations of a +% subfamily compared to the remaining set of sequences. Here, +% typical residues of AQP3 are shown (upright) which deviate +% from the remaining four aquaporins of this alignment (upside-down). +% The output can be directly compared to the sequence logo above, +% which displays the same section of the alignment. +% Note, that five sequences are far too few to obtain meaningful +% results with this method. This is just to illustrate the +% approach. +% \medskip +% +% \begin{texshade}{AQPpro.MSF} +% \setends{AQP3.PRO}{203..235} +% \residuesperline*{33} +% \setsubfamily{3} +% \showsubfamilylogo{top} \showlogoscale{leftright} +% \namesubfamilylogo[others]{AQP3} +% \namessf \namessl +% \showruler{bottom}{AQP3.PRO} \rulersteps{1} +% \hideseqs +% \hideconsensus +% \dofrequencycorrection +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \setends{AQP3.PRO}{203..235} +% \residuesperline*{33} +% \setsubfamily{3} +% \showsubfamilylogo{top} \showlogoscale{leftright} +% \namesubfamilylogo[others]{AQP3} +% \namessf \namessl +% \showruler{bottom}{AQP3.PRO} \rulersteps{1} +% \hideseqs +% \hideconsensus +% \dofrequencycorrection +% \end{texshade} +% \end{verbatim}} +% +% +% +% +% \subsection{Customization of the alignment output} +% +% Extensive possibilities are given to the user to customize +% the final output of an alignment. Thus, all parameters defining the +% appearance of letters can be changed individually for sequence +% residues, names and numbering or the describing feature texts. +% Additional manual shading can be applied to any region or +% block of residues. Sequences are easily re-ordered, separated, hidden +% or blanked out without recalculation of the entire alignment; +% sections of the alignment can also be shown. +% Numbering and rulers can be displayed and set to any value. +% A powerful tool is the |\feature| +% command which allows one to label stretches of residues with bars, +% arrows, braces or any fill character and describing text. +% Legends are set automatically if desired, but user commands +% are also provided to build individual legends. +% +% +% \newpage +% \section{Format of alignment input files} +% +% \label{alignfilestruc} +% +% \TeXshade{} can handle two common alignment input formats, i.\,e.\ +% the MSF format (\underline{m}ultiple \underline{s}equence +% \underline{f}ormat) and the ALN format +% (\underline{al}ig\underline{n}ment format). The MSF +% format is used by |PILEUP| of the Unix GCG sequence +% analysis package\footnote{For a description see +% |http://gene.md.huji.ac.il/Computer/GCG9doc|}. Files in the +% ALN format are produced by |CLUSTAL| which is +% available for free for Unix, DOS and Macintosh. Further, upon +% request, the FASTA format is supported since version 1.6. +% In addition to the mentioned software many alignment programs have +% export filters for the MSF, ALN or FASTA +% format, e.\,g.\ |MACAW| produces ALN files. If +% you are not sure whether your favorite sequence aligner +% produces one of the required formats compare its output to +% the following examples. \TeXshade{} determines the format from +% the internal file structure, thus extensions like MSF, ALN +% or FASTA +% are not required. If you can choose the alignment format +% MSF is recommended, because this format gives information +% about the sequence type, i.\,e.\ peptide or nucleotide sequences, +% and length (for the correct setting of gaps at the sequence end). +% +% \subsection{The MSF file format} +% Files of this type are divided into a header section and the +% multiple sequence alignment. The header may contain the +% following components: +% +% +% \begin{itemize} +% \item[\textbf{File Type}:] (optional) The first header line +% reads for nucleic acids alignments +% |!!NA_MULTIPLE_ALIGNMENT 1.0| and for amino acid sequences +% |!!AA_MULTIPLE_ALIGNMENT 1.0| (all uppercase). +% \item[\textbf{Description}:] (optional) Informative text +% describing what is in the file. +% \item[\textbf{Dividing line}:] (required!) Must include the +% following attributes: +% \begin{itemize} +% \item[|MSF|:] Displays the number of bases or residues in +% the multiple sequence alignment. +% \item[|Type|:] Displays the sequence type, `P' for a peptide +% and `N' for a nucleotide alignment. +% \item[|Checksum|:] Displays an integer value that +% characterizes the contents of the file. +% \item[|..|] The two periods act as a divider between the +% descriptive information and the following +% sequence information. +% \end{itemize} +% \item[\textbf{Name/Weight}:] (required!) Must include the name of +% each sequence included in the alignment, as well as its +% length, checksum and weight. +% \item[\textbf{Two slashes} (|//|):] (required!) This separating +% line divides the name/weight information from the +% sequence alignment +% \end{itemize} +% +% The alignment section consists of sequence blocks divided by an +% empty line. Each sequence line starts out with the sequence name. +% An example file is shown here: +% \medskip +% +% \parindent-1mm +% \begin{fmpage} +% \begin{verbatim} +% +% AQP.MSF MSF: 87 Type: P May 1st, 1998 Check: 2586 .. +% Name: AQP1.PRO Len: 66 Check: 1367 Weight: 1.00 +% Name: AQP2.PRO Len: 58 Check: 2176 Weight: 1.00 +% Name: AQP3.PRO Len: 83 Check: 1893 Weight: 1.00 +% Name: AQP4.PRO Len: 63 Check: 3737 Weight: 1.00 +% Name: AQP5.PRO Len: 59 Check: 3413 Weight: 1.00 +% // +% 1 45 +% AQP1.PRO MAS........................EIKKKLFWRAVVAEFLAM +% AQP2.PRO MW.........................ELRSIAFSRAVLAEFLAT +% AQP3.PRO M.........NRCG.....EMLHIRYR......LLRQALAECLGT +% AQP4.PRO MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM +% AQP5.PRO MK........................KEVCSLAFFKAVFAEFLAT +% +% 45 87 +% AQP1.PRO TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL +% AQP2.PRO LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL +% AQP3.PRO LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA +% AQP4.PRO LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM +% AQP5.PRO LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL +% \end{verbatim} +% \end{fmpage} +% \bigskip +% +% \parindent0mm +% \TeXshade{} extracts only the information from the file it +% really needs. So, do not mind all the checksums listed +% in the file---\TeXshade{} does not either. The same is true +% for |Weight|. Required are the string |MSF:| +% for the identification of the file format and |Type:| for the +% determination of the sequence type (both in the dividing line), +% further all |Name:| definitions and finally |//|. The MSF format +% allows one to comment out sequences. This is done +% by putting an exclamation point directly infront of the respective +% |Name|. These sequences are neither displayed nor used for the +% calculation of the consensus. This works for \TeXshade, too. +% To comment out sequences without changing +% the input file use the \TeXshade{} command +% |\killseq{|\meta{seqref}|}| (\ref{kill}). +% \medskip +% +% \parindent-1mm +% \begin{fmpage}\label{commout} +% \begin{verbatim} +% +% AQP.MSF MSF: 87 Type: P May 1st, 1998 Check: 2586 .. +% Name: AQP1.PRO Len: 66 Check: 1367 Weight: 1.00 +% !Name: AQP2.PRO Len: 58 Check: 2176 Weight: 1.00 +% !Name: AQP3.PRO Len: 83 Check: 1893 Weight: 1.00 +% Name: AQP4.PRO Len: 63 Check: 3737 Weight: 1.00 +% Name: AQP5.PRO Len: 59 Check: 3413 Weight: 1.00 +% // +% 1 45 +% AQP1.PRO MAS........................EIKKKLFWRAVVAEFLAM +% AQP2.PRO MW.........................ELRSIAFSRAVLAEFLAT +% AQP3.PRO M.........NRCG.....EMLHIRYR......LLRQALAECLGT +% AQP4.PRO MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM +% AQP5.PRO MK........................KEVCSLAFFKAVFAEFLAT +% +% 45 87 +% AQP1.PRO TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL +% AQP2.PRO LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL +% AQP3.PRO LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA +% AQP4.PRO LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM +% AQP5.PRO LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL +% \end{verbatim} +% \end{fmpage} +% \parindent0mm +% \bigskip +% +% The sequence lengths given after |Len:| are not used by +% \TeXshade. Due to the fact that most alignment programms calculate the +% sequence length by summing up residues and additionally gaps which +% is not really correct. In order to have the sequence break right +% after the last residue without printing further gap symbols +% \TeXshade{} counts the number of residues by itself. You can +% also use the command |\seqlength| in the \TeXshade{} +% environment to set the values manually if you do not trust a machine. +% +% \subsection{The ALN file format} +% ALN files are quite similar to the above described MSF files. +% They simply lack a defined header section. Nevertheless, +% describing text is allowed before the alignment part. \TeXshade{} +% determines the number of sequences and their names from the last +% sequence block---so, no further text lines are allowed after this block! +% Due to a lacking declaration in the file the sequence type has +% to be set in the |texshade| environment by |\seqtype{|\meta{type}|}| +% \label{Lseqtype} with `P' for peptide and `N' for nucleotide sequences; +% for the example below: |\seqtype{P}|. If no |\seqtype| command +% is used \TeXshade{} assumes a nucleotide sequence. +% \bigskip +% +% \parindent-1mm +% \begin{fmpage} +% \begin{verbatim} +% +% profalign May 1st, 1998, 16:58 +% +% of AQPpro.MSF{} +% +% Muliple alignment parameter: +% +% Gap Penalty (fixed): 10.00 +% Gap Penalty (varying): .05 +% Gap separation penalty range: 8 +% Percent. identity for delay: 0% +% List of hydrophilic residue: GPSNDQEKRH +% Protein Weight Matrix: blosom +% +% 10 20 30 40 +% . . . . +% AQP1.PRO MAS........................EIKKKLFWRAVVAEFLAM +% AQP2.PRO MW.........................ELRSIAFSRAVLAEFLAT +% AQP3.PRO M.........NRCG.....EMLHIRYR......LLRQALAECLGT +% AQP4.PRO MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM +% AQP5.PRO MK........................KEVCSLAFFKAVFAEFLAT +% * . ** *. +% +% AQP1.PRO TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL +% AQP2.PRO LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL +% AQP3.PRO LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA +% AQP4.PRO LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM +% AQP5.PRO LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL +% .. * .** . ** . +% \end{verbatim} +% \end{fmpage} +% \bigskip +% +% The minimal contents of an ALN file are shown below; this +% is fully sufficient. Many sequence alignment programs can +% produce such an output. Have a look at |seqpup| by +% \textsc{Don Gilbert} if you need a comprehensive conversion +% program\footnote{Sorry, |seqpup| is much more!}. +% \bigskip +% +% \parindent-1mm +% \begin{fmpage} +% \begin{verbatim} +% +% AQP1.PRO MAS........................EIKKKLFWRAVVAEFLAM +% AQP2.PRO MW.........................ELRSIAFSRAVLAEFLAT +% AQP3.PRO M.........NRCG.....EMLHIRYR......LLRQALAECLGT +% AQP4.PRO MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM +% AQP5.PRO MK........................KEVCSLAFFKAVFAEFLAT +% +% AQP1.PRO TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL +% AQP2.PRO LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL +% AQP3.PRO LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA +% AQP4.PRO LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM +% AQP5.PRO LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL +% \end{verbatim} +% \end{fmpage} +% \bigskip +% +% \subsection{The FASTA file format} +% In FASTA files each sequence is led +% by a single description line starting with a `|>|'. \TeXshade{} uses +% the first word delimited by the leading `|>|' and a space as +% the sequence name. If no descriptive text is present \TeXshade{} +% generates a sequence name consisting of `|seq|' plus a consecutive +% number. The lines following the description line +% contain the sequence. +% \bigskip +% +% \begin{fmpage} +% \begin{verbatim} +% +% >AQP1.PRO +% MAS........................EIKKKLFWRAVVAEFLAM +% TLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATL +% +% >AQP2.PRO +% MW.........................ELRSIAFSRAVLAEFLAT +% LLFVFFGLGSALQWA...SS....PPSVLQIAVAFGLGIGIL +% +% >AQP3.PRO +% M.........NRCG.....EMLHIRYR......LLRQALAECLGT +% LILVMFGCGSVAQVVLSRGTHGGF....LTINLAFGFAVTLA +% +% >AQP4.PRO +% MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAM +% LIFVLLSVGSTINWG...GSENPLPVDMVLISLCFGLSIATM +% +% >AQP5.PRO +% MK........................KEVCSLAFFKAVFAEFLAT +% LIFVFFGLGSALKWP...SA....LPTILQISIAFGLAIGTL +% \end{verbatim} +% \end{fmpage} +% \bigskip +% +% +% \parindent0mm +% \newpage +% \section{Use of a \TeX{}shade parameter file} +% +% \label{paramfilestruc} +% +% Using predefined parameter files for repeatedly occuring situations +% can save a lot of typing and makes the output throughout the +% publication or presentation more consistent. Further, such +% files are an easy way to exchange self-defined shading +% modes or new color schemes (i.\,e.\ for a satisfying grayscale output) +% with other users. If you have created a +% parameter file, which you think is of interest for others, please +% submit it to me\footnote{|ebeitz@pharmazie.uni-kiel.de|} as an e-mail +% attachment together with a short +% description. I will take care of those files and post them---with +% a reference to the author---together with the next \TeXshade{} +% distribution to make them available for all interested users. +% +% No special file format is required for parameter +% files. \TeXshade{} simply calls the file using the |\input| +% command right after resetting all parameters to default. An +% example parameter file is present containing the standard +% parameters of \TeXshade{} called |texshade.def|. This file can be +% changed freely and can be used as a template for the creation of +% personal parameter files. +% +% Five steps are executed by \TeXshade{} when +% processing the |texshade| environment: +% +% \bigskip +% \begin{minipage}{12cm} +% |\begin{texshade}[|\meta{parameterfile}|]{|\meta{alignmentfile}|}| +% +% \begin{enumerate} +% \item Analysis of the \meta{alignmentfile}; determination of +% the number of sequences and sequence names +% +% \item Setting parameters to default +% +% \item Setting parameters to the definitions of the +% \meta{parameterfile}, if existent +% +% \item Execution of further \TeXshade{} commands within the +% evironment, if existent +% +% \parindent-1cm +% \medskip +% |\end{texshade}| +% +% \parindent0cm +% \item Loading and setting the alignment on a line by line basis +% \end{enumerate} +% \end{minipage} +% +% \newpage +% \section{\texttt{texshade} user commands} +% +% The \TeXshade{} package must be loaded by the |\usepackage| +% command in the document header section. +% \medskip +% +% \quad|\usepackage[|\meta{option}|]{texshade}| +% \medskip +% +% Then, the |texshade| environment is ready to use as described +% in \ref{tsenvironment}. See also section \ref{paramfilestruc} for +% a description of the optional parameter file. All other +% commands provided by \TeXshade{} (except |\shadebox| [\ref{Lshadebox}], |\molweight| and +% |\charge| [\ref{molcharge}], and |\percentsimilarity|, |\percentidentity| and +% |\similaritytable| [\ref{Lpercentidentity}]) must +% be used within the |texshade| environment. +% +% +% +% \subsection{Using predefined shading modes} +% +% \label{predef} +% +% \label{Lshadingmode} +% If no |\shadingmode| command is given in the |texshade| +% environment the default shading mode (\emph{identical}, see +% \ref{ident}) is active. For the selection of one of the other +% predefined shading modes the following command is provided. +% \bigskip +% +% \quad |\shadingmode[|\meta{option}|]{|\meta{mode}|}| +% \bigskip +% +% You can choose from four shading modes and declare one option +% which depends on the selected mode. +% +% \begin{enumerate} +% +% \item |\shadingmode[|\meta{allmatchspecial/number}|]{identical}| +% +% See \ref{ident} for examples. Use the +% option |allmatchspecial| to shade positions with a special color +% where all residues are identical. Or use a percentage number +% (0--100) as an option to set an additional threshold for highly +% conserved residues, e.\,g.\ |\shadingmode[90]{identical}|. +% \label{Lallmatchspecial}|\allmatchspecial| can also be +% used as a command with or without an optional parameter for +% setting the high conservation threshold. As both, option or command, +% |allmatchspecial| is only active in the \emph{identical} and +% \emph{similar} shading modes. +% +% \label{Lshadingcolors} +% One can choose from five predefined shading color schemes with +% the command +% |\shadingcolors{|\meta{scheme}|}|. The sets are named `blues' +% (used in the example, \ref{ident}), `reds', `greens', +% `grays' and `black'. Default is |\shadingcolors{blues}|. Further, the colors +% for the non matching, the +% conserved and all matching (or highly conserved) residues can be set individually +% plus the letter case (lower or upper) or any character +% can be chosen: \label{Lnomatchresidues} +% \label{Lconservedresidues} +% \label{Lallmatchresidues} +% \bigskip +% +% |\nomatchresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}| +% +% |\conservedresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}| +% +% |\allmatchresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}| +% \bigskip +% +% For how to handle colors for the foreground \meta{res.col.} and +% the background \meta{shad.col.} see section \ref{colors}. +% The third parameter \meta{case} tells \TeXshade{} to print the +% corresponding residue as a lowercase or an uppercase letter or +% even to print any other character. Finally, the \meta{style} +% parameter tells \TeXshade{} which shape to use for the letters. +% Use one of the following styles +% for \meta{style}. +% +% \begin{center} +% \begin{tabular}{cl} +% \meta{style} & \emph{effect} \\ \hline +% |bf| & bold face series\\ +% |md| & normal series \\ +% |up| & upright shape (normal shape)\\ +% |it| & italics shape \\ +% |sl| & slanted shape \\ +% |rm| & modern roman family \\ +% |sf| & sans serif family \\ +% |tt| & typewriter family \\ +% \end{tabular} +% \end{center} +% \medskip +% +% In order to change only some +% of the parameters it is sufficient to declare these +% and use empty braces for the others. Examples: +% \bigskip +% +% \quad|\conservedresidues{White}{Blue}{upper}{bf}|: the conserved +% residues are printed as bold face white uppercase letters on blue. +% \bigskip +% +% \quad|\nomatchresidues{}{}{{$\bullet$}}{}|: instead of the non +% matching residues a `$\bullet$' is printed. The colors and style +% are not changed. +% Note the double curly braces which make \TeXshade{} +% interpret this complex symbol description as one single +% character. +% +% Once a set of shading colors is redefined, it can be saved using +% |\defshadingcolors{|\meta{name}|}|\label{Ldefshadingcolors} for +% later use in the document (see \ref{shaderegion}). +% +% \bigskip +% +% +% \item |\shadingmode[|\meta{allmatchspecial/number}|]{similar}| +% +% \label{Lsimilarresidues} +% See \ref{similar} for an example output and an explanation +% of the shading. In addition to the described commands +% for changing shading colors this shading mode provides +% the command |\similarresidues|. +% Use it in analogy to the commands above. +% +% \label{Lpepsims}\label{Lpepgroups} +% \label{LDNAsims}\label{LDNAgroups} +% How does \TeXshade{} know which residues are +% considered to be similar? These definitions are set by two command +% couples, i.\,e.\ +% |\pepsims|,|\pepgroups| for peptides and +% |\DNAsims|,|\DNAgroups| for nucleotides. With |\pepsims| and +% |\DNAsims| residues are defined which are similar to the +% consensus residue. Examples: +% +% \quad |\pepsims{S}{TA}|\quad If a serine is the consensus +% residue then all threonins and alanines at this +% position are shaded in the color for similars. This +% definition does \emph{not} imply that threonine and +% alanine are similar to each other! This becomes +% obvious when you inspect the next definition: +% +% \quad |\pepsims{T}{S}|\quad Serine but not alanine is declared +% to be similar to threonine. +% +% What happens if there is no consensus residue? How does +% \TeXshade{} decide if a group of similars is greater than +% the threshold? For this groups are pre-defined: +% +% \quad |\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ}| This command allows +% one to set up to nine groups of similars, separated by commas. +% Each residue can belong to only one group. If one residue +% is assigned to several groups only the last assignment is +% carried out. +% +% \quad |\DNAgroups{GAR,CTY}| This command is used in analogy to +% the amino acid groups. Here, two ambiguity codes (`R' for +% pu\underline{r}ine base and `Y' for p\underline{y}rimidine +% base) are assigned in addition. +% +% Residues which do not appear in any of the four commands are +% considered not to belong to a group. The default +% settings for similars are listed below: +% \bigskip +% +% \begin{verbatim} +% \pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} +% +% \pepsims{F}{YW} % Y and W are similar to F +% \pepsims{Y}{WF} % W and F are similar to Y +% \pepsims{W}{YF} % Y and F are similar to W +% +% \pepsims{I}{LVM} % L, V and M are similar to I +% \pepsims{L}{VMI} % V, M and I are similar to L +% \pepsims{V}{MIL} % M, I and L are similar to V +% +% \pepsims{R}{KH} % K and H are similar to R +% \pepsims{K}{HR} % H and R are similar to K +% \pepsims{H}{RK} % R and K are similar to H +% +% \pepsims{A}{GS} % G and S are similar to A +% \pepsims{G}{A} % A (but not S) is similar to G +% +% \pepsims{S}{TA} % T and A are similar to S +% \pepsims{T}{S} % S (but not A) is similar to T +% +% \pepsims{D}{EN} % E and N (but not Q) are similar to D +% \pepsims{E}{DQ} % D and Q (but not N) are similar to E +% \pepsims{N}{QD} % Q and D (but not E) are similar to N +% \pepsims{Q}{NE} % N and E (but not D) are similar to Q +% +% \DNAgroups{GAR,CTY} +% +% \DNAsims{A}{GR} % G and R are similar to A +% \DNAsims{G}{AR} % A and R are similar to G +% \DNAsims{R}{AG} % A and G are similar to R +% +% \DNAsims{C}{TY} % T and Y are similar to C +% \DNAsims{T}{CY} % C and Y are similar to T +% \DNAsims{Y}{CT} % C and T are similar to Y +% \end{verbatim} +% +% +% \item |\shadingmode[|\meta{filename}|]{T-Coffee}| +% +% Enter a \meta{filename} to load the shading +% information from a |T-Coffee| |score_ascii| file (|www.tcoffee.org|); +% see example in \ref{TCoffee}. Make sure +% that the alignment file specified in the |\texshade| command +% and this shading file correspond to each other. +% +% If you do not enter a \meta{filename} here, a separate +% command |\includeTCoffee{|\meta{filename}|}| must be used. +% +% |T-Coffee| shading can also be used in the consensus +% p.\,\pageref{Lshowconsensus} and in the feature lines, +% in particular color scales and bar plots p.\,\pageref{Lgraphs}, +% for the display of shading information. +% +% +% \item |\shadingmode[|\meta{seqref}|]{diverse}| +% +% \ref{diverse} depicts an example alignment. Choose the +% number or the name of the sequence \meta{seqref} which will be treated +% as the consensus and to which the other sequences are compared. +% If no \meta{seqref} is declared the first sequence is set as +% consensus (\meta{seqref} = 1). +% +% Standard definitions for |diverse| +% mode are: +% +% \begin{verbatim} +% \nomatchresidues{Black}{White}{lower}{up} +% \similarresidues{Black}{White}{lower}{up} +% \conservedresidues{Black}{White}{{.}}{up} +% \allmatchresidues{Black}{White}{{.}}{up} +% \gapchar{-} +% \end{verbatim} +% +% After calling |\shadingmode{diverse}| these commands can be +% used to redefine the |diverse| mode settings (mind the double +% curly braces around the dot-symbol!). +% +% \label{Lhideallmatchpositions} +% Since alignment positions where all residues match do not contain +% much information, those sites can be blanked out using +% Ê|\hideallmatchpositions|. The resulting break in the alignment is +% indicated by a gap and a vertical line. See the |\setdomain| +% command (\ref{Lsetdomain}) +% for further information on how to change the gap and ruler colors. +% A single-stepped ruler is also recommended (\ref{Lshowruler}). +% Ê|\hideallmatchpositions| can be combined with |\setends| +% (\ref{Lsetends}). +% +% +% \item |\shadingmode[|\meta{type}|]{functional}|\label{funcdef} +% There are seven different functional shading modes available for +% peptide sequences; nucleotide sequences can not be shaded due +% to functional aspects. Five of \TeXshade's functional modes +% correspond to the four `alphabets' employed by \textsc{Karlin} +% and \textsc{Ghandour} for peptide alignments [2] or by the +% rasmol software. Additional +% `alphabets' to the standard 20-letter array of amino acids +% can highlight peptide similarities which were otherwise not visible. +% For the `alphabet' definitions see below: +% +% \begin{itemize} +% \item \meta{type} = |charge|\quad Acidic (D, E) and basic (H, +% K, R). +% +% \item \meta{type} = |hydropathy|\quad Acidic and basic (as +% above), polar uncharged (C, G, N, Q, S, +% T, Y) and hydrophobic nonpolar (A, F, I, L, M, +% P, V, W), see also \textsc{Kyte} \& +% \textsc{Doolittle} [3]. +% +% \item \meta{type} = |structure|\quad External (D, E, H, K, N, Q, R), +% internal (F, I, L, M, V) and ambivalent (A, C, +% G, P, S, T, W, Y). +% +% \item \meta{type} = |chemical|\quad Acidic (D, E), aliphatic +% (I, L, V), aliphatic (small) (A, G), +% amide (N, Q), aromatic +% (F, W, Y), basic (H, K, R), hydroxyl +% (S, T), imino (P) and sulfur (C, M). +% +% \item \meta{type} = |rasmol|\quad (D, E), (K, R, H), (F, Y, W), +% (A, G), (C, M), (S, T), (N, Q), (I, L, V), +% (P). +% +% \end{itemize} +% +% The two modes described below highlight sidechain sizes and +% hydrophobicity, respectively, according to \textsc{Rose} +% \emph{et al.}\ [4,5]. Standard area stands for the surface area +% of the residue in \AA$^2$, i.\,e. it is a measure for the size +% of a residue's sidechain. The accessible area value (also in +% \AA$^2$) gives information about the size of the surface area +% which is accessible by solvent molecules within the folded +% protein. A very small area means that the residue is +% strongly buried and is thus very hydrophobic. Hydrophilic +% residues in turn possess large accessible areas due +% to their prefered location at the protein surface. Therefore, +% this kind of shading provides another method, in addition +% to |hydropathy| and |structure|, for the +% visualization of structural protein properties. +% +% \begin{itemize} +% +% \item \meta{type} = |standard area|\quad for the area values +% see legend of the alignment in \ref{starea} +% +% \item \meta{type} = |accessible area|\quad for values see +% \ref{accarea} +% +% \end{itemize} +% +% \label{Lclearfuncgroups} +% If no \meta{type} or an unknown \meta{type} is designated as option +% all functional groups and shading colors are cleared. This is +% also achieved by the command +% |\clearfuncgroups|. With all groups cleared one can start to +% build new shading modes from scratch. How to do this is explained +% in the next section. +% +% \label{Lfuncshadingstyle} +% In order to exchange the colors but to keep the group definitions +% and descriptions the command +% |\funcshadingstyle| can be +% employed. Usage: +% \medskip +% +% \quad|\funcshadingstyle{|\meta{residue}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}| +% +% \hfill|{|\meta{case}|}{|\meta{style}|}| +% \medskip +% +% \meta{residue} is one representative of the whole amino acid group. The +% colors which are declared by the next four parameters are used +% for all residues in this group. \meta{case} and \meta{style} are +% as described for example in |\nomatchresidues|. +% \end{enumerate} +% +% With |\shadeallresidues| \label{Lshadeallresidues} the +% threshold is ignored and +% all residues are shaded due to their group assignment. +% +% \subsection{Creating new functional shading modes} +% +% The grouping of amino acids due to other properties can make sense as +% suggested by \textsc{Karlin} and \textsc{Ghandour} [2], e.\,g.\ +% physical properties (molecular weight, shape), kinetic properties +% (reaction velocity, Michaelis-Menton constant), or structure +% ($\alpha$-helices, $\beta$-sheets, turns). +% +% \label{Lfuncgroup} +% New amino acid groups are defined with the +% |\funcgroup| command. This command needs six parameters: +% \medskip +% +% \quad|\funcgroup{|\meta{descr}|}{|\meta{residues}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}| +% +% \hfill|{|\meta{case}|}{|\meta{style}|}| +% \medskip +% +% \meta{descr} contains descriptive text which is displayed in the legend. +% The second parameter \meta{residues} holds the amino acids to be +% grouped. The colors for the foreground and background are set +% with the following two parameters, the case and style is declared by the +% last parameters. The example below defines a +% funcional group named `acidic ($-$)' containing the amino acids +% aspartic and glutamic acid with white letters on a red background: +% \bigskip +% +% \quad|\funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up}| +% \bigskip +% +% For the usage of colors see section \ref{colors}. Up to nine +% individual groups can be defined. New groups are simply added to the +% already existing groups, i.\,e.\ if an extension of the group +% definitions of an existing shading mode is desired there is +% no need to clear these groups und re-define them again. Just +% add the new groups with the |\funcgroup| command. To create +% completely new modes use the command +% |\shadingmode{functional}| without an option +% \emph{before} setting the new groups. The new definitions are active +% only in the functional shading mode---so be sure to +% have it switched on before setting the new groups. +% Remember, |\shadingmode{functional}| without an optional parameter +% clears all groups defined before, see above. The following example +% shows the definitions needed to produce an output which is identical +% to the functional mode `charge': +% \bigskip +% +% \quad|\begin{texshade}{|\meta{alignmentfile}|}| +% \medskip +% +% \quad\quad |\shadingmode{functional}| +% +% \quad\quad |\funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up}| +% +% \quad\quad |\funcgroup{basic ($+$)}{HKR}{White}{Blue}{upper}{up}| +% \medskip +% +% \quad|\end{texshade}| +% +% +% \subsection{Appearance of the consensus line} +% +% \label{Lthreshold} +% An important parameter for the calculation of the consensus is the +% threshold percentage. Default setting is 50\%, i.\,e.\ to become +% the consensus residue more than half of the residues at this +% position must be identical or similar, depending on the shading +% mode. Any percentage between 0 and 100 is allowed and can be +% set with +% |\threshold{|\meta{percentage}|}|, e.\,g.\ |\threshold{50}|. +% +% Additionally, an optional parameter can be set, e.\,g.\, +% |\threshold[90]{50}|, to label residues that are highly conserved +% in a special color (see example on page \pageref{ident}). +% +% \label{Lconstosingleseq} +% Another possibility is to set one sequence of the alignment +% as consensus and +% compare the other sequences to this one. Therefore, the +% command +% |\constosingleseq{|\meta{seqref}|}| is provided. The +% \meta{seqref} selects the sequence to be used as consensus +% (numbering according to the appearance in the alignment file; +% top sequence is number~1, or use the sequence name). +% Nevertheless, the threshold percentage is also taken into +% account, i.\,e.\ with a threshold of 50\% half +% of the sequences must be identical or similar compared to the +% specified consensus sequence in order to be shaded. +% \label{Lconstoallseqs} With |\constoallseqs| the +% consensus is calculated considering all sequences (the case +% described in the paragraph above). +% +% \label{Lshowconsensus}\label{Lhideconsensus} +% \label{Lnameconsensus} +% Consensus lines are displayed either on the top or at the bottom +% of the alignment by calling +% \medskip +% +% |\showconsensus[|\meta{color/scale}|[,|\meta{color/scale}|]]{|\meta{position}|}| +% \medskip +% +% with +% \meta{scale} |Gray|, |BlueRed|, |RedBlue|, |GreenRed|, |RedGreen|, +% |ColdHot| (recommended), |HotCold|, or |T-Coffee| \ref{TCoffee}, and \meta{position} |top| +% or |bottom|. +% +% The first color defines the foreground, i.e. the letters, the +% second color---if specified---defines the background. +% If a color scale is named the consensus will be shaded according +% to the level of sequence conservation (see section \ref{resweight} on residue +% weight tables below). For an example output see page +% \pageref{shadecons}. You can find more information on color scales +% on page \pageref{Lgraphs}. The calculated consensus colors can be exported +% as a Pymol [8] \label{Lexportconsensus} +% script by |\exportconsensus[|\meta{filename}|]{|\meta{seqref}|}|. +% If no \meta{filename} is specified |export.txt| will be used. The +% generated file can be opened in Pymol in order to shade a 3D model +% of the sequence \meta{seqref}. +% +% To hide the consensus use +% |\hideconsensus|. The consensus +% line is named `consensus' in english texts, `consenso' in spanish +% or `Konsensus' if the |german.sty| is used. With +% |\nameconsensus{|\meta{name}|}| any name can be set. +% +% \label{Ldefconsensus} +% You can tell \TeXshade{} which symbols or letters to use in +% the consensus line for different matching qualities by +% \bigskip +% +% \quad|\defconsensus{|\meta{symbol1}|}{|\meta{symbol2}|}{|\meta{symbol3}|}|. +% \bigskip +% +% The following parameters are allowed for symobols 1--3: +% +% \begin{enumerate} +% +% \item \meta{symbol1} = no match symbol (if below threshold) +% +% \begin{itemize} +% \item any character or letter +% \item |{}| (empty braces) for blank space +% \end{itemize} +% +% \item \meta{symbol2} = conserved symbol (if threshold is exceeded) +% +% \begin{itemize} +% \item |upper| (prints the consensus residue in uppercase) +% \item |lower| (prints the consensus residue in lowercase) +% \item any character or letter +% \item |{}| (empty braces) for blank space +% \end{itemize} +% +% \item \meta{symbol3} = highly conserved symbol (if +% +% \hfill|\allmatchspecial| is active) +% +% \begin{itemize} +% \item see \meta{symbol2} +% \end{itemize} +% +% \end{enumerate} +% +% Example: |\defconsensus{{}}{*}{upper}| does not show non matching +% residues in the consensus line, marks conserved residues +% with `|*|', and displays the uppercase letter of the consensus +% residue at positions with high conservation. +% +% +% \label{Lconsensuscolors} +% Finally, the colors of the above defined symbols are adjustable +% by the command: +% +% \begin{tabbing} +% \quad|\consensuscolors|\=|{|\meta{res.col.1}|}{|\meta{shad.col.1}|}|\\ +% +% \>|{|\meta{res.col.2}|}{|\meta{shad.col.2}|}|\\ +% +% \>|{|\meta{res.col.3}|}{|\meta{shad.col.3}|}|\\ +% \end{tabbing} +% +% The color definitions are in the same order as in the +% |\defconsensus| command: +% +% \begin{enumerate} +% +% \item \meta{res.col.1} = no match residue color (if below threshold) +% +% \meta{shad.col.1} = no match background color +% +% \item \meta{res.col.2} = conserved residue color (if threshold is exceeded) +% +% \meta{shad.col.2} = conserved background color +% +% \item \meta{res.col.3} = highly conserved residue color (if +% +% \hfill|\allmatchspecial| is active) +% +% \meta{shad.col.3} = highly conserved background color +% +% \end{enumerate} +% +% For colors which are not to be changed empty braces can be used. +% +% Example:\medskip +% +% \quad|\consensuscolors{}{}{Blue}{White}{Red}{Green}| +% \medskip +% +% Non matching symbol colors are not changed, +% conserved residues are displayed blue on white and highly conserved residues +% appear as red symbols on a green background in the +% consensus line. +% +% +% \subsubsection{Residue weight tables} \label{resweight} +% +% The degree of similarity between two amino acid residues is defined using +% so-called \emph{residue weight tables}. The values usually range roughly +% from $-10$ to 10, with positive values denoting similarity and negative +% values dissimilarity. The most simple table sets pairs +% of identical residues to a value of 10 and all others to 0, i.e. the +% |identity| matrix. Several more matrices based on extensive protein alignments +% exist and can be used, e.g. |PAM250| (|Point Accepted Mutations|), |PAM100|, +% or |BLOSUM62| (|BLOcks of amino acid SUbstitution Matrix|); for details see +% respective sources and section \ref{weightmatrix}. \TeXshade{} further contains a +% |structural| matrix where +% similarity is defined on simple comparisons of the sidechain properties with +% respect to volume and hydropathy. +% +% For calculation of the consensus color shading or for bar graphs or color scales +% in the |\feature| lines (\ref{Lfeature}), a residue weight table can be selected +% by \label{Lweighttable} |\weighttable{|\meta{table}|}| with \meta{table} +% being |identity|, |structural|, |PAM250|, |PAM100|, or |BLOSUM62| (default is +% |identity|). Which matrix suits the analysis best needs to be decided case by case. +% Due to the all-positive values of the |structural| matrix (section \ref{weightmatrix}) the similarity level +% appears usually very high; the |identity| matrix simply represents the number +% of identical residues at each position. The |PAM| and |BLOSUM| matrices provide +% more differentiated results. +% One can change individual values or even define his own weight table +% using the command \label{Lsetweight} +% |\setweight{|\meta{res.1}|}{|\meta{res.2}|}{|\meta{value}|}|, e.g. +% |\setweight{E}{Q}{2}| or |\setweight{K}{C}{-5}|. A full table, thus, needs 200 +% entries ($20 * 20 / 2$). \label{Lgappenalty} +% A value for the gap penalty is set with |\gappenalty{|\meta{value}|}|. +% +% \subsection{Display of logos} +% +% \subsubsection{Sequence logos} +% +% \label{Lshowsequencelogo}\label{Lhidesequencelogo} +% In a sequence logo [7], the information content $I(P_i)$ of +% each alignment position $i$ is defined as +% +% \[ +% I(P_i) = \log_2 \vert\Sigma\vert + \sum P_{ij} \cdot \log_2 P_{ij} +% \] +% +% \noindent +% with $\vert\Sigma\vert$ being the cardinality of the used alphabet, +% i.\,e. 4 for DNA and 20 for protein sequences, and $P_{ij}$ +% being the frequency of residue $j$ at this position. Each position +% is displayed as a stack of residue symbols whose heights +% represent their proportion of the information content (example on +% p.\pageref{logo}). +% +% The display of sequence logos can be either on the top or at the bottom +% of a nucleotide or protein alignment. Logos will be shown after the +% command: |\showsequencelogo[|\meta{colorset}|]{|\meta{top/bottom}|}|. If no optional +% \meta{colorset} is selected the residues will be shaded as follows:\medskip +% +% \begin{itemize} +% \item Nucleotide sequences +% +% \begin{itemize} +% \item[G]: Black +% \item[A]: Green +% \item[T,U]: Red +% \item[C]: Blue +% \end{itemize} +% +% +% \item Protein sequences (similar to rasmol) +% +% \begin{itemize} +% \item[D,E]: Red +% \item[C,M]: Yellow +% \item[K,R]: Blue +% \item[S,T]: Orange +% \item[F,Y]: MidnightBlue +% \item[N,Q]: Cyan +% \item[G]: LightGray +% \item[L,V,I]: Green +% \item[A]: DarkGray +% \item[W]: CarnationPink +% \item[H]: CornflowerBlue +% \item[P]: Apricot +% \item[B,Z]: LightMagenta +% \end{itemize} +% \end{itemize} +% +% Optional color sets correspond to the functional shading modes +% |chemical|, |rasmol|, |hydropathy|, |structure|, |standard area|, +% |accessible area| (see p.\pageref{funcdef}). The |\showsequencelogo| +% command can be reversed by |\hidesequencelogo|. +% +% \label{Llogocolor}\label{Lclearlogocolors} +% Logo colors can be turned to `Black' with the command +% |\clearlogocolors[|\meta{color}|]| with the optional parameter +% not set. The optional parameter can be used to set all +% residue colors to \meta{color}, e.g.\ |\clearlogocolors[Blue]|. +% User specific logo color sets are defined by using +% |\logocolor{|\meta{residues}|}{|\meta{color}|}|, e.g.\ +% |\logocolor{DE}{Red} \logocolor{CM}{Yellow}| etc. +% +% \label{Ldofrequencycorrection}\label{Lundofrequencycorrection} +% It is common practice for protein sequence logos to correct +% amino acid frequencies to the background frequency in the +% alignment, which usually differs from the equal distribution +% of 5\% for each residue. Frequency correction can be turned on +% by |\dofrequencycorrection| and off by |\undofrequencycorrection|. +% +% \label{Llogostretch}The vertical extent of the logo can be changed by +% |\logostretch{|\meta{factor}|}|, e.g.\ |\logostretch{1.5}|. +% The width of the logo characters is dependent on the character +% width set for the alignment, see |\charstretch| on p.\pageref{Lcharstretch}. +% +% \label{Lshowlogoscale}\label{Lhidelogoscale}Finally, the bit-scale +% can be turned off and on using |\hidelogoscale| and +% |\showlogoscale[|\meta{color}|]{|\meta{position}|}|, respectively, with +% \meta{position} |left|, |right|, or |leftright| and an optional +% \meta{color}. +% \label{Lnamesequencelogo} +% A name for the sequence logo can be set, which is displayed +% next to the scale by |\namesequencelogo{|\meta{name}|}|. +% +% +% \subsubsection{Subfamily logos} +% +% Subfamily logos provide a novel tool to visualize +% subfamily-specific sequence deviations at alignment positions with +% a high information content in an intuitive way [14]. +% +% This is achieved by subtracting from the frequency of a residue within +% a pre-defined subset of sequences, i.\,e. a subfamily, the frequency of +% this residue in the remaining set of sequences. The difference is then +% weighted by the information content, see above section on sequence logos. +% An example is shown on p.\pageref{sublogo}. +% +% Subtraction of frequencies produces values from $-1$ to $1$. Positive +% values correspond to residues which are characteristic for the subfamily +% (shown upright in the output), negative values to those that are typical +% for the remaining sequences (shown upside-down). Positions with an equal +% distribution of the residue result in a zero value. +% +% \label{Lshowsubfamilylogo}\label{Lhidesubfamilylogo}\label{Lsetsubfamily} +% Subfamily logos are displayed analogous to sequence logos by the command +% |\showsubfamilylogo[|\meta{colorset}|]{|\meta{top/bottom}|}| and hidden by +% |\hidesubfamilylogo|. To calculate a subfamily logo, it is further required +% to define a subfamily within the alignment by +% |\setsubfamily{|\meta{seqrefs}|}|, e.g. |\setsubfamily{1-10,20,AQP3}|. +% +% For coloring residues, display/stretching of the scales, and frequency +% correction the same commands as for sequence logos apply with two exceptions. +% \label{Lshownegatives}\label{Lhidenegatives} +% First, subfamily logos contain negative values, which can be displayed +% |\shownegatives[|\meta{weak, medium, strong}|]| or hidden +% |\hidenegatives|. Without the optional parameter negative residues will +% be tinted by 50\%, i.e. |medium|. This greatly improves readability. +% \label{Lnamesubfamilylogo} +% Second, a name for the subfamily logo is set by +% |\namesubfamilylogo[|\meta{neg.name}|]{|\meta{pos.name}|}| with a required +% name for the positive part of the logo and an optional name for the negative +% part. +% +% \label{Lrelevance}\label{Lshowrelevance}\label{Lhiderelevance} +% In order to better recognize relevant positions in the subfamily logo, a +% bit-value can be set above which the deviation is considered relevant +% by the command |\relevance{|\meta{bit-value}|}|. If this command is +% not given 2.321\,bit is assumed for proteins, i.\,e. +% $\log_2 5$, and 1\,bit for DNA, i.\,e. $\log_2 2$. Such positions will +% be labeled by +% |\showrelevance[|\meta{color}|]{|\meta{symbol}|}|, e.\,g. +% |\showrelevance[Blue]{$\nabla$}|. The symbol will be hidden with +% |\hiderelevance|. +% +% \subsection{Appearance of the sequence lines} +% +% \label{seqlines} +% +% \subsubsection{Names, numbers and gaps} +% \label{Lshownames}\label{Lshownumbering} +% Many parameters that influence the appearance of the actual sequence +% lines can be changed for customization. +% Thus, the sequence names can be shown colored via \meta{color} +% either left or right by +% \medskip +% +% \quad|\shownames[|\meta{color}|]{|\meta{position}|}| +% \medskip +% +% with \meta{position} set to |left| or |right|. The numbering can be +% displayed either left or right and even on both sides by +% \medskip +% +% \quad|\shownumbering[|\meta{color}|]{|\meta{position}|}| +% \medskip +% +% with \meta{position} |left|, |right| or |leftright|. Both, +% names and numbering can be displayed on the same side. +% \label{Lnamescolor}\label{Lnumberingcolor} +% The colors can also be set with |\namescolor{|\meta{color}|}| and +% |\numberingcolor{|\meta{color}|}|, respectively. +% +% \label{Lnameseq} +% \TeXshade{} uses the sequence names from the +% alignment input file. This can cause some +% problems during the \TeX-run when special characters are present +% in those names! \TeXshade{} does not accept the following characters +% in sequence names: |\ { } @| spaces and the tilde. Those have to be replaced in +% the input file. The characters |#| and |%| can only be used with a +% leading backslash, e.\,g. |\#|. This must also be changed in the +% input file. All other special characters should be displayed +% properly. +% +% Sequence names that are accepted by \TeXshade{} can further be +% changed in the |texshade| environment: +% \medskip +% +% \quad|\nameseq{|\meta{seqref}|}{|\meta{name}|}| +% \medskip +% +% \meta{seqref} selects the sequence whose name is to be changed. +% The basis for the \meta{seqref} is the appearance in +% the alignment input file with the top sequence = 1, or the old +% name. +% \label{Lnamecolor}\label{Lnumbercolor} +% In order to change the colors only of some sequence names or numbers +% the commands +% |\namecolor{|\meta{seq1}|, ... ,|\meta{seq n}|}{|\meta{color}|}| and +% |\numbercolor{|\meta{seq1}|, ... ,|\meta{seq n}|}{|\meta{color}|}| +% are provided. +% +% \label{Lhidenames}\label{Lhidename} +% \label{Lhidenumbering}\label{Lhidenumber} +% In order to hide all names or the numbering use the command +% |\hidenames| or |\hidenumbering|. If only the names or numbers of +% some sequences should be hidden apply +% +% |\hidename{|\meta{seq1}|, ... ,|\meta{seq n}|}| or +% +% |\hidenumber{|\meta{seq1}|, ... ,|\meta{seq n}|}|, respectively. +% +% \label{Lstartnumber} \label{Lallowzero} \label{Ldisallowzero} +% In some situations, e.\,g.\ when only sections of sequences are +% displayed, one +% may not want to have the residue numbering start out with number~1. +% The command +% |\startnumber[|\meta{start..stop}|]{|\meta{seqref}|}{|\meta{startnumber}|}| +% allows one to set the starting number of any sequence to any value +% incl.\ negative values but except `0' which is not usually used in +% sequence numbering (the transition from negative to positive +% values is like this: \ldots\ $-2$, $-1$, 1, 2 \ldots). If, however, +% the use of the number `0' is wanted as sometimes in sequence logos +% this can be turned on by |\allowzero| and off with |\disallowzero|. +% The optional parameter can be used to truncate the sequence display +% to a certain section (see also |\setends| below). +% +% \label{Lseqlength} +% \TeXshade{} needs to know the correct length of the sequences +% to be able to break them right after the last residue. If +% MSF files are used as an input the length is already given +% but the calculation is usually wrong because the gaps are +% also counted. Thus, \TeXshade{} counts the number of residues +% during each run by itself and stores the values in the |.aux| file. That +% means that it needs two runs to get the numbers right. Again, +% this is only important if the gap symbol after the sequence end +% should be suppressed, see below (|\hideleadinggaps|). +% +% If you know the correct length of the sequences you can use the +% command +% \medskip +% +% \quad|\seqlength{|\meta{seqref}|}{|\meta{length}|}| +% \medskip +% +% in order to set the values by hand and have the gaps break +% properly already in the first \TeX{} run. +% \medskip +% +% Example: |\seqlength{1}{346}| means that sequence no.~1 is 346 +% residues long. +% +% +% \label{Lshowruler}\label{Lhideruler} +% \label{Lrulersteps}\label{Lrulercolor} +% \label{Lrotateruler}\label{Lunrotateruler} +% \label{Lnamerulerpos}\label{Lrulerspace} +% Another possibility to label sequence positions is to switch +% on a ruler on the top or at the bottom of the sequence block +% using \label{ruler} +% |\showruler[|\meta{color}|]{|\meta{position}|}{|\meta{seqref}|}|. +% The residue ruler of one sequence \meta{seqref} or the consensus +% (declare `|consensus|' as \meta{seqref}) can be +% displayed at \meta{position} |top| or |bottom|. +% The ruler is hidden with |\hideruler|. The steps between two +% numbers are set by |\rulersteps{|\meta{number}|}|. If the steps +% are set to be very close ($< 4$) or when every position is numbered, the +% numbering is automatically rotated by 90$^\circ$. Using |\rotateruler| +% and |\unrotateruler| this can be done and undone manually. +% In order to change the +% ruler color use the optional parameter or the command +% |\rulercolor{|\meta{color}|}|. Also, the label and its color at individual +% ruler positions can be changed by the user to a string using +% |\namerulerpos{|\meta{number}|}{|\meta{text}|[|\meta{color}|]}| +% (see example on p.\ \pageref{ras}). Finally, to adjust the distance +% between the ruler and the top or bottom sequence row use +% |\rulerspace{|\meta{length}|}|, e.\,g. |\rulerspace{1mm}|. +% +% \label{Lgapchar}\label{Lgaprule} +% \label{Lgapcolors}\label{gapchar} +% Further, the symbol which is displayed in sequence gaps is freely +% selectable with +% |\gapchar{|\meta{symbol}|}|. \meta{symbol} can be any character +% or symbol. If math symbols are to be used math mode must be +% activated by |$| characters, i.\,e. |\gapchar{{$\triangle$}}|. +% Note the double curly braces in the last command. Everytime a +% `complex' character is used, i.\,e. a character definition consisting +% of more than one letter, it must be braced in order to be interpreted as one +% character. One exception is |\gapchar{rule}|; with this +% parameter lines are drawn in the sequence gaps with a certain +% thickness defined by |\gaprule{|\meta{thickness}|}|, e.\,g. +% |\gaprule{1.5pt}|. The colors of the gaps and gap symbols are set by +% |\gapcolors{|\meta{symbol color}|}{|\meta{background color}|}|. +% +% There are some discussions whether or not to display gap symbols before +% and after the actual sequence. Since v1.3a one can control the +% appearance of those gap symbols by the commands +% \label{Lshowleadinggaps} \label{Lhideleadinggaps} +% |\showleadinggaps| and |\hideleadinggaps|. By default, leading +% gaps are indicated by symbols despite my personal +% thinking that it could suggest that +% there are some not displayed residues upstream resp.\ downstream of the +% gap. +% +% At certain instances a protein alignment input file may contain stop +% positions, e.\,g. due to frame shifts in the underlying DNA sequence. +% If such positions are labeled in the input with an |*| this will be +% shown in the output as well as an asterisk, i.\,e. distinguishable from +% a normal gap symbol. The character shown at stop positions can be +% changed by |\stopchar{|\meta{symbol}|}|. \label{Lstopchar} +% +% \subsubsection{Displaying selected residues in the alignment} +% +% \label{Lsetends} +% \TeXshade{} can display a section of the complete alignment +% without the need to edit the alignment input file or even +% to re-calculate +% the entire alignment. This allows one to use one single +% alignment of the full length proteins or open reading frames for +% multiple visualizations of different sections in a document as +% done in this manual. Thus, the file |AQPpro.MSF| contains +% the full-length multiple protein alignment of five aquaporins but +% only sections are displayed as examples in +% \ref{ident} through \ref{accarea}. The definition of a section +% is done by +% \medskip +% +% \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}|. +% \medskip +% +% Again, \meta{seqref} is the sequence number based on the +% appearance in the alignment file, or the name; further, in order to use +% the consensus as a measure for the sequence section the +% string `|consensus|' as \meta{seqref} is accepted. The +% specified sequence is truncated at +% positions \meta{start} and \meta{stop}. All other +% sequences are cut accordingly. If the number of the first +% residue in the sequence is set to a new value with the +% |\startnumber| command (s.\,a.) this is taken into account. The +% \meta{startnumber} can be set as an optional parameter directly +% in the |\setends| command as well. +% \medskip +% +% Some examples: +% \medskip +% +% \quad a) |\setends{1}{21..100}| +% \medskip +% +% \quad b) |\startnumber{1}{101} \setends{1}{121..200}| +% \medskip +% +% Both commands select the same sequence section from the alignment but +% numbering for sequence 1 starts at position~21 in the first example and at +% position~121 in the latter. +% \medskip +% +% \quad c) |\setends[101]{1}{121..200}| equals example b. +% \medskip +% +% \medskip +% +% \quad d) |\startnumber[121..200]{1}{101}| also equals example b. +% \medskip +% +% \medskip +% +% \quad e) |\setends{consensus}{21..100}| +% \medskip +% +% This may describe a very different section of the multiple +% sequence alignment because the consensus counts every position +% including gaps. +% +% \label{Lsetdomain} +% The output can be even further restricted to +% individually selected residues, e.g.\ to eliminate uninteresting alignment stretches or +% to condense the output, by: +% \medskip +% +% \quad|\setdomain{|\meta{seqref}|}{|\meta{selection}|}| +% \medskip +% +% Here, \meta{seqref} denotes the reference sequence by its number or name. +% This sequence is used to define the alignment positions \meta{selection} +% to be shown. +% \meta{selection} can have two different formats +% depending on whether (a) the user wants to select the positions manually +% or (b) \TeXshade{} is supposed to select the residues based on 3D +% coordinates provided by a PDB file. +% +% To select the residues manually, the user provides a position list of +% the following format: +% \medskip +% +% \quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}| +% \medskip +% +% For how to select positions by 3D coordinates +% provided by a PDB file, see \ref{Lshaderegion}. +% \medskip +% +% Examples (see also p.\,\pageref{ident}ff): +% +% \quad|\setdomain{1}{20..80}| +% +% \quad|\setdomain{consensus}{20..80,100..150,200..220}| +% +% \quad|\setdomain{AQP1}{point[6]:1FX8.pdb,173[side]}| +% +% \quad|\setdomain{3}{plane[0.5]:1JN4.pdb,66[CA],73[side],199[CA]}| +% \medskip +% +% +% It is helpful to show a ruler (e.g. single-stepped, see p.\,\pageref{Lshowruler}) to +% label the residue positions. +% +% The resulting gaps between sequence stretches are marked by a vertical rule, which +% can be changed in thickness by +% \medskip +% +% \quad|\domaingaprule{|\meta{thickness}|}|, e.\,g.\ +% |\domaingaprule{1pt}|. \label{Ldomaingaprule} +% \medskip +% +% Also, the colors can be set by +% \medskip +% +% \quad|\domaingapcolors{|\meta{foreground}|}{|\meta{background}|}| \label{Ldomaingapcolors} +% \medskip +% +% e.\,g.\ |\domaingapcolors{Blue}{Yellow}|. +% +% +% \subsubsection{Hiding, killing, separating and ordering} +% +% \label{kill} +% +% \label{Lhideseq}\label{Lhideseqs}\label{Lshowseqs}\label{Lkillseq} +% If one or more sequences from the alignment input file should be used for +% the calculation of the consensus but it is desired not to +% display these sequences in the final output use the command +% |\hideseq{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}|. +% For consecutive sequence numbers a dash can be used, e.\,g. +% |\hideseq{1-3}| instead of |\hideseq{1,2,3}|. Decending series +% are also permitted, e.\,g. |\hideseq{3-1}|. +% This command allows one for example to hide +% the sequence which has been defined as the consensus sequence +% with |\constosingleseq|. When all sequences should be hidden, e.g. to +% show a sequence logo alone, one can simply say |\hideseqs|. This +% command is reversed by |\showseqs|. +% +% In order to completely exclude sequences the command +% |\killseq{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}| is +% provided. Again, for number series the dash can be used (s.\,a.). The +% designated sequences are neither displayed nor +% considered for the calculation of the consensus. This is +% another possibility to comment out sequences in addition +% to the use of an exclamation point infront of the |Name:| +% definition in an MSF-file (see figure on page \pageref{commout}). +% +% \label{Ldonotshade} +% The command +% |\donotshade{|\meta{seq1}|,|\meta{seq2}\ldots|,|\meta{seq n}|}| +% makes +% one or more sequences (remember the dash, s.\,a.) appear unshaded +% in black letters on white background. +% This does not influence any other sequences or the consensus +% calculation. +% +% \label{Lhideresidues}\label{Lshowresidues} +% If a very graphical output of the sequences is desired, the +% residue symbols or letters can be blanked out by +% |\hideresidues|. Now, only the shaded boxes are printed. +% In combination with |\gapchar{rule}| one obtains alignments +% in a style \`a la Mondrian. +% The residues reappear with |\showresidues|. +% +% \label{Lseparationline}\label{Lsmallsep} +% \label{Lmedsep}\label{Lbigsep} +% \label{Lvsepspace} +% If an alignment contains members of several subgroups of a +% protein or a gene family it may be rather helpful to visualize the group +% divisions by a separation line. Therefore, the command +% |\separationline{|\meta{seqref}|}| is applicable. This +% command inserts vertical space after the sequence which is +% refered to by \meta{seqref}. How much space is inserted +% is defined by one of the following commands: +% |\smallsep|, |\medsep| (default) or |\bigsep|. These lengths +% correspond to the known |\small|-, |\med|- and |\bigskip| commands. +% With |\vsepspace{|\meta{length}|}| any length with any +% \TeX{} unit can be assigned, e.\,g. |\vsepspace{2mm}|. +% +% \label{Lorderseqs} +% The sequence order given by the alignment input file is easily +% reorganized by +% |\orderseqs{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}| +% without the need for editing the alignment input file (which +% would be a big copy'n'paste job). +% Make sure that all sequences are assigned in this +% command. If there are more sequences present than numbers or names in the +% command an error message will occur. Here also, the dash can be +% used for sequence number series. Example: |\orderseqs{1-3,6-4,7}| +% is equivalent to |\orderseqs{1,2,3,6,5,4,7}|. +% Reordering of sequences only changes the output; all commands using +% the parameter \meta{seqref} are not influenced, because \meta{seqref} +% always corresponds to the appearance in the alignment file. Thus, +% to completely reverse the order of a five sequence alignment simply type +% |\orderseqs{5-1}|. +% +% +% \subsubsection{Residues per line and further settings} +% +% \label{Lresiduesperline}\label{Lresiduesperline*} +% By default \TeXshade{} puts the highest possible by five +% divisible number of residues in one line depending on the +% |\linewidth|. With |\residuesperline{|\meta{number}|}| a new +% value can be set. If this value exceeds the highest possible +% number of residues per line it is ignored; lower values are +% accepted of course. But also in the latter case the number +% of residues printed per line is rounded such to be divisible by five. +% To force \TeXshade{} +% to set lines with exactly the desired number of residues use +% the asterisk-extended command |\residuesperline*{|\meta{number}|}|. +% You have to take care yourself of the alignment width after this command, +% because in this mode \TeXshade{} does not check the length of the +% lines any more. +% +% \label{Lcharstretch}\label{Llinestretch} +% \TeXshade{} calculates the dimensions of a shaded box from +% the width and height of the uppercase letter `M' and the depth of +% the lowercase `g'. Depending on the font used for the +% sequence residues the box dimensions might not be fully +% satisfactory. With |\charstretch{|\meta{factor}|}| and +% |\linestretch{|\meta{factor}|}| the width and height/depth, +% respectively, of the boxes can be multiplied individually by a +% \meta{factor} to stretch ($>1$) or shrink ($<1$) the dimensions. +% +% \label{Lnumberingwidth} +% The reserved space for the sequence numbering is set by the +% command |\numberingwidth{|\meta{n digits}|}|. Here, the default setting +% is four-digit numbering, i.\,e.\ $-999$ through 9999. If this range +% is to be changed assign the desired number as parameter +% \meta{n digits}, e.\,g.\ |\numberingwidth{111111}| reserves +% space for 6 digit numbering. +% +% The vertical space between the sequence blocks can be controlled +% by the commands |\smallblockskip|, |\medblockskip| (default +% setting), +% \label{Lsmallblockskip}\label{Lmedblockskip} +% \label{Lbigblockskip}\label{Lnoblockskip} +% \label{Lvblockspace} +% |\bigblockskip| or |\noblockskip|. Further, the command +% |\vblockspace{|\meta{length}|}| allows one to set a defined space +% length using any \TeX{} unit, e.\,g.\ |\vblockspace{0.4in}|. +% +% Two more commands set the space between the sequence blocks to be +% \label{Lflexblockspace}\label{Lfixblockspace} +% flexible (|\flexblockspace|) (default) or fixed (|\fixblockspace|). +% Flexible means, that only the vertical white space between the +% blocks is kept to the settings by +% e.\,g. |\medblockskip|. This results in flexible space between +% the actual blocks depending on the presence of feature lines. When +% switching to fixed space the distance of the blocks is kept constant +% by using more white space between blocks without feature lines. +% Thus, a difference between flexible and fixed space will only be +% noticeable when features are used. +% +% \label{Lalignment} +% The position of the output can be aligned left, right +% or centered on the page by |\alignment{|\meta{position}|}| +% with the \meta{position} parameter |left|, |center| or +% |right|. +% +% +% +% \subsubsection{Fingerprinting} +% +% \label{fingerprint} +% +% \label{Lfingerprint} +% An easy way to gain an overview on complete alignments is +% provided by displaying a so called alignment `fingerprint'. +% In this style the whole sequence can be shown in one line. Due to +% the lacking space the residue names are hidden and the shaded +% boxes are reduced to thin vertical colored lines. The command +% |\fingerprint{|\meta{res. per line}|}| takes one argument stating +% the desired number of residues per line, e.\,g. |\fingerprint{1000}|. +% All \TeXshade{} commands are compatible with |\fingerprint|, +% i.\,e. all shading modes are applicable for displaying overviews +% on similarity or every functional aspect. Also, all kinds of +% labeling---as described in the following---work with this +% command. +% +% +% \subsection{Individual shading and labeling of sequence stretches} +% +% Computer calculated conservation shading is informative---but +% even more information can be visualized by additional labeling +% of positions and regions of interest with different colors, +% text styles or graphical marks and descriptive text. All this +% is provided by easy to handle \TeXshade{} commands. +% +% +% \subsubsection{Shading of regions and blocks} +% \label{shaderegion} +% +% \label{Lshaderegion} +% Besides the shading calculated by \TeXshade{} any region can be +% additionally shaded with a color specified by the user. This is very +% useful to highlight secondary protein modification +% sites such as phosphorylation or glycosylation sites, or longer +% motifs for example protein/protein interaction sites or protein domains. +% This is done with the following command: +% \medskip +% +% \quad|\shaderegion{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}| +% \medskip +% +% Here, \meta{seqref} refers to the sequence by its name or number +% within the alignment. The +% foreground and background colors can be set with the last two +% parameters. +% \meta{selection} can have three different formats +% depending on whether (a) the user wants to select the positions manually, +% (b) the selection should be based on a sequence motif to be found by \TeXshade{}, +% or (c) \TeXshade{} is supposed to select the residues based on 3D +% coordinates provided by a PDB file. +% \medskip +% +% (a) To select the residues manually, the user provides a position list of +% the following format: +% \medskip +% +% \quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}| +% \medskip +% +% In order to shade residue number 13 and the region +% 20--30 of sequence number 1 in red letters on a green background +% type the following command: +% \medskip +% +% \quad|\shaderegion{1}{13..13,20..30}{Red}{Green}| +% \medskip +% +% If the consensus is to be shaded use |consensus| as +% \meta{seqref}. +% \medskip +% +% (b) A sequence motif can be given, which will be found and labeled. A simple +% example selecting all sequence motifs `NNAD' in sequence `1' would be: +% \medskip +% +% \quad|\shaderegion{1}{NNAD}{Red}{Green}| +% \medskip +% +% The definition can further include `X' for any residue and groups of residues in brackets +% at uncertain positions. The example below will find all motifs in sequence `1' +% that start with an asparagine, followed by any two residues, an acidic, a +% basic residue, again any two residues and finally a glutamine. +% \medskip +% +% \quad|\shaderegion{1}{NXX[DE][KR]XXQ}{Red}{Green}| +% \medskip +% +% (c) In order to select positions based on the 3D structure a PDB +% structure file is required. \TeXshade{} can select residues within +% a given distance in \AA{} around a point, along a line, or above and +% below a plane, which are defined by one to three residues. The points +% can be further specified to be the $\alpha$-carbon atom, i.\,e.\ the +% protein backbone, or the most distant atom of the sidechain. Accordingly, +% \meta{selection} has one of the formats: +% \medskip +% +% \quad|{point[|\meta{dist}|]:|\meta{file}|,|\meta{num}|[CA/side]}| +% \medskip +% +% \quad|{line[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side]}| +% \medskip +% +% \vbox{% +% \quad|{plane[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side],| +% \medskip +% +% \hfill\meta{num3}|[CA/side]}| +% } +% \medskip +% +% +% Example: in order to select and shade as above all residues that are within an 8\ \AA{} +% sphere around the $\alpha$-carbon of residue 81 and the data are +% provided in the PDB file |1J4N.pdb|, type: +% \medskip +% +% \quad|\shaderegion{1}{point[8]:1J4N.pdb,81[CA]}{Red}{Green}| +% \medskip +% +% Example: two points denote a line, hence, give two residues to select +% everything within 1\ \AA{} along the line between the $\alpha$-carbon of +% residue 81 and the sidechain of residue 168 with: +% \medskip +% +% \quad|\shaderegion{1}{line[1]:1J4N.pdb,81[CA],168[side]}| +% \medskip +% +% \hfill|{Red}{Green}| +% \medskip +% +% Definition of a plane follows the same format but requires three points. +% If the optional parameters |[\meta{dist}]| and |[CA/side]| are not given, +% \TeXshade{} assumes |[1]| and |[side]|, respectively. +% +% In case one needs the position numbers of the selected residues for usage +% in other applications, those can be either printed in the \TeX{} document with +% |\printPDBlist{|\meta{selection}|}| or shown during the \TeX{} run with +% |\messagePDBlist{|\meta{selection}|}|. The commands can be used outside of the +% \TeXshade{} environment. \label{LprintPDBlist}\label{LmessagePDBlist} +% +% Both selection formats, i.\,e. a manually given list and the 3D selection, +% can be used with |\shadeblock| (see below), +% |\tintregion|, |\tintblock|, |\emphregion|, |\emphblock|, |\lowerregion|, |\lowerblock|, +% |\frameblock| (all in \ref{Lframeblock}), and |\feature| (\ref{Lfeature}). +% +% +% \label{Lshadeblock} +% In analogy to |\shaderegion| which is restricted to a single +% sequence, |\shadeblock| shades the corresponding region in all +% other sequences as well +% except the consensus. If also the consensus is to be shaded +% define the region using |consensus| as \meta{seqref}. +% \medskip +% +% \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}| +% \medskip +% +% +% Another option is to change the whole set of shading colors for certain +% sequence blocks, e.\,g.\ from |blues| to |reds| or self-defined color sets (see \ref{Lshadingmode}). +% Therefore, the following command was implemented: +% \medskip +% +% \quad |\changeshadingcolors{|\meta{seqref}|}{|\meta{selection}|}{|\meta{name}|}| +% \medskip \label{Lchangeshadingcolors} +% +% Examples: +% \medskip +% +% \quad |\changeshadingcolors{1}{10..50}{reds}| +% \medskip +% +% \quad |\changeshadingcolors{AQP1}{[AS]NKD}{my_set}| +% \medskip +% +% etc. +% +% \subsubsection{Emphasizing, tinting, lowercasing, and framing} +% +% \label{Lemphregion}\label{Lemphblock} +% If it is preferred to keep the calculated shading colors +% but distinct regions or blocks are yet to be emphasized one +% can use the following commands to change the font style of +% such regions: +% \medskip +% +% \quad|\emphregion{|\meta{seqref}|}{|\meta{selection}|}| +% \medskip +% +% and +% \medskip +% +% \quad|\emphblock{|\meta{seqref}|}{|\meta{selection}|}| +% \medskip +% +% For the format possibilities of the \meta{selection} parameter please see \ref{Lshaderegion}. +% +% \label{Lemphdefault} +% Which style \TeXshade{} uses for emphasizing regions is defined by +% |\emphdefault{|\meta{style}|}|. Default setting is the +% \emph{italics} font shape (set by |\emphdefault{it}|). In order to change +% this setting choose one of the styles |bf, md, up, it, sl, rm, sf, tt|. +% +% Example: |\emphdefault{bf}| +% \medskip +% +% \label{Ltintregion}\label{Ltintblock} +% Further, it is possible to tint the region or block in question +% or to switch the characters to lowercase +% by using the commands (for example see hydropathy-figure on page +% \pageref{hydro}): +% \medskip +% +% \quad|\tintregion{|\meta{seqref}|}{|\meta{selection}|}| +% \medskip +% +% and +% \medskip +% +% \quad|\tintblock{|\meta{seqref}|}{|\meta{selection}|}| +% \medskip +% +% \label{Ltintdefault} +% The level of tinting in the region in question can be set by +% |\tintdefault{|\meta{level}|}| with |weak|, |normal|, and +% |strong| as possible \meta{level}s. +% \medskip +% +% \label{Llowerregion}\label{Llowerblock} +% \quad|\lowerregion{|\meta{seqref}|}{|\meta{selection}|}| +% \medskip +% +% and +% \medskip +% +% \quad|\lowerblock{|\meta{seqref}|}{|\meta{selection}|}| +% \medskip +% +% +% Another option is to draw a bounding box around the sequence block +% in question (for an example see diversity mode-figure on page +% \pageref{frame}) with the +% command:\footnote{Thanks to Alan Robinson for inspiration.} +% \medskip\label{Lframeblock} +% +% \quad|\frameblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{color}|[|\meta{length}|]}| +% \medskip +% +% With the optional parameter the default line thickness of the frame can +% be changed, example: |\frameblock{1}{10..20,50..70}{Red[2pt]}| +% +% +% +% +% \subsubsection{Graphical labeling of sequence features} +% +% \label{feature} +% +% \label{Lfeature} +% The |\feature| command is designed to fulfill most needs for the +% graphical labeling of sequence stretches and the setting of descriptive +% text. It needs five parameters: +% \medskip +% +% \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{selection}|}{|\meta{labelstyle}|}{|\meta{text}|}| +% \medskip +% +% In the following paragraphs all possible parameter settings of +% this rather complex but mighty command are discussed in detail. +% The parameter \meta{position} tells \TeXshade{} where to display +% the feature label, i.\,e. on the top of the alignment (|top|), +% or at the bottom (|bottom|). Further, there can be three more feature lines +% ontop of the top feature line (|ttop|, |tttop|, and |ttttop|) or below the bottom +% feature line (|bbottom|, |bbbottom|, |bbbbottom|). Thus, up to eight features +% overlapping in eight different lines may be displayed. +% Depending on the content of the feature lines the gaps between +% them might be not satisfactory. +% \label{Ltopspace}\label{Lttopspace} +% \label{Ltttopspace}\label{Lttttopspace} +% \label{Lbottomspace}\label{Lbbottomspace} +% \label{Lbbbottomspace}\label{Lbbbbottomspace} +% Therefore, eight separate commands can be employed to change the +% space below |ttttop|, |tttop|, |ttop|, or |top| +% (|\topspace{|\meta{length}|}| etc.), and above +% |bottom|, |bbottom|, |bbbottom|, or |bbbbottom| +% (|\bottomspace{|\meta{length}|}| etc.). Use positive +% values to further separate the lines, e.\,g. +% |\ttopspace{3mm}| or negative values to reduce the space, e.\,g. +% |\bottomspace{-0.1in}|. +% +% The argument \meta{seqref} and the third +% parameter containing the \meta{selection} of the specified residues +% are identical to the ones described before in several commands, e.\,g. +% |\shaderegion| (\ref{shaderegion}). +% +% New is the fourth parameter for the definition of the label style. +% There are many possibilities like braces, helices, boxes, arrows, bars, any +% fill character, bar graphs, color scales or even translations of the +% specified regions. +% \medskip +% +% \textbf{Braces:}\\ +% In order to display an over- or underbrace as +% a label use the parameter |{brace}|. Depending on the +% \meta{position} (|ttttop|, |tttop|, |ttop|, |top|, |bottom|, +% |bbottom|, |bbbottom|, or |bbbbottom|) the respective brace is +% displayed. The standard color of braces is +% black. It can be changed by an optional parameter directly after +% the definition of the symbol, e.\,g. |{brace[Red]}|. +% \medskip +% +% \textbf{Protein $\alpha$-Helices:}\\ +% The parameter |{helix}| will plot a symbolized $\alpha$-helix +% as a label. The standard color of the helix spiral is +% black. It can be changed by an optional parameter directly after +% the definition of the symbol, e.\,g. |{helix[Red]}|. +% \medskip +% +% \textbf{Filling a stretch with a symbol:}\\ +% A region can be filled with any character for +% labeling purposes using the parameter |{fill:|\meta{symbol}|}|. +% The \meta{symbol} is freely selectable; the usage is like +% in |\gapchar| (\ref{gapchar}). Do not use spaces before or after +% the expression \meta{symbol}; this will shift the symbols to the +% respective direction. The standard color of the fill symbol is +% black. It can be changed by an optional parameter directly after +% the definition of the symbol, e.\,g. |{fill:$\bullet$[Red]}|. +% +% The |\feature| command does not like special characters in +% text mode, e.\,g. |\dag|. One has to use the math version of +% those symbols between |$|-signs. The following quite common +% text symbols have also a math equivalent\footnote{Thanks to +% Darrell Conklin for reporting this problem}: +% +% \begin{center} +% \begin{tabular}{cll} +% \emph{symbol} & \emph{command} & \emph{description} \\ \hline +% $\dagger$ & |$\dagger$| & dagger\\ +% $\ddagger$ & |$\ddagger$| & double dagger\\ +% $\mathparagraph$ & |$\mathparagraph$| & paragraph mark\\ +% $\mathsection$ & |$\mathsection$| & section mark\\ +% $\mathdollar$ & |$\mathdollar$| & dollar\\ +% $\lbrace$ & |$\lbrace$| & left brace\\ +% $\rbrace$ & |$\rbrace$| & right brace\\ +% \end{tabular} +% \end{center} +% \medskip +% +% \textbf{Labeling restriction or protease cutting sites:}\\ +% If a label is needed that points between two residues, e.\,g. +% for showing restriction sites, simply use the feature style +% |{restriction[|\meta{color}|]}|. This will show a filled +% triangle with the tip right between the residues to be labeled, +% e.\,g. |\feature{top}{1}{25..26}{restriction[Blue]}{EcoR I}|. +% +% \medskip +% +% \textbf{Boxes:}\\ +% Boxed text is printed using the parameter |{box:|\meta{text}|}|. +% By default black letters in a white framed box are displayed. In +% order to change these colors optional parameters can be included +% in the argument: +% \medskip +% +% \quad|{box[|\meta{framecolor,boxcolor}|][|\meta{length}|]:|\meta{text}|[|\meta{textcolor}|]}|. +% \medskip +% +% If the box frame and fill colors are the same it is sufficient to +% use only this one color as an argument in the command. The optional +% parameter \meta{length} defines the thickness of the box frame. If +% this parameter is not set in the command the value from the +% |\featurerule{|\meta{length}|}| command (see below) is used. +% \medskip +% +% Examples: +% \medskip +% +% \quad|{box[Blue]:$\alpha$-helix[Yellow]}| +% \smallskip +% +% \quad|{box[Blue,Red]:$\alpha$-helix[Yellow]}| +% \smallskip +% +% \quad|{box[Blue,Red][2pt]:$\alpha$-helix[Yellow]}| +% \medskip +% +% \medskip +% +% \textbf{Horizontal bars and arrows:}\\ +% For displaying bars and arrows a simple selection scheme +% consisting of three consecutive characters is +% used as the \meta{labelstyle} parameter. Each bar or arrow is +% defined by its left end, the middle part, and the right end. +% The following table gives some examples for the construction +% of arrows and bars. +% +% \begin{center} +% \begin{tabular}{cl} +% middle & \\ +% \hbox to 1.6cm{\hss left end} \raisebox{1mm}{$\downarrow$} \hbox to 1.6cm{right end} & \\ \hline +% |---|& plain bar \\ +% |===|& double bar \\ +% |-->|& right arrow \\ +% |'->|& right arrow with up hook \\ +% |<-|$\vert$ & left \emph{maps to} arrow \\ +% |<-o|& left arrow with ball at right end\\ +% |<=>|& double arrow, two heads \\ +% |,-,|& plain bar with down hooks\\ +% $\vert$|=|$\vert$ & double bar with vertical ends\\ +% |S-S|& labels disulfide bridges\\ +% \end{tabular} +% \end{center} +% +% Combinations of the left-end-characters +% (|-=<',|$\vert$o), the middle-characters (|-=|), +% and the right-end-characters (|-=>',|$\vert$o) are +% allowed and produce the desired arrow or bar. +% The color is changed as described above. +% \label{Lfeaturerule} The thickness can be generally +% set by the separate command |\featurerule{|\meta{length}|}| +% with any \TeX{} measure as \meta{length}, e.\,g.\ |\featurerule{3pt}|. +% This value is then used for all arrows, bars, and boxes (see above) +% throughout the alignment. If an individual thickness for a +% particular arrow should be set one can add an optional +% parameter to the \meta{labelstyle} parameter, e.g. +% |{o->[Red][1mm]}|. Similar to the boxes described above, a text can be put on +% the arrow or bar, e.\,g.\ |{<->[Red][1mm]:$\beta$-sheet[Blue]}|. +% +% +% In \TeXshade{} versions before v1.9, the original \LaTeX{}-arrows +% were used. These have now been replaced by more modern looking +% arrows with scalable line thickness. If the classical look is +% requested, use |v| instead of |<| or |>| in the arrow definition, +% e.\,g.\ |{--v}|, to get them back. The new arrow style makes use of +% of the AMS math symbol font (amssymb.sty). Thus, in order to +% display the arrow heads correctly make sure that this style is +% present on your system (usually it is in a common \LaTeX{} installation). +% \medskip +% +% \textbf{Sequence translations:}\\ +% With the option |{translate}|, sequence stretches can be +% translated from nucleotide to peptide sequences as well as +% backtranslations from peptide to nucleotide sequences are +% possible. Default setting for the translations is the standard +% genetic code. Of course, the codons can be re-defined by the +% user. The command \label{Lcodon} +% |\codon{|\meta{amino acid}|}{|\meta{triplet1, \ldots, triplet n}|}| +% has been implemented for this issue. The usage is simple. Replace +% \meta{amino acid} by the single letter code of the amino acid +% to be defined and add a list of triplets for this residue. +% Example definition for the amino acid \emph{alanine}: +% \medskip +% +% \quad |\codon{A}{GCA,GCG,GCC,GCT,GCU,GCN}| +% \medskip +% +% Note the last triplet in the list. It contains an ambiguity code +% |N| which stands for \emph{any} nucleotide. This triplet has been +% added at the last position because the last triplet is used +% for the generation of the backtranslated nucleotide sequence from +% a peptide. Two files are included in the \TeXshade{} +% distribution as examples (|standard.cod, ciliate.cod|). If you +% want to define a new genetic code store your commands in a file +% like the examples. Such files with the suffix |.cod| can be +% loaded in the \TeXshade{} environment by \label{Lgeneticcode} +% |\geneticcode{|\meta{filename}|}|, e.\,g. |\geneticcode{ciliate}|. +% Do not designate the suffix |.cod| in \meta{filename}. Please +% note, when inspecting the example files, that only the exchanges +% compared to the standard code need to be defined in a new genetic code file. +% +% When DNA sequences are translated to protein the resulting amino +% acids are aligned to the second nucleotide of each triplet. +% It is more difficult to produce a satisfactory display of +% backtranslated nucleotide sequences due to the lack of space. +% You need thrice as much space than the original peptide sequence, +% because single letter amino acid code is translated to a triplet +% code. Therefore, the user can choose from five display styles +% for backtranslations depending on personal preferences: +% \medskip\label{Lbacktranslabel} +% +% \quad |\backtranslabel[|\meta{size}|]{|\meta{style}|}|, with +% \medskip +% +% \begin{tabbing} +% \qquad\qquad|{|\meta{style}|}|\ \= = |{horizontal}|\\ +% \> = |{alternating}|\\ +% \> = |{zigzag}|\\ +% \> = |{oblique}|\\ +% \> = |{vertical}| +% \end{tabbing} +% +% \meta{size} can be any \TeX{} size from |tiny| up to |Huge|, but +% |tiny| is recommended (and default setting). Translations +% can be colored as all other labels, see above. +% \medskip +% +% \textbf{Bar graphs and color scales:}\label{Lgraphs}\\ +% Sequence related numeral data, such as hydropathy or solvent +% accessibility data etc., can be shown in a feature line as bar graphs +% or color scales. The data are (a) pre-defined or calculated by +% \TeXshade{} due to amino acid properties or conservation, (b) are +% provided in a separate file or (c) may be entered by hand in the +% |\feature| command. +% +% (a) Currently, three different +% properties can be plotted, i.e. |hydrophobicity|, |molweight|, and +% |charge|. Further, the level of sequence conservation at the given +% protein sequence stretch can be shown (|conservation|). See +% \ref{resweight} for selecting an appropriate \emph{residue weight table}. +% +% (b) The format of a data file is simple: every value must +% appear in a separate line. Numbers and the Java-typical `NaN' for +% `Not a Number' are permitted. Comments are allowed, because \TeXshade{} +% ignores all lines starting with a letter except `NaN' lines (avoid +% `|-|' as the first +% character of a comment line as this is interpreted as a negative number). +% Make sure that there are as many values as positions defined as the +% sequence stretch in the feature command. +% \TeXshade{} will read this file and determine the minimal and maximal +% values. These data are then normalized for plotting. +% Due to \TeX's limited calculation capabilities no values above 10\,737 +% are allowed and the difference between minimum and maximum must not +% exceed this very number. Values below 0.001 may be susceptible to major +% rounding errors. Thus, try to provide your data already normalized to +% moderate scales, e.g. 0.0\,--\,1.0 or -100\,--\,100. + +% (c) Data which is +% directly entered in the |\feature| command must be normalized to integer +% values with a maximal difference of 100 between the highest and lowest +% value, e.g. -50\,--\,50 or 0\,--\,100. +% +% For (b) and (c), the range to be plotted can be set by hand as an optional parameter +% in the |\feature| command. This can be necessary when the data file +% contains values between e.g. $-0.44$ and $0.87$. Without help \TeXshade{} +% will assume $-0.44$ as minimum and $0.87$ as maximum. But if the actual +% range to be plotted should be $-1.0$\,--\,$1.0$ this needs to be set +% manually, see examples below. Be aware of the fact, that if you +% define a scale by hand, which is more narrow than the values of the +% input, this will stretch the bars accordingly. It is NOT recommended +% to use this method for stretching bars vertically. Instead another +% command has been introduced. +% \label{Lbargraphstretch}\label{Lcolorscalestretch} +% The plotted bars can be stretched by a factor if the appearance is +% not as desired: |\bargraphstretch{|\meta{factor}|}|. Here, the factor +% is multiplied with the bar length, e.g |\bargraphstretch{2}| will double +% the bar height, |\bargraphstretch{0.5}| will make them half as high. +% Similarly, color scales can be stretched vertically with +% |\colorscalestretch{|\meta{factor}|}|. +% +% The default color of bar graphs is gray and can be changed by an +% optional parameter at the end of the |label| definition. Further, an optional +% background color can be chosen for the bars. Doing so will visualize +% the maximal bar extension. +% +% Default for +% color scales is a 5\% gray scale from very light gray to black (|Gray|). +% More colorful scales have been implemented, i.e. |BlueRed|, |RedBlue|, |GreenRed|, +% |RedGreen|, |ColdHot| and |HotCold|, the latter two being particularly +% useful for ranges from negative to positive values. Further, a scale called |T-Coffee| +% is available if |T-Coffee| shading information has been imported as the +% |\shadingmode| \ref{Lshadingmode}. +% +% +% +% The general format of this feature label definition for bar graphs is: +% \medskip +% +% \quad |{bar[|\meta{min}|,|\meta{max}|]:|\meta{properties/file/data}|[|\meta{color(,bgcolor)}|]}| +% \medskip +% +% and for color scales: +% \medskip +% +% \quad|{color[|\meta{min}|,|\meta{max}|]:|\meta{properties/file/data}|[|\meta{scale}|]}| +% \medskip +% +% Some examples: +% \medskip +% +% \qquad |{bar:conservation}| +% \medskip +% +% \qquad |{bar:conservation[T-Coffee]}| +% \medskip +% +% \qquad |{bar:hydrophobicity}| +% \medskip +% +% \qquad |{bar:charge[Red]}| +% \medskip +% +% \qquad |{bar:molweight[Red,Gray10]}| +% \medskip +% +% \qquad |{bar:10,20,30,40,50[Red]}| +% \medskip +% +% \qquad |{bar[-20,40]:-10,0,10,20,30[Red,Gray10]}| +% \medskip +% +% \qquad |{bar:data.txt}| +% \medskip +% +% \qquad |{bar[-10,10]:data.txt[Red,Gray10]}| +% \medskip +% +% \qquad |{color:conservation[BlueRed]}| +% \medskip +% +% \qquad |{color:conservation[T-Coffee]}| +% \medskip +% +% \qquad |{color:hydrophobicity[GreenRed]}| +% \medskip +% +% \qquad |{color:charge}| +% \medskip +% +% \qquad |{color:molweight}| +% \medskip +% +% \qquad |{color[-10,10]:data.txt[ColdHot]}| +% \medskip +% +% \qquad |{color[-0.1,0.1]:otherdata.txt[ColdHot]}| +% \medskip +% +% See also the example output in section \ref{graphs} on page +% \pageref{graphs}. +% +% \medskip +% +% \textbf{No graphical label, only text:}\\ +% If no graphical label is +% wanted the fourth parameter of |\feature| can be empty +% braces. +% \medskip +% +% Finally, the fifth parameter of the |\feature| command contains +% the descriptive text +% for the labeled region. Type whatever you want incl. symbols and +% math chars. The text field can also contain sequence translations. +% In this case just set \meta{text} = |{translate}|. There is a +% command for setting the size and style of backtranslated sequences +% in the feature \meta{text} which corresponds to the one +% described above: \label{Lbacktranstext} +% \medskip +% +% \quad |\backtranstext[|\meta{size}|]{|\meta{style}|}| +% \medskip +% +% Again, the color can be set by an +% optional parameter appended to the text. For how to change the +% font size of text or symbols in the feature style line +% (|featurestyles|) or the in descriptive text line (|features|) +% see section \ref{Lsetsize}, page \pageref{Lsetsize}. +% +% Another set of commands can be used to set a name for a feature +% line, which is printed together with the sequence names at the +% left or right side of the alignment, i.\,e.\ +% \medskip +% +% \label{Lshowfeaturename} \label{Lshowfeaturestylename} +% \label{Lhidefeaturename} \label{Lhidefeaturestylename} +% \label{Lhidefeaturenames} \label{Lhidefeaturestylenames} +% \quad |\showfeaturename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}|, +% \medskip +% +% \quad |\showfeaturestylename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}| +% \medskip +% +% \quad |\hidefeaturename{|\meta{ttttop...bbbbottom}|}| +% \medskip +% +% \quad |\hidefeaturestylename{|\meta{ttttop...bbbbottom}|}| +% \medskip +% +% \quad |\hidefeaturenames|, and |\hidefeaturestylenames|. +% \medskip +% +% Using |\showfeaturename| will print the name in the same line as +% the descriptive text of the feature whereas | \showfeaturestylename| +% will put the name in the same line as the feature symbols. +% +% The color of such names can be generally changed with \label{Lfeaturenamescolor} +% \medskip +% +% \quad |\featurenamescolor{|\meta{color}|}| and \label{Lfeaturestylenamescolor} +% \medskip +% +% \quad |\featurestylenamescolor{|\meta{color}|}| +% \medskip +% +% or individually with \label{Lfeaturenamecolor} +% \medskip +% +% \quad |\featurenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}| and \label{Lfeaturestylenamecolor} +% \medskip +% +% \quad |\featurestylenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}| +% \medskip +% +% See section \ref{colors} for how to select colors in \TeX{}shade. +% +% Font styles can be set as usual (see section \ref{Lsetfamily}), e.\,g.\ +% \medskip +% +% |\setsize{featurenames}{large}| or |\featurestylenamesrm| etc. +% \medskip +% +% +% +% Examples for the appearance of features are given in the +% overview section (\ref{over}), see: +% \medskip +% +% \emph{similarity mode} (\ref{similar}): fill-character; here, only +% one position is labeled. It is also possible to label a longer +% stretch, then, the character is printed several times to +% fill the specified region. +% +% \quad|\feature{top}{1}{93..93}{fill:$\downarrow$}{first...}| +% +% \quad|\feature{bottom}{1}{98..98}{fill:$\uparrow$}{second...}| +% \medskip +% +% \emph{T-Coffee mode} (\ref{TCoffee}): |T-Coffee| color scale +% +% \quad|\feature{top}{1}{30..63}{color:conservation[T-Coffee]}{}| +% +% \quad|\showfeaturestylename{bottom}{cons}| +% \medskip +% +% \emph{diversity mode} (\ref{diverse}): frames, text only +% +% \quad|\feature{top}{1}{77..109}{}{AQP2 species variants}| +% +% \quad|\frameblock{1}{82..82,106..106}{Red[1pt]}| +% \medskip +% +% \emph{functional mode} (\ref{func}): bar graph, color scale, tinting, box, arrow, +% translation, brace, helix +% +% \quad|\feature{top}{3}{153..165}| +% +% \quad\quad\quad\quad\quad|{bar[-50,50]:-50,-45,-40,...,40,45,50}{}| +% \medskip +% +% \quad|\feature{top}{3}{167..186}| +% +% \quad\quad\quad\quad\quad|{color:5,10,15,...,90,95,100[ColdHot]}{}| +% \medskip +% +% \quad |\feature{top}{1}{158..163}{brace}{tinted}| +% +% \quad|\tintblock{1}{158..163}| +% \medskip +% +% \quad|\feature{top}{1}{138..157}| +% +% \quad\quad\quad\quad\quad|{box[Blue,Red][0.5pt]:$\alpha$-helix[Yellow]}| +% +% \quad\quad\quad\quad\quad|{transmembrane domain 4}| +% +% \quad|\feature{top}{1}{164..170}{o->[Red]}{trans. dom. 5}| +% +% \quad|\feature{top}{1}{158..163}{translate[Blue]}{}| +% +% \quad|\backtranslabel{oblique}| +% +% \quad|\feature{bottom}{1}{158..163}| +% +% \quad\quad\quad\quad\quad|{brace[Blue]}{loop D[Blue]}| +% \medskip +% +% \quad|\feature{top}{1}{138..157,164..170}{helix}{membr.}| +% +% \quad|\feature{top}{1}{158..163}{---}{loop}| +% +% \quad|\featurerule{1mm}| +% \medskip +% +% \emph{bar graphs and color scales} (\ref{graphs}): sequence conservation, +% charge, molecular weight, hydrophobicity +% +% \quad|\feature{ttop}{1}{138..170}{bar:conservation}{}| +% +% \quad|\feature{top}{1}{138..170}{color:charge}{}| +% +% \quad|\feature{bottom}{1}{138..170}| +% +% \quad\quad\quad\quad\quad|{color:molweight[ColdHot]}{}| +% +% \quad|\feature{bbottom}{1}{138..170}| +% +% \quad\quad\quad\quad\quad|{bar:hydrophobicity[Red,Gray10]}{}| +% \medskip +% +% \subsubsection{Including secondary structure information} +% +% \label{structure} +% +% \label{LincludeDSSP} +% \label{LincludeSTRIDE} +% \label{LincludePHDsec} +% \label{LincludePHDtopo} +% \label{LincludeHMMTOP} +% The DSSP [9], STRIDE [10], PHD [11] and HMMTOP [12] algorithms produce +% secondary protein structure predictions. PHD files contain both, +% secondary structure information and topology data. This information can be +% displayed in an alignment by one of the commands: +% \bigskip +% +% \begin{tabular}{ll} +% |\includeDSSP| & sec. structure calculated by DSSP\\ +% +% |\includeSTRIDE| & sec. structure calculated by STRIDE \\ +% +% |\includePHDsec| & sec. structure calculated by PHD \\ +% +% |\includePHDtopo| & topology data calculated by PHD \\ +% +% |\includeHMMTOP| & topology data calculated by HMMTOP \\ +% \end{tabular} +% \bigskip +% +% The syntax is |\includeDSSP{|\meta{seqref}|}{|\meta{filename}|}|, +% with |seqref| indicating the number or name of the sequence for which +% the secondary structure data is calculated and |filename| designating the +% corresponding structure file to be included. +% +% Several types of secondary structures are predicted by these +% programs; in order to designate them in \TeXshade{} use the names +% from the right column: +% +% \begin{center} +% \begin{tabular}{ll} +% secondary structure & designation\\[3mm] +% \emph{DSSP and STRIDE} & \\[2mm] +% 4-helix ($\alpha$-helix) & |alpha| \\ +% isolated $\beta$-bridge & |bridge| \\ +% extended strand ($\beta$-strand) & |beta| \\ +% 3-helix (3$_{10}$-helix) & |3-10| \\ +% 5-helix ($\pi$-helix) & |pi| \\ +% H-bonded turn & |turn| \\[3mm] +% \emph{PHDsec} & \\[2mm] +% helix & |alpha| \\ +% sheet & |beta| \\[3mm] +% \emph{PHDtopo and HMMTOP} & \\[2mm] +% internal region & |internal| \\ +% external region & |external| \\ +% transmembrane domain & |TM| \\ +% \end{tabular} +% \end{center} +% +% \label{LshowonDSSP} +% \label{LshowonSTRIDE} +% \label{LshowonPHDsec} +% \label{LshowonPHDtopo} +% \label{LshowonHMMTOP} +% \label{LhideonDSSP} +% \label{LhideonSTRIDE} +% \label{LhideonPHDsec} +% \label{LhideonPHDtopo} +% \label{LhideonHMMTOP} +% By default all three types of helices and the strands are +% displayed whereas turns and bridges are skipped. If it is +% desired to shown them as well, call for example |\shownonDSSP{bridge,turn}|. +% In analogy to this example all structure features can be activated +% in DSSP, STRIDE, PHDsec, PHDtopo and HMMTOP. In order to hide +% certain structure types use for example |\hideonDSSP{3-10,pi}|. +% +% The DSSP format has two columns of sequence numberings. The first +% column is consecutive, whereas the second column contains the +% actual sequence numbering. This can be different from the first +% column when sequence parts are missing in the DSSP file. One can +% choose which column will be read by \TeXshade{} by +% \label{LfirstcolumnDSSP} \label{LsecondcolumnDSSP} +% `|\firstcolumnDSSP|' and |\secondcolumnDSSP|'. The second column +% is still default. +% +% The HMMTOP algorithm can present its results as plain text or +% as HTML---plain text needs to be selected here. Further, the +% output can be formatted in a single line or in an extended form +% (see the HMMTOP documentation). Both can be read and interpreted +% by \TeXshade{}. Importantly, HMMTOP files can contain topology +% predictions of multiple sequences. \TeXshade{} tries to find +% the correct data based on the respective sequence name. If the +% sequence name is not found in the file, the first topology data +% is used. Using an optional parameter (number of the prediction +% in the file or name) one can define which data from the file is +% to be used: +% \medskip +% +% |\includeHMMTOP{|\meta{seqref in texshade}|[|\meta{seqref in file}|]}{|\meta{filename}|}| +% \medskip +% +% PHD predictions: when starting the PHD software do not +% restrict the prediction to secondary structure or topology alone. +% This leads to changes in the PHD output file which are not +% correctly interpretable by \TeXshade{} due to ambiguities. There +% is no way around it---thus, run the full prediction. +% +% Now, some information on how \TeXshade{} extracts and displays +% secondary structure features. In short, it is a two step process. +% First, \TeXshade{} analyzes the secondary structure file and +% extracts all necessary data. This data is converted into a +% format which is readable and processable by \TeXshade{} using the +% |feature| command (see \ref{feature}). This command allows one to +% label sequence stretches graphically. For a detailed explanation +% see the indicated reference. A list of feature commands is saved +% in a file with the ending `|.sec|' for DSSP, STRIDE and PHDsec +% or `|.top|' for PHDtopo. Then, in a second step, this file is loaded +% again and executed. When \TeXshade{} encouters this file a +% second time, i.\,e. in a second \TeX{} run, it uses the already +% existing file for the output. The great advantage of this method +% is its flexibility. Due to the simple reason that the feature +% file can be edited in the meantime. Thus, the user has the +% ability to change the computer-generated file according to his +% personal needs. On the other hand, one can force \TeXshade{} to +% write a new file every time by the optional argument |[make new]| in the +% include command, e.\,g. |\includePHDsec[make new]{1}{AQP.phd}|. +% +% \label{Lappearance} +% Finally, the appearance of the feature labels can be assigned by +% the command +% +% |\appearance{|\meta{filetype}|}{|\meta{type}|}{|\meta{position}|}{|\meta{labelstyle}|}{|\meta{text}|}|. +% +% Here, \meta{filetype} stands for one of the following secondary structure +% file types: |DSSP|, |STRIDE|, |PHDsec|, |PHDtopo| or |HMMTOP| and +% \meta{type} designates the secondary structure type as shown in +% the right column of the table above. The other +% arguments \meta{position}, \meta{labelstyle} and \meta{text} +% are almost as described in \ref{feature}. +% \label{Lnumcount} +% \label{Lalphacount} +% \label{LAlphacount} +% \label{Lromancount} +% \label{LRomancount} +% One further possibility +% is to include internal counters for each secondary structure type. +% Just add one of the following commands +% to the text in the feature description. +% +% \begin{center} +% \begin{tabular}{ll} +% \emph{counter} & \emph{display} \\[2mm] +% |\numcount| & 1, 2, 3 \ldots \\ +% |\alphacount| & a, b, c \ldots \\ +% |\Alphacount| & A, B, C \ldots \\ +% |\romancount| & i, ii, iii \ldots \\ +% |\Romancount| & I, II, III \ldots \\ +% \end{tabular} +% \end{center} +% +% Examples: +% +% \quad|\appearance{DSSP}{alpha}{ttop}| +% +% \quad\quad\quad\quad\quad\quad\quad|{-->}{$\alpha$-helix~\Alphacount}| +% +% \quad|\appearance{PHDtopo}{TM}{bottom}| +% +% \quad\quad\quad\quad\quad\quad\quad|{box[Blue]:TM\numcount[Yellow]}{}| +% +% +% \subsection{Displaying and building legends} +% +% \label{Lshowlegend}\label{Lhidelegend}\label{Lmovelegend} +% \label{Lgermanlanguage}\label{Lenglishlanguage}\label{Llegendcolor} +% \label{Lspanishlanguage} +% For each predefined shading mode \TeXshade{} can print an appropriate +% legend to explain the used +% shading colors. The commands |\showlegend| and |\hidelegend| +% display or clear the legend at the end of the alignment. +% The legend is displayed by default beneath the first residue +% of the last alignment line. The location can be changed by +% |\movelegend{|\meta{x-offset}|}{|\meta{y-offset}|}|. Both +% parameters require a \TeX{} length, e.\,g. |\movelegend{5cm}{-2cm}| +% moves the legend 5\,cm to the right and 2\,cm up. +% +% The language for the descriptions is english by default; +% if the |\german.sty| package is active legend texts are in +% german. So far, german, spanish and english are implemented. With the +% commands |\germanlanguage|, |\spanishlanguage| and |\englishlanguage| +% switching between the languages +% is made possible. For the addition of other languages contact me. +% Finally, the color of the describing legend texts can be set +% with the command |\legendcolor{|\meta{color}|}|. +% +% User defined legends are easily built with the following command +% \label{Lshadebox}|\shadebox{|\meta{color}|}|. Use this command outside +% the \TeXshade{} environment, e.\,g. in the text or in the caption. As +% \meta{color} any color can be designated (see section \ref{colors}) or +% one of the following parameters: +% +% \begin{itemize} +% \item |nomatch| = the color used for nonmatching residues +% +% \item |similar| = the color used for similar residues +% +% \item |conserved| = the color used for conserved residues +% +% \item |allmatch| = the color used for highly conserved residues +% (if |\allmatchspecial| is active) +% +% \end{itemize} +% +% The command simply prints a shaded box in the specified color +% then a describing text can be appended. Examples: +% \medskip +% +% \quad|\shadebox{nomatch}---nonmatching residues| +% +% \quad|\shadebox{similar}: similar residues| +% +% \quad|\shadebox{conserved}~conserved residues| +% +% \quad|\shadebox{Yellow}\quad PKA phosphorylation sites| +% +% +% +% \subsection{Adding captions to the alignment} +% +% Since \TeXshade{} v1.5 captions can be added to the alignment. +% So far, captions were difficult to use when the alignment was +% bigger than one page and therefore did not fit into a +% figure environment. The \TeXshade{} captions behave exactly as +% normal figure captions. They +% adopt their style, use the figure counter number and appear in +% the list of figures as any other figure. +% +% The usage is slightly different from normal captions but +% intuitive: \label{Lshowcaption} +% \medskip +% +% \quad |\showcaption[|\meta{position}|]{|\meta{text}|}| +% \medskip +% +% The optional \meta{position} tells \TeXshade{} to put the caption on +% |top| or at the |bottom| of the alignment. If nothing is stated here +% the caption will appear at the bottom. The parameter +% \meta{text} just holds the caption text as in the normal |\caption|. +% The command can be used at any position within the |texshade| +% environment. A simple example would be: +% \medskip +% +% \quad |\showcaption{A beautiful \TeXshade{} alignment.}| +% \medskip +% +% \label{Lshortcaption} +% In order to show a short version of the caption in the +% "List of Figures" the |\shortcaption{|\meta{short caption text}|}| +% command can be used. +% +% \subsection{Font handling} +% +% \subsubsection{Changing font styles} +% +% \label{Lsetfamily}\label{Lsetseries} +% \label{Lsetshape}\label{Lsetsize} +% The font styles for the numbering, the sequence names, +% the sequence residues, the descriptive feature texts +% and the legends can be changed by several commands. +% \medskip +% +% \quad|\setfamily{|\meta{text}|}{|\meta{family}|}| +% +% \quad|\setseries{|\meta{text}|}{|\meta{series}|}| +% +% \quad|\setshape{|\meta{text}|}{|\meta{shape}|}| +% +% \quad|\setsize{|\meta{text}|}{|\meta{size}|}| +% \medskip +% +% The first parameter selects the text whose style is to be +% changed. Possible first parameters are +% |numbering|, |names|, |residues|, |features|, |featurestyles|, +% |hideblock|, |ruler|, and |legend|. +% \medskip +% +% The style is set by the second parameter: +% +% \begin{center} +% \begin{tabular}{lll} +% command & \meta{2. parameter} & \\ +% \hline +% |\setfamily| & |rm| & modern roman font family \\ +% & |sf| & sans serif font family \\ +% & |tt| & typewriter font family \\ \hline +% |\setseries| & |bf| & bold face series \\ +% & |md| & normal series \\ \hline +% |\setshape| & |it| & italics shape \\ +% & |sl| & slanted shape \\ +% & |sc| & small capitals shape \\ +% & |up| & upright shape \\ \hline +% |\setsize| & |tiny| & the known \TeX{} sizes \\ +% & |scriptsize| & \\ +% & |footnotesize| & \\ +% & |small| & \\ +% & |normalsize| & \\ +% & |large| & \\ +% & |Large| & \\ +% & |LARGE| & \\ +% & |huge| & \\ +% & |Huge| & \\ \hline +% \end{tabular} +% \end{center} +% +% Example: |\setfamily{features}{it} \setseries{features}{bf}| +% \medskip +% +% \label{Lsetfont} +% With the command +% \medskip +% +% \quad|\setfont{|\meta{text}|}{|\meta{family}|}{|\meta{series}|}{|\meta{shape}|}{|\meta{size}|}| +% \medskip +% +% all four font attributes of one \meta{text} can be changed +% simultaneously. The order of the parameters is as indicated. +% \medskip +% +% Example: |\setfont{features}{rm}{it}{bf}{normalsize}| +% \medskip +% +% Further, short commands are provided to change single font +% attributes quickly. The following commands set attributes +% of feature texts. +% \medskip +% \enlargethispage{\baselineskip} +% +% \quad |\featuresrm| \quad |\featurestiny| \label{Lfeaturesrm} +% +% \quad |\featuressf| \quad |\featuresscriptsize| +% +% \quad |\featurestt| \quad |\featuresfootnotesize| +% +% \quad |\featuresbf| \quad |\featuressmall| +% +% \quad |\featuresmd| \quad |\featuresnormalsize| +% +% \quad |\featuresit| \quad |\featureslarge| +% +% \quad |\featuressl| \quad |\featuresLarge| +% +% \quad |\featuressc| \quad |\featuresLARGE| +% +% \quad |\featuresup| \quad |\featureshuge| +% +% \quad | | \quad |\featuresHuge| +% \medskip +% +% Corresponding sets are provided for the +% numbering (|\numberingrm| etc.), +% featurestyles (|featurestylesrm| etc.), names (|\namesrm| etc.), +% featurenames (|\featurenamesrm| etc.), +% featurestylenames (|\featurestylenames| etc.), +% residues (|\residuesrm| etc.), +% hideblock labels (|hideblockrm| etc.), +% rulers (|\rulerrm| etc.), and +% legend texts (|legendrm| etc.). +% +% +% \subsubsection{Using PostScript fonts} +% +% As already mentioned \TeXshade{} makes intensive use of +% \textsc{PostScript} for shading. Now, that +% \textsc{PostScript} output is active anyway, including \textsc{PostScript} +% fonts is very easy. Just declare in the document header +% \medskip +% +% \quad |\usepackage{|\meta{PS-font}|}|. +% \medskip +% +% +% The typewriter font of \TeX{} is always a topic of discussions. +% By including the package |\usepackage{courier}| \TeX's +% typewriter font is replaced by the widely accepted \textsc{Courier}. +% Have a look into the directory |..texinputs:latex:psnfss|; there, +% some styles are located which exchange the common \TeX{} fonts by +% \textsc{PostScript} fonts, e.\,g.\ |avant.sty|, |bookman.sty|, +% |chancery.sty|, |courier.sty|, |helvet.sty| or |utopia.sty|. +% Depending on the style used the |\rmdefault|-, |\sfdefault|-, +% and |\ttdefault| fonts are substituted partly or completely. +% Thus, |courier.sty| for instance exchanges only the typewriter font, +% whereas |bookman.sty| sets \textsc{Bookman} as |\rmdefault|, +% \textsc{Avantgarde} as |\sfdefault| and \textsc{Courier} as +% |\ttdefault|. +% +% For further information see \textsc{Tomas Rokicki}'s +% |dvips| manual [13]. +% +% +% +% +% \subsection{Goodies} +% +% The following commands give information on sequence properties, +% such as molecular weight, charge or similarity data. They can +% be used outside the |texshade| environment directly in the +% document or in a caption text. +% +% \subsubsection{Molweight and charge} +% +% \label{molcharge} +% +% \label{Lmolweight}\label{Lcharge} +% During the process of sequence setting \TeXshade{} +% sums up the molecular weight and charge of the +% aligned proteins. This data can be accessed by the +% following commands. +% \medskip +% +% \quad|\molweight{|\meta{seqref}|}{|\meta{Da/kDa}|}| +% +% \quad|\charge{|\meta{seqref}|}{|\meta{i/o/N/C}|}| +% \medskip +% +% The first parameter \meta{seqref} selects the sequence. The +% second parameter in the |\molweight| command allows one to +% switch the units between Dalton (|Da|) and kilo-Dalton +% (|kDa|). The |\charge| command needs the second parameter +% for the correct consideration of the charged protein termini. +% Thus, `|i|' refers to internal sequences, `|o|' to the +% overall charge, `|N|' to N-terminal sequence parts, and +% `|C|' to the C-terminal end of a protein. +% \medskip +% +% Example: \quad Charge: |\charge{1}{o}|; Weight: |\molweight{1}{Da}| +% +% \subsubsection{Similarity/identity data and tables} +% +% \label{simtable} +% The degree of similarity and identity in percent for any two +% sequences in the displayed alignment section can be read out +% with the commands +% \label{Lpercentsimilarity} \label{Lpercentidentity} +% |\percentsimilarity{|\meta{seqref1}|}{|\meta{seqref2}|}| and +% |\percentidentity{|\meta{seqref1}|}{|\meta{seqref2}|}|. +% +% Using the example alignment on page \pageref{simtableEx} and +% typing outside the |texshade| environment in the document text the +% following phrase: +% \bigskip +% +% \quad\quad |AQP1 and AQP2 share a sequence similarity| +% +% \quad\quad |of \percentsimilarity{AQP1.pro}{AQP2.pro}\%| +% \bigskip +% +% will result in the text: +% \bigskip +% +% \quad\quad AQP1 and AQP2 share a sequence similarity of 69.6\% +% \bigskip +% +% Likewise, |\percentidentity{1}{2}| will give the value |48.4|; note that +% sequences can be referred to by their number or their assigned name. The +% percent value is calculated by dividing the number of identical or similar +% positions, respectively, by the total of non-gap positions shared by both +% sequences. Here, only the part of the alignment is taken into account that +% is actually displayed. Two residues are considered similar when this is +% defined by the command |\pepsims| (see page \pageref{Lpepsims}). +% +% A full similarity/identity table showing values for all sequences of the +% alignment can be set using |\similaritytable|.\label{Lsimilaritytable} +% The labels and number format will be adjusted according to the language +% settings (\ref{Lgermanlanguage}). +% \medskip +% +% Example (see section \ref{simtableEx}): +% \medskip +% +% \vbox{% +% \quad |\begin{center}| +% \medskip +% +% \quad\quad|\similaritytable| +% \medskip +% +% \quad |\end{center}| +% } +% \bigskip +% +% The command generates a valid \LaTeX{} |tabular| +% environment, which can be embedded into a |table| environment, e.g. +% \medskip +% +% \vbox{% +% \quad |\begin{table}[htdp]| +% +% \quad |\caption{Text ...}| +% +% \quad |\begin{center}| +% \medskip +% +% \quad\quad|\similaritytable| +% \medskip +% +% \quad |\end{center}| +% +% \quad |\end{table}| +% } +% +% \newpage +% \section{The PostScript color selection scheme} +% +% \label{colors} +% +% \textsc{PostScript} provides 64 standard colors. All these +% colors are predefined in the |color.sty|. Each color +% has a pictorial name such as |Bittersweet| and a distinct +% composition, e.\,g.\ 0\% cyan + 75\% magenta + 100\% yellow + +% 24\% black---the so-called CMYK scheme. \TeXshade{} enhances this +% color scheme by gray scales in 5\% steps. +% The following colors and grays can be used in \TeXshade{} by +% simply declaring the name of the color in the respective +% command, e.\,g.\ |\consensuscolors|: +% +% +% \begin{footnotesize} +% \begin{tabbing} +% \emph{name}\hspace{2.7cm}\= \emph{CMYK}\hspace{1.6cm} +% \=\emph{name}\hspace{2.5cm}\= \emph{CMYK}\\ +% +% \textcolor{GreenYellow}{$\bullet$}GreenYellow \>{0.15,0,0.69,0}\>\textcolor{Yellow}{$\bullet$}Yellow \>{0,0,1,0}\\ +% \textcolor{Goldenrod}{$\bullet$}Goldenrod \>{0,0.10,0.84,0}\>\textcolor{Dandelion}{$\bullet$}Dandelion \>{0,0.29,0.84,0}\\ +% \textcolor{Apricot}{$\bullet$}Apricot \>{0,0.32,0.52,0}\>\textcolor{Peach}{$\bullet$}Peach \>{0,0.50,0.70,0}\\ +% \textcolor{Melon}{$\bullet$}Melon \>{0,0.46,0.50,0}\>\textcolor{YellowOrange}{$\bullet$}YellowOrange \>{0,0.42,1,0}\\ +% \textcolor{Orange}{$\bullet$}Orange \>{0,0.61,0.87,0}\>\textcolor{BurntOrange}{$\bullet$}BurntOrange \>{0,0.51,1,0}\\ +% \textcolor{Bittersweet}{$\bullet$}Bittersweet \>{0,0.75,1,0.24}\>\textcolor{RedOrange}{$\bullet$}RedOrange \>{0,0.77,0.87,0}\\ +% \textcolor{Mahagony}{$\bullet$}Mahagony \>{0,0.85,0.87,0.35}\>\textcolor{Maroon}{$\bullet$}Maroon \>{0,0.87,0.68,0.32}\\ +% \textcolor{BrickRed}{$\bullet$}BrickRed \>{0,0.89,0.94,0.28}\>\textcolor{Red}{$\bullet$}Red \>{0,1,1,0}\\ +% \textcolor{OrangeRed}{$\bullet$}OrangeRed \>{0,1,0.50,0}\>\textcolor{RubineRed}{$\bullet$}RubineRed \>{0,1,0.13,0}\\ +% \textcolor{WildStrawberry}{$\bullet$}WildStrawberry\>{0,0.96,0.39,0}\>\textcolor{Salmon}{$\bullet$}Salmon \>{0,0.53,0.38,0}\\ +% \textcolor{CarnationPink}{$\bullet$}CarnationPink \>{0,0.63,0,0}\>\textcolor{Magenta}{$\bullet$}Magenta \>{0,1,0,0}\\ +% \textcolor{VioletRed}{$\bullet$}VioletRed \>{0,0.81,0,0}\>\textcolor{Rhodamine}{$\bullet$}Rhodamine \>{0,0.82,0,0}\\ +% \textcolor{Mulberry}{$\bullet$}Mulberry \>{0.34,0.90,0,0.02}\>\textcolor{RedViolet}{$\bullet$}RedViolet \>{0.07,0.90,0,0.34}\\ +% \textcolor{Fuchsia}{$\bullet$}Fuchsia \>{0.47,0.91,0,0.08}\>\textcolor{Lavender}{$\bullet$}Lavender \>{0,0.48,0,0}\\ +% \textcolor{Thistle}{$\bullet$}Thistle \>{0.12,0.59,0,0}\>\textcolor{Orchid}{$\bullet$}Orchid \>{0.32,0.64,0,0}\\ +% \textcolor{DarkOrchid}{$\bullet$}DarkOrchid \>{0.40,0.80,0.20,0}\>\textcolor{Purple}{$\bullet$}Purple \>{0.45,0.86,0,0}\\ +% \textcolor{Plum}{$\bullet$}Plum \>{0.50,1,0,0}\>\textcolor{Violet}{$\bullet$}Violet \>{0.79,0.88,0,0}\\ +% \textcolor{RoyalPurple}{$\bullet$}RoyalPurple \>{0.75,0.90,0,0}\>\textcolor{BlueViolet}{$\bullet$}BlueViolet \>{0.86,0.91,0,0.04}\\ +% \textcolor{Periwinkle}{$\bullet$}Periwinkle \>{0.57,0.55,0,0}\>\textcolor{CadetBlue}{$\bullet$}CadetBlue \>{0.62,0.57,0.23,0}\\ +% \textcolor{CornflowerBlue}{$\bullet$}CornflowerBlue\>{0.65,0.13,0,0}\>\textcolor{MidnightBlue}{$\bullet$}MidnightBlue \>{0.98,0.13,0,0.43}\\ +% \textcolor{NavyBlue}{$\bullet$}NavyBlue \>{0.94,0.54,0,0}\>\textcolor{RoyalBlue}{$\bullet$}RoyalBlue \>{1,0.50,0,0}\\ +% \textcolor{Blue}{$\bullet$}Blue \>{1,1,0,0}\>\textcolor{Cerulean}{$\bullet$}Cerulean \>{0.94,0.11,0,0}\\ +% \textcolor{Cyan}{$\bullet$}Cyan \>{1,0,0,0}\>\textcolor{ProcessBlue}{$\bullet$}ProcessBlue \>{0.96,0,0,0}\\ +% \textcolor{SkyBlue}{$\bullet$}SkyBlue \>{0.62,0,0.12,0}\>\textcolor{Turquoise}{$\bullet$}Turquoise \>{0.85,0,0.20,0}\\ +% \textcolor{TealBlue}{$\bullet$}TealBlue \>{0.86,0,0.34,0.02}\>\textcolor{Aquamarine}{$\bullet$}Aquamarine \>{0.82,0,0.30,0}\\ +% \textcolor{BlueGreen}{$\bullet$}BlueGreen \>{0.85,0,0.33,0}\>\textcolor{Emerald}{$\bullet$}Emerald \>{1,0,0.50,0}\\ +% \textcolor{JungleGreen}{$\bullet$}JungleGreen \>{0.99,0,0.52,0}\>\textcolor{SeaGreen}{$\bullet$}SeaGreen \>{0.69,0,0.50,0}\\ +% \textcolor{Green}{$\bullet$}Green \>{1,0,1,0}\>\textcolor{ForestGreen}{$\bullet$}ForestGreen \>{0.91,0,0.88,0.12}\\ +% \textcolor{PineGreen}{$\bullet$}PineGreen \>{0.92,0,0.59,0.25}\>\textcolor{LimeGreen}{$\bullet$}LimeGreen \>{0.50,0,1,0}\\ +% \textcolor{YellowGreen}{$\bullet$}YellowGreen \>{0.44,0,0.74,0}\>\textcolor{SpringGreen}{$\bullet$}SpringGreen \>{0.26,0,0.76,0}\\ +% \textcolor{OliveGreen}{$\bullet$}OliveGreen \>{0.64,0,0.95,0.40}\>\textcolor{RawSienna}{$\bullet$}RawSienna \>{0,0.72,1,0.45}\\ +% \textcolor{Sepia}{$\bullet$}Sepia \>{0,0.83,1,0.70}\>\textcolor{Brown}{$\bullet$}Brown \>{0,0.81,1,0.60}\\ +% \textcolor{Tan}{$\bullet$}Tan \>{0.14,0.42,0.56,0}\>\>\\ +% \textcolor{White}{$\bullet$}White (Gray0) \>{0,0,0,0}\>\textcolor{Black}{$\bullet$}Black (Gray100) \>{0,0,0,1}\\ +% \textcolor{Gray5}{$\bullet$}Gray5 \>{0,0,0,0.05}\>\textcolor{Gray10}{$\bullet$}Gray10 \>{0,0,0,0.10}\\ +% \textcolor{Gray15}{$\bullet$}Gray15 \>{0,0,0,0.15}\>\textcolor{Gray20}{$\bullet$}Gray20 \>{0,0,0,0.20}\\ +% \textcolor{Gray25}{$\bullet$}Gray25 \>{0,0,0,0.25}\>\textcolor{Gray30}{$\bullet$}Gray30 \>{0,0,0,0.30}\\ +% \textcolor{LightGray}{$\bullet$}LightGray \>{0,0,0,0.33}\>\textcolor{Gray35}{$\bullet$}Gray35 \>{0,0,0,0.35}\\ +% \textcolor{Gray40}{$\bullet$}Gray40 \>{0,0,0,0.40}\>\textcolor{Gray45}{$\bullet$}Gray45 \>{0,0,0,0.45}\\ +% \textcolor{Gray50}{$\bullet$}Gray50 \>{0,0,0,0.50}\>\textcolor{Gray}{$\bullet$}Gray \>{0,0,0,0.50}\\ +% \textcolor{Gray55}{$\bullet$}Gray55 \>{0,0,0,0.55}\>\textcolor{Gray60}{$\bullet$}Gray60 \>{0,0,0,0.60}\\ +% \textcolor{Gray65}{$\bullet$}Gray65 \>{0,0,0,0.65}\>\textcolor{DarkGray}{$\bullet$}DarkGray \>{0,0,0,0.66}\\ +% \textcolor{Gray70}{$\bullet$}Gray70 \>{0,0,0,0.70}\>\textcolor{Gray75}{$\bullet$}Gray75 \>{0,0,0,0.75}\\ +% \textcolor{Gray80}{$\bullet$}Gray80 \>{0,0,0,0.80}\>\textcolor{Gray85}{$\bullet$}Gray85 \>{0,0,0,0.85}\\ +% \textcolor{Gray90}{$\bullet$}Gray90 \>{0,0,0,0.90}\>\textcolor{Gray95}{$\bullet$}Gray95 \>{0,0,0,0.95}\\ +% \textcolor{LightGreenYellow}{$\bullet$}LightGreenYellow\>{0.08,0,0.35,0}\>\textcolor{LightYellow}{$\bullet$}LightYellow \>{0,0,0.50,0}\\ +% \textcolor{LightGoldenrod}{$\bullet$}LightGoldenrod \>{0,0.05,0.42,0}\>\textcolor{LightDandelion}{$\bullet$}LightDandelion\> {0,0.15,0.42,0}\\ +% \textcolor{LightApricot}{$\bullet$}LightApricot \>{0,0.16,0.26,0}\>\textcolor{LightPeach}{$\bullet$}LightPeach \>{0,0.25,0.35,0}\\ +% \textcolor{LightMelon}{$\bullet$}LightMelon \>{0,0.23,0.25,0}\>\textcolor{LightYellowOrange}{$\bullet$}LightYellowOrange \>{0,0.21,0.50,0}\\ +% \textcolor{LightOrange}{$\bullet$}LightOrange \>{0,0.31,0.44,0}\>\textcolor{LightBurntOrange}{$\bullet$}LightBurntOrange \>{0,0.26,0.50,0}\\ +% \textcolor{LightBittersweet}{$\bullet$}LightBittersweet\>{0,0.38,0.50,0.12}\>\textcolor{LightRedOrange}{$\bullet$}LightRedOrange\>{0,0.39,0.44,0}\\ +% \textcolor{LightMahagony}{$\bullet$}LightMahagony \>{0,0.43,0.44,0.18}\>\textcolor{LightMaroon}{$\bullet$}LightMaroon \>{0,0.44,0.34,0.16}\\ +% \textcolor{LightBrickRed}{$\bullet$}LightBrickRed \>{0,0.45,0.47,0.14}\>\textcolor{LightRed}{$\bullet$}LightRed \>{0,0.50,0.50,0}\\ +% \textcolor{LightOrangeRed}{$\bullet$}LightOrangeRed \>{0,0.50,0.25,0}\>\textcolor{LightRubineRed}{$\bullet$}LightRubineRed \>{0,0.50,0.07,0}\\ +% \textcolor{LightWildStrawberry}{$\bullet$}LightWildStrawberry\>{0,0.48,0.20,0}\>\textcolor{LightSalmon}{$\bullet$}LightSalmon \>{0,0.27,0.19,0}\\ +% \textcolor{LightCarnationPink}{$\bullet$}LightCarnationPink \>{0,0.32,0,0} \>\textcolor{LightMagenta}{$\bullet$}LightMagenta \>{0,0.50,0,0}\\ +% \textcolor{LightVioletRed}{$\bullet$}LightVioletRed \>{0,0.40,0,0} \>\textcolor{LightRhodamine}{$\bullet$}LightRhodamine \>{0,0.41,0,0}\\ +% \textcolor{LightMulberry}{$\bullet$}LightMulberry \>{0.17,0.45,0,0.01}\>\textcolor{LightRedViolet}{$\bullet$}LightRedViolet \>{0.04,0.45,0,0.17}\\ +% \textcolor{LightFuchsia}{$\bullet$}LightFuchsia \>{0.24,0.46,0,0.04}\>\textcolor{LightLavender}{$\bullet$}LightLavender \> {0,0.24,0,0}\\ +% \textcolor{LightThistle}{$\bullet$}LightThistle \>{0.06,0.30,0,0} \>\textcolor{LightOrchid}{$\bullet$}LightOrchid \>{0.16,0.32,0,0}\\ +% \textcolor{LightDarkOrchid}{$\bullet$}LightDarkOrchid \>{0.20,0.40,0.10,0}\>\textcolor{LightPurple}{$\bullet$}LightPurple \>{0.23,0.43,0,0}\\ +% \textcolor{LightPlum}{$\bullet$}LightPlum \>{0.25,0.50,0,0} \>\textcolor{LightViolet}{$\bullet$}LightViolet \>{0.40,0.44,0,0}\\ +% \textcolor{LightRoyalPurple}{$\bullet$}LightRoyalPurple\>{0.38,0.45,0,0} \>\textcolor{LightBlueViolet}{$\bullet$}LightBlueViolet \>{0.43,0.46,0,0.02}\\ +% \textcolor{LightPeriwinkle}{$\bullet$}LightPeriwinkle \>{0.29,0.28,0,0} \>\textcolor{LightCadetBlue}{$\bullet$}LightCadetBlue \> {0.31,0.29,0.12,0}\\ +% \textcolor{LightCornflowerBlue}{$\bullet$}LightCornflowerBlue\>{0.33,0.07,0,0}\>\textcolor{LightMidnightBlue}{$\bullet$}LightMidnightBlue\>{0.49,0.07,0,0.22}\\ +% \textcolor{LightNavyBlue}{$\bullet$}LightNavyBlue \>{0.47,0.27,0,0} \>\textcolor{LightRoyalBlue}{$\bullet$}LightRoyalBlue \> {0.50,0.25,0,0}\\ +% \textcolor{LightBlue}{$\bullet$}LightBlue \>{0.50,0.50,0,0} \>\textcolor{LightCerulean}{$\bullet$}LightCerulean \> {0.47,0.06,0,0}\\ +% \textcolor{LightCyan}{$\bullet$}LightCyan \>{0.50,0,0,0} \>\textcolor{LightProcessBlue}{$\bullet$}LightProcessBlue \> {0.48,0,0,0}\\ +% \textcolor{LightSkyBlue}{$\bullet$}LightSkyBlue \>{0.31,0,0.06,0} \>\textcolor{LightTurquoise}{$\bullet$}LightTurquoise \>{0.43,0,0.10,0}\\ +% \textcolor{LightTealBlue}{$\bullet$}LightTealBlue \>{0.43,0,0.17,0.01}\>\textcolor{LightAquamarine}{$\bullet$}LightAquamarine \>{0.41,0,0.15,0}\\ +% \textcolor{LightBlueGreen}{$\bullet$}LightBlueGreen \>{0.43,0,0.17,0}\>\textcolor{LightEmerald}{$\bullet$}LightEmerald \>{0.50,0,0.25,0}\\ +% \textcolor{LightJungleGreen}{$\bullet$}LightJungleGreen\>{0.50,0,0.26,0} \>\textcolor{LightSeaGreen}{$\bullet$}LightSeaGreen \>{0.35,0,0.25,0}\\ +% \textcolor{LightGreen}{$\bullet$}LightGreen \>{0.50,0,0.50,0} \>\textcolor{LightForestGreen}{$\bullet$}LightForestGreen\>{0.46,0,0.44,0.06}\\ +% \textcolor{LightPineGreen}{$\bullet$}LightPineGreen \>{0.46,0,0.30,0.13}\>\textcolor{LightLimeGreen}{$\bullet$}LightLimeGreen\>{0.25,0,0.50,0}\\ +% \textcolor{LightYellowGreen}{$\bullet$}LightYellowGreen\>{0.22,0,0.37,0} \>\textcolor{LightSpringGreen}{$\bullet$}LightSpringGreen \>{0.13,0,0.38,0}\\ +% \textcolor{LightOliveGreen}{$\bullet$}LightOliveGreen \>{0.32,0,0.48,0.20} \>\textcolor{LightRawSienna}{$\bullet$}LightRawSienna\>{0,0.36,0.50,0.23}\\ +% \textcolor{LightSepia}{$\bullet$}LightSepia \>{0,0.44,0.50,0.35} \>\textcolor{LightBrown}{$\bullet$}LightBrown \>{0,0.41,0.50,0.30}\\ +% \textcolor{LightTan}{$\bullet$}LightTan \>{0.07,0.21,0.28,0}\\ +% LightLight- and LightLightLight-versions were derived by dividing all values\\ +% from Light-color definitions by 2 and 4, respectively. +% \end{tabbing} +% +% \begin{tabbing} +% \emph{name}\hspace{2.5cm}\= \emph{RGB\quad}\hspace{1.8cm} +% \=\emph{name}\hspace{2.5cm}\= \emph{RGB\quad}\\ +% +% \textcolor{BlueRed5}{$\bullet$}BlueRed5 \>{0.15,0.17,0.55} \>\textcolor{BlueRed10}{$\bullet$}BlueRed10 \> {0.20,0.23,0.57}\\ +% \textcolor{BlueRed15}{$\bullet$}BlueRed15 \> {0.24,0.29,0.60} \>\textcolor{BlueRed20}{$\bullet$}BlueRed20 \> {0.33,0.35,0.64}\\ +% \textcolor{BlueRed25}{$\bullet$}BlueRed25 \> {0.43,0.43,0.68} \>\textcolor{BlueRed30}{$\bullet$}BlueRed30 \> {0.52,0.52,0.73}\\ +% \textcolor{BlueRed35}{$\bullet$}BlueRed35 \> {0.60,0.60,0.78} \>\textcolor{BlueRed40}{$\bullet$}BlueRed40 \> {0.70,0.70,0.84}\\ +% \textcolor{BlueRed45}{$\bullet$}BlueRed45 \> {0.80,0.80,0.85} \>\textcolor{BlueRed50}{$\bullet$}BlueRed50 \> {0.86,0.82,0.82}\\ +% \textcolor{BlueRed55}{$\bullet$}BlueRed55 \> {0.87,0.73,0.73} \>\textcolor{BlueRed60}{$\bullet$}BlueRed60 \> {0.89,0.64,0.64}\\ +% \textcolor{BlueRed65}{$\bullet$}BlueRed65 \> {0.90,0.55,0.55} \>\textcolor{BlueRed70}{$\bullet$}BlueRed70 \> {0.91,0.47,0.46}\\ +% \textcolor{BlueRed75}{$\bullet$}BlueRed75 \> {0.91,0.39,0.37} \>\textcolor{BlueRed80}{$\bullet$}BlueRed80 \> {0.90,0.33,0.28}\\ +% \textcolor{BlueRed85}{$\bullet$}BlueRed85 \> {0.89,0.25,0.20} \>\textcolor{BlueRed90}{$\bullet$}BlueRed90 \> {0.88,0.23,0.14}\\ +% \textcolor{BlueRed95}{$\bullet$}BlueRed95 \> {0.87,0.21,0.09} \>\textcolor{BlueRed100}{$\bullet$}BlueRed100\> {0.87,0.16,0.04}\\ +% \textcolor{GreenRed5}{$\bullet$}GreenRed5 \> {0,1,0} \>\textcolor{GreenRed10}{$\bullet$}GreenRed10\> {0.05,0.95,0}\\ +% \textcolor{GreenRed15}{$\bullet$}GreenRed15 \> {0.10,0.90,0} \>\textcolor{GreenRed20}{$\bullet$}GreenRed20\> {0.15,0.85,0}\\ +% \textcolor{GreenRed25}{$\bullet$}GreenRed25 \> {0.20,0.80,0} \>\textcolor{GreenRed30}{$\bullet$}GreenRed30\> {0.25,0.75,0}\\ +% \textcolor{GreenRed35}{$\bullet$}GreenRed35 \> {0.30,0.70,0} \>\textcolor{GreenRed40}{$\bullet$}GreenRed40\> {0.35,0.65,0}\\ +% \textcolor{GreenRed45}{$\bullet$}GreenRed45 \> {0.40,0.60,0} \>\textcolor{GreenRed50}{$\bullet$}GreenRed50\> {0.45,0.55,0}\\ +% \textcolor{GreenRed55}{$\bullet$}GreenRed55 \> {0.50,0.50,0} \>\textcolor{GreenRed60}{$\bullet$}GreenRed60\> {0.55,0.45,0}\\ +% \textcolor{GreenRed65}{$\bullet$}GreenRed65 \> {0.60,0.40,0} \>\textcolor{GreenRed70}{$\bullet$}GreenRed70\> {0.65,0.35,0}\\ +% \textcolor{GreenRed75}{$\bullet$}GreenRed75 \> {0.70,0.30,0} \>\textcolor{GreenRed80}{$\bullet$}GreenRed80\> {0.75,0.25,0}\\ +% \textcolor{GreenRed85}{$\bullet$}GreenRed85 \> {0.80,0.20,0} \>\textcolor{GreenRed90}{$\bullet$}GreenRed90\> {0.85,0.15,0}\\ +% \textcolor{GreenRed95}{$\bullet$}GreenRed95 \> {0.90,0.10,0} \>\textcolor{GreenRed100}{$\bullet$}GreenRed100\> {0.95,0.05,0}\\ +% \textcolor{ColdHot5}{$\bullet$}ColdHot5 \> {0,0.08,1} \>\textcolor{ColdHot10}{$\bullet$}ColdHot10 \> {0,0.29,1}\\ +% \textcolor{ColdHot15}{$\bullet$}ColdHot15 \> {0,0.49,1} \>\textcolor{ColdHot20}{$\bullet$}ColdHot20 \> {0,0.70,1}\\ +% \textcolor{ColdHot25}{$\bullet$}ColdHot25 \> {0,0.90,1} \>\textcolor{ColdHot30}{$\bullet$}ColdHot30 \> {0,1,0.87}\\ +% \textcolor{ColdHot35}{$\bullet$}ColdHot35 \> {0,1,0.68} \>\textcolor{ColdHot40}{$\bullet$}ColdHot40 \> {0,1,0.46}\\ +% \textcolor{ColdHot45}{$\bullet$}ColdHot45 \> {0,1,0.25} \>\textcolor{ColdHot50}{$\bullet$}ColdHot50 \> {0,1,0.04}\\ +% \textcolor{ColdHot55}{$\bullet$}ColdHot55 \> {0.16,1,0} \>\textcolor{ColdHot60}{$\bullet$}ColdHot60 \> {0.35,1,0}\\ +% \textcolor{ColdHot65}{$\bullet$}ColdHot65 \> {0.56,1,0} \>\textcolor{ColdHot70}{$\bullet$}ColdHot70 \> {0.79,1,0}\\ +% \textcolor{ColdHot75}{$\bullet$}ColdHot75 \> {0.98,1,0} \>\textcolor{ColdHot80}{$\bullet$}ColdHot80 \> {1,0.82,0}\\ +% \textcolor{ColdHot85}{$\bullet$}ColdHot85 \> {1,0.60,0} \>\textcolor{ColdHot90}{$\bullet$}ColdHot90 \> {1,0.40,0}\\ +% \textcolor{ColdHot95}{$\bullet$}ColdHot95 \> {1,0.20,0} \>\textcolor{ColdHot100}{$\bullet$}ColdHot100\> {0.91,0,0}\\ +% and reverse definitions: |RedBlue|, |RedGreen|, |HotCold|.\\ +% \end{tabbing} +% \end{footnotesize} +% +% Type the color names with the upper case letters exactly as described above. +% For the definition of new colors use one of the |color.sty| commands: +% \medskip +% +% \quad|\definecolor{|\meta{name}|}{cmyk}{|\meta{C,M,Y,K}|}| +% \medskip +% +% \quad|\definecolor{|\meta{name}|}{rgb}{|\meta{R,G,B}|}| +% \medskip +% +% The \meta{name} can be chosen freely, the values for the color +% composition must be in the range 0--1, i\,e.\ 0--100\% of the +% respective component (`C' -- cyan, `M' -- magenta, `Y' -- yellow, +% `K' -- black; or `R' -- red, `G' -- green, `Blue' -- blue) separated by +% commas. +% \medskip +% +% Examples: +% \medskip +% +% |\definecolor{Salmon}{cmyk}{0,0.53,0.38,0}| +% \medskip +% +% |\definecolor{ColdHot15}{rgb}{0,0.49,1}| +% \medskip +% +% \newpage +% \section{Listing of the \texttt{texshade} default settings} +% +% \subsection{Standard definitions} +% +% The file |texshade.def| mirrors all commands which are +% carried out at the beginning of the |texshade| environment. +% Short comments are also included, thus, it is refered to +% this file for further information. +% +% \subsection{Colors used in the different shading modes} +% +% \vspace{5mm} +% +% Color scheme \emph{blues}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>Black \> Magenta \> similar \\ +% \>White \> RoyalBlue \> identical \\ +% \>Goldenrod \> RoyalPurple \> all match\\ +% \end{tabbing} +% \medskip +% +% Color scheme \emph{greens}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>Black \> GreenYellow \> similar \\ +% \>White \> PineGreen \> identical \\ +% \>YellowOrange \> OliveGreen \> all match\\ +% \end{tabbing} +% \medskip +% +% Color scheme \emph{reds}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>Black \> YellowOrange \> similar \\ +% \>White \> BrickRed \> identical \\ +% \>YellowGreen \> Mahagony \> all match\\ +% \end{tabbing} +% \medskip +% +% \newpage +% Color scheme \emph{grays}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>Black \> LightGray \> similar \\ +% \>White \> DarkGray \> identical \\ +% \>White \> Black \> all match\\ +% \end{tabbing} +% \medskip +% +% Color scheme \emph{black}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>Black \> White \> similar \\ +% \>White \> Black \> identical \\ +% \>White \> Black \> all match\\ +% \end{tabbing} +% \medskip +% +% Functional mode \emph{charge}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>White \> Red \> acidic \\ +% \>White \> Blue \> basic \\ +% \end{tabbing} +% \medskip +% +% Functional mode \emph{hydropathy}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>White \> Red \> acidic \\ +% \>White \> Blue \> basic \\ +% \>Black \> Yellow \> polar uncharged \\ +% \>White \> Green \> hydrophobic nonpolar \\ +% \end{tabbing} +% \medskip +% +% \newpage +% Functional mode \emph{chemical}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>White \> Red \> acidic \\ +% \>White \> Black \> aliphatic \\ +% \>White \> Gray \> aliphatic (small) \\ +% \>White \> Green \> amide \\ +% \>White \> Brown \> aromatic \\ +% \>White \> Blue \> basic \\ +% \>Black \> Magenta \> hydroxyl \\ +% \>Black \> Orange \> imino \\ +% \>Black \> Yellow \> sulfur \\ +% \end{tabbing} +% \medskip +% +% Functional mode \emph{rasmol}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>Red \> White \> Asp, Glu \\ +% \>Blue \> White \> Arg, Lys, His \\ +% \>MidnightBlue \> White \> Phe, Tyr, Trp \\ +% \>Gray \> White \> Ala, Gly \\ +% \>Yellow \> White \> Cys, Met \\ +% \>Orange \> White \> Ser, Thr \\ +% \>Cyan \> White \> Asn, Gln \\ +% \>Gree \> White \> Leu, Val, Ile \\ +% \>Apricot \> White \> Pro \\ +% \end{tabbing} +% \medskip +% +% Functional mode \emph{structure}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>Black \> Orange \> external \\ +% \>Black \> Yellow \> ambivalent \\ +% \>White \> Green \> internal \\ +% \end{tabbing} +% \medskip +% +% \newpage +% Functional mode \emph{standard area}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>Black \> BrickRed \> G\\ +% \>Black \> Orange \> A, S\\ +% \>Black \> Yellow \> C, P \\ +% \>Black \> YellowGreen \> T, D, V, N \\ +% \>White \> PineGreen \> I, E \\ +% \>Black \> SkyBlue \> L, Q, H, M \\ +% \>White \> RoyalPurple \> F, K \\ +% \>White \> RedViolet \> Y \\ +% \>White \> Black \> R, W \\ +% \end{tabbing} +% \medskip +% +% Functional mode \emph{accessible area}: +% \medskip +% +% \begin{tabbing} +% \hspace{1cm}\=\emph{res.color}\hspace{1.5cm}\=\emph{shad.color}\hspace{1.5cm} \= \emph{residues} \\ +% \>Black \> White \> no match \\ +% \>Black \> BrickRed \> C \\ +% \>Black \> Orange \> I, V, G \\ +% \>Black \> Yellow \> F, L, M, A \\ +% \>Black \> YellowGreen \> W, S, T, H \\ +% \>White \> PineGreen \> P \\ +% \>Black \> SkyBlue \> Y, D, N \\ +% \>White \> RoyalPurple \> E, Q \\ +% \>White \> RedViolet \> R \\ +% \>White \> Black \> K \\ +% \end{tabbing} +% \medskip +% +% +% \newpage +% \subsection{Residue weight tables}\label{weightmatrix} +% \bigskip +% +% |identity| +% \bigskip +% \bigskip +% +%{\footnotesize\tt +% +%\weighttable{identity} +%\hspace*{-2cm} +%\begin{tabular}{lrrrrrrrrrrrrrrrrrrrr} +% +%C & \consCC &&&&&&&&&&&&&&&&&&& \\ +% +%S & \consSC & \consSS &&&&&&&&&&&&&&&&&& \\ +% +%T & \consTC & \consTS & \consTT &&&&&&&&&&&&&&&&& \\ +% +%P & \consPC & \consPS & \consPT & \consPP &&&&&&&&&&&&&&&& \\ +% +%A & \consAC & \consAS & \consAT & \consAP & \consAA +%&&&&&&&&&&&&&&& \\ +% +%G & \consGC & \consGS & \consGT & \consGP & \consGA +%& \consGG &&&&&&&&&&&&&& \\ +% +%N & \consNC & \consNS & \consNT & \consNP & \consNA +%& \consNG & \consNN &&&&&&&&&&&&& \\ +% +%D & \consDC & \consDS & \consDT & \consDP & \consDA +%& \consDG & \consDN & \consDD &&&&&&&&&&&& \\ +% +%E & \consEC & \consES & \consET & \consEP & \consEA +%& \consEG & \consEN & \consED & \consEE &&&&&&&&&&& \\ +% +%Q & \consQC & \consQS & \consQT & \consQP & \consQA +%& \consQG & \consQN & \consQD & \consQE & \consQQ +%&&&&&&&&&& \\ +% +%H & \consHC & \consHS & \consHT & \consHP & \consHA +%& \consHG & \consHN & \consHD & \consHE & \consHQ +%& \consHH &&&&&&&&& \\ +% +%R & \consRC & \consRS & \consRT & \consRP & \consRA +%& \consRG & \consRN & \consRD & \consRE & \consRQ +%& \consRH & \consRR &&&&&&&& \\ +% +%K & \consKC & \consKS & \consKT & \consKP & \consKA +%& \consKG & \consKN & \consKD & \consKE & \consKQ +%& \consKH & \consKR & \consKK &&&&&&& \\ +% +%M & \consMC & \consMS & \consMT & \consMP & \consMA +%& \consMG & \consMN & \consMD & \consME & \consMQ +%& \consMH & \consMR & \consMK & \consMM &&&&&& \\ +% +%I & \consIC & \consIS & \consIT & \consIP & \consIA +%& \consIG & \consIN & \consID & \consIE & \consIQ +%& \consIH & \consIR & \consIK & \consIM & \consII +%&&&&& \\ +% +%L & \consLC & \consLS & \consLT & \consLP & \consLA +%& \consLG & \consLN & \consLD & \consLE & \consLQ +%& \consLH & \consLR & \consLK & \consLM & \consLI +%& \consLL &&&& \\ +% +%V & \consVC & \consVS & \consVT & \consVP & \consVA +%& \consVG & \consVN & \consVD & \consVE & \consVQ +%& \consVH & \consVR & \consVK & \consVM & \consVI +%& \consVL & \consVV &&& \\ +% +%F & \consFC & \consFS & \consFT & \consFP & \consFA +%& \consFG & \consFN & \consFD & \consFE & \consFQ +%& \consFH & \consFR & \consFK & \consFM & \consFI +%& \consFL & \consFV & \consFF && \\ +% +%Y & \consYC & \consYS & \consYT & \consYP & \consYA +%& \consYG & \consYN & \consYD & \consYE & \consYQ +%& \consYH & \consYR & \consYK & \consYM & \consYI +%& \consYL & \consYV & \consYF & \consYY & \\ +% +%W & \consWC & \consWS & \consWT & \consWP & \consWA +%& \consWG & \consWN & \consWD & \consWE & \consWQ +%& \consWH & \consWR & \consWK & \consWM & \consWI +%& \consWL & \consWV & \consWF & \consWY & \consWW \\[1.5ex] +% +%& C & S & T & P & A & G & N & D & E & Q & H & R & K & M & I & L & V & F & Y & W \\ +% +%\end{tabular} +%} +% \newpage +% +% |structural| +% \bigskip +% \bigskip +% +%{\footnotesize\tt +% +%\weighttable{structural} +%\hspace*{-2cm} +%\begin{tabular}{lrrrrrrrrrrrrrrrrrrrr} +% +%C & \consCC &&&&&&&&&&&&&&&&&&& \\ +% +%S & \consSC & \consSS &&&&&&&&&&&&&&&&&& \\ +% +%T & \consTC & \consTS & \consTT &&&&&&&&&&&&&&&&& \\ +% +%P & \consPC & \consPS & \consPT & \consPP &&&&&&&&&&&&&&&& \\ +% +%A & \consAC & \consAS & \consAT & \consAP & \consAA +%&&&&&&&&&&&&&&& \\ +% +%G & \consGC & \consGS & \consGT & \consGP & \consGA +%& \consGG &&&&&&&&&&&&&& \\ +% +%N & \consNC & \consNS & \consNT & \consNP & \consNA +%& \consNG & \consNN &&&&&&&&&&&&& \\ +% +%D & \consDC & \consDS & \consDT & \consDP & \consDA +%& \consDG & \consDN & \consDD &&&&&&&&&&&& \\ +% +%E & \consEC & \consES & \consET & \consEP & \consEA +%& \consEG & \consEN & \consED & \consEE &&&&&&&&&&& \\ +% +%Q & \consQC & \consQS & \consQT & \consQP & \consQA +%& \consQG & \consQN & \consQD & \consQE & \consQQ +%&&&&&&&&&& \\ +% +%H & \consHC & \consHS & \consHT & \consHP & \consHA +%& \consHG & \consHN & \consHD & \consHE & \consHQ +%& \consHH &&&&&&&&& \\ +% +%R & \consRC & \consRS & \consRT & \consRP & \consRA +%& \consRG & \consRN & \consRD & \consRE & \consRQ +%& \consRH & \consRR &&&&&&&& \\ +% +%K & \consKC & \consKS & \consKT & \consKP & \consKA +%& \consKG & \consKN & \consKD & \consKE & \consKQ +%& \consKH & \consKR & \consKK &&&&&&& \\ +% +%M & \consMC & \consMS & \consMT & \consMP & \consMA +%& \consMG & \consMN & \consMD & \consME & \consMQ +%& \consMH & \consMR & \consMK & \consMM &&&&&& \\ +% +%I & \consIC & \consIS & \consIT & \consIP & \consIA +%& \consIG & \consIN & \consID & \consIE & \consIQ +%& \consIH & \consIR & \consIK & \consIM & \consII +%&&&&& \\ +% +%L & \consLC & \consLS & \consLT & \consLP & \consLA +%& \consLG & \consLN & \consLD & \consLE & \consLQ +%& \consLH & \consLR & \consLK & \consLM & \consLI +%& \consLL &&&& \\ +% +%V & \consVC & \consVS & \consVT & \consVP & \consVA +%& \consVG & \consVN & \consVD & \consVE & \consVQ +%& \consVH & \consVR & \consVK & \consVM & \consVI +%& \consVL & \consVV &&& \\ +% +%F & \consFC & \consFS & \consFT & \consFP & \consFA +%& \consFG & \consFN & \consFD & \consFE & \consFQ +%& \consFH & \consFR & \consFK & \consFM & \consFI +%& \consFL & \consFV & \consFF && \\ +% +%Y & \consYC & \consYS & \consYT & \consYP & \consYA +%& \consYG & \consYN & \consYD & \consYE & \consYQ +%& \consYH & \consYR & \consYK & \consYM & \consYI +%& \consYL & \consYV & \consYF & \consYY & \\ +% +%W & \consWC & \consWS & \consWT & \consWP & \consWA +%& \consWG & \consWN & \consWD & \consWE & \consWQ +%& \consWH & \consWR & \consWK & \consWM & \consWI +%& \consWL & \consWV & \consWF & \consWY & \consWW \\[1.5ex] +% +%& C & S & T & P & A & G & N & D & E & Q & H & R & K & M & I & L & V & F & Y & W \\ +% +%\end{tabular} +%} +% \newpage +% +% |PAM250| +% \bigskip +% \bigskip +% +%{\footnotesize\tt +% +%\weighttable{PAM250} +%\hspace*{-2cm} +%\begin{tabular}{lrrrrrrrrrrrrrrrrrrrr} +% +%C & \consCC &&&&&&&&&&&&&&&&&&& \\ +% +%S & \consSC & \consSS &&&&&&&&&&&&&&&&&& \\ +% +%T & \consTC & \consTS & \consTT &&&&&&&&&&&&&&&&& \\ +% +%P & \consPC & \consPS & \consPT & \consPP &&&&&&&&&&&&&&&& \\ +% +%A & \consAC & \consAS & \consAT & \consAP & \consAA +%&&&&&&&&&&&&&&& \\ +% +%G & \consGC & \consGS & \consGT & \consGP & \consGA +%& \consGG &&&&&&&&&&&&&& \\ +% +%N & \consNC & \consNS & \consNT & \consNP & \consNA +%& \consNG & \consNN &&&&&&&&&&&&& \\ +% +%D & \consDC & \consDS & \consDT & \consDP & \consDA +%& \consDG & \consDN & \consDD &&&&&&&&&&&& \\ +% +%E & \consEC & \consES & \consET & \consEP & \consEA +%& \consEG & \consEN & \consED & \consEE &&&&&&&&&&& \\ +% +%Q & \consQC & \consQS & \consQT & \consQP & \consQA +%& \consQG & \consQN & \consQD & \consQE & \consQQ +%&&&&&&&&&& \\ +% +%H & \consHC & \consHS & \consHT & \consHP & \consHA +%& \consHG & \consHN & \consHD & \consHE & \consHQ +%& \consHH &&&&&&&&& \\ +% +%R & \consRC & \consRS & \consRT & \consRP & \consRA +%& \consRG & \consRN & \consRD & \consRE & \consRQ +%& \consRH & \consRR &&&&&&&& \\ +% +%K & \consKC & \consKS & \consKT & \consKP & \consKA +%& \consKG & \consKN & \consKD & \consKE & \consKQ +%& \consKH & \consKR & \consKK &&&&&&& \\ +% +%M & \consMC & \consMS & \consMT & \consMP & \consMA +%& \consMG & \consMN & \consMD & \consME & \consMQ +%& \consMH & \consMR & \consMK & \consMM &&&&&& \\ +% +%I & \consIC & \consIS & \consIT & \consIP & \consIA +%& \consIG & \consIN & \consID & \consIE & \consIQ +%& \consIH & \consIR & \consIK & \consIM & \consII +%&&&&& \\ +% +%L & \consLC & \consLS & \consLT & \consLP & \consLA +%& \consLG & \consLN & \consLD & \consLE & \consLQ +%& \consLH & \consLR & \consLK & \consLM & \consLI +%& \consLL &&&& \\ +% +%V & \consVC & \consVS & \consVT & \consVP & \consVA +%& \consVG & \consVN & \consVD & \consVE & \consVQ +%& \consVH & \consVR & \consVK & \consVM & \consVI +%& \consVL & \consVV &&& \\ +% +%F & \consFC & \consFS & \consFT & \consFP & \consFA +%& \consFG & \consFN & \consFD & \consFE & \consFQ +%& \consFH & \consFR & \consFK & \consFM & \consFI +%& \consFL & \consFV & \consFF && \\ +% +%Y & \consYC & \consYS & \consYT & \consYP & \consYA +%& \consYG & \consYN & \consYD & \consYE & \consYQ +%& \consYH & \consYR & \consYK & \consYM & \consYI +%& \consYL & \consYV & \consYF & \consYY & \\ +% +%W & \consWC & \consWS & \consWT & \consWP & \consWA +%& \consWG & \consWN & \consWD & \consWE & \consWQ +%& \consWH & \consWR & \consWK & \consWM & \consWI +%& \consWL & \consWV & \consWF & \consWY & \consWW \\[1.5ex] +% +%& C & S & T & P & A & G & N & D & E & Q & H & R & K & M & I & L & V & F & Y & W \\ +% +%\end{tabular} +%} +% \newpage +% +% |PAM100| +% \bigskip +% \bigskip +% +%{\footnotesize\tt +% +%\weighttable{PAM100} +%\hspace*{-3cm} +%\begin{tabular}{lrrrrrrrrrrrrrrrrrrrr} +% +%C & \consCC &&&&&&&&&&&&&&&&&&& \\ +% +%S & \consSC & \consSS &&&&&&&&&&&&&&&&&& \\ +% +%T & \consTC & \consTS & \consTT &&&&&&&&&&&&&&&&& \\ +% +%P & \consPC & \consPS & \consPT & \consPP &&&&&&&&&&&&&&&& \\ +% +%A & \consAC & \consAS & \consAT & \consAP & \consAA +%&&&&&&&&&&&&&&& \\ +% +%G & \consGC & \consGS & \consGT & \consGP & \consGA +%& \consGG &&&&&&&&&&&&&& \\ +% +%N & \consNC & \consNS & \consNT & \consNP & \consNA +%& \consNG & \consNN &&&&&&&&&&&&& \\ +% +%D & \consDC & \consDS & \consDT & \consDP & \consDA +%& \consDG & \consDN & \consDD &&&&&&&&&&&& \\ +% +%E & \consEC & \consES & \consET & \consEP & \consEA +%& \consEG & \consEN & \consED & \consEE &&&&&&&&&&& \\ +% +%Q & \consQC & \consQS & \consQT & \consQP & \consQA +%& \consQG & \consQN & \consQD & \consQE & \consQQ +%&&&&&&&&&& \\ +% +%H & \consHC & \consHS & \consHT & \consHP & \consHA +%& \consHG & \consHN & \consHD & \consHE & \consHQ +%& \consHH &&&&&&&&& \\ +% +%R & \consRC & \consRS & \consRT & \consRP & \consRA +%& \consRG & \consRN & \consRD & \consRE & \consRQ +%& \consRH & \consRR &&&&&&&& \\ +% +%K & \consKC & \consKS & \consKT & \consKP & \consKA +%& \consKG & \consKN & \consKD & \consKE & \consKQ +%& \consKH & \consKR & \consKK &&&&&&& \\ +% +%M & \consMC & \consMS & \consMT & \consMP & \consMA +%& \consMG & \consMN & \consMD & \consME & \consMQ +%& \consMH & \consMR & \consMK & \consMM &&&&&& \\ +% +%I & \consIC & \consIS & \consIT & \consIP & \consIA +%& \consIG & \consIN & \consID & \consIE & \consIQ +%& \consIH & \consIR & \consIK & \consIM & \consII +%&&&&& \\ +% +%L & \consLC & \consLS & \consLT & \consLP & \consLA +%& \consLG & \consLN & \consLD & \consLE & \consLQ +%& \consLH & \consLR & \consLK & \consLM & \consLI +%& \consLL &&&& \\ +% +%V & \consVC & \consVS & \consVT & \consVP & \consVA +%& \consVG & \consVN & \consVD & \consVE & \consVQ +%& \consVH & \consVR & \consVK & \consVM & \consVI +%& \consVL & \consVV &&& \\ +% +%F & \consFC & \consFS & \consFT & \consFP & \consFA +%& \consFG & \consFN & \consFD & \consFE & \consFQ +%& \consFH & \consFR & \consFK & \consFM & \consFI +%& \consFL & \consFV & \consFF && \\ +% +%Y & \consYC & \consYS & \consYT & \consYP & \consYA +%& \consYG & \consYN & \consYD & \consYE & \consYQ +%& \consYH & \consYR & \consYK & \consYM & \consYI +%& \consYL & \consYV & \consYF & \consYY & \\ +% +%W & \consWC & \consWS & \consWT & \consWP & \consWA +%& \consWG & \consWN & \consWD & \consWE & \consWQ +%& \consWH & \consWR & \consWK & \consWM & \consWI +%& \consWL & \consWV & \consWF & \consWY & \consWW \\[1.5ex] +% +%& C & S & T & P & A & G & N & D & E & Q & H & R & K & M & I & L & V & F & Y & W \\ +% +%\end{tabular} +%} +% \newpage +% +% |BLOSUM62| +%\bigskip +%\bigskip +% +%{\footnotesize\tt +% +%\weighttable{BLOSUM62} +%\hspace*{-2cm} +%\begin{tabular}{lrrrrrrrrrrrrrrrrrrrr} +% +%C & \consCC &&&&&&&&&&&&&&&&&&& \\ +% +%S & \consSC & \consSS &&&&&&&&&&&&&&&&&& \\ +% +%T & \consTC & \consTS & \consTT &&&&&&&&&&&&&&&&& \\ +% +%P & \consPC & \consPS & \consPT & \consPP &&&&&&&&&&&&&&&& \\ +% +%A & \consAC & \consAS & \consAT & \consAP & \consAA +%&&&&&&&&&&&&&&& \\ +% +%G & \consGC & \consGS & \consGT & \consGP & \consGA +%& \consGG &&&&&&&&&&&&&& \\ +% +%N & \consNC & \consNS & \consNT & \consNP & \consNA +%& \consNG & \consNN &&&&&&&&&&&&& \\ +% +%D & \consDC & \consDS & \consDT & \consDP & \consDA +%& \consDG & \consDN & \consDD &&&&&&&&&&&& \\ +% +%E & \consEC & \consES & \consET & \consEP & \consEA +%& \consEG & \consEN & \consED & \consEE &&&&&&&&&&& \\ +% +%Q & \consQC & \consQS & \consQT & \consQP & \consQA +%& \consQG & \consQN & \consQD & \consQE & \consQQ +%&&&&&&&&&& \\ +% +%H & \consHC & \consHS & \consHT & \consHP & \consHA +%& \consHG & \consHN & \consHD & \consHE & \consHQ +%& \consHH &&&&&&&&& \\ +% +%R & \consRC & \consRS & \consRT & \consRP & \consRA +%& \consRG & \consRN & \consRD & \consRE & \consRQ +%& \consRH & \consRR &&&&&&&& \\ +% +%K & \consKC & \consKS & \consKT & \consKP & \consKA +%& \consKG & \consKN & \consKD & \consKE & \consKQ +%& \consKH & \consKR & \consKK &&&&&&& \\ +% +%M & \consMC & \consMS & \consMT & \consMP & \consMA +%& \consMG & \consMN & \consMD & \consME & \consMQ +%& \consMH & \consMR & \consMK & \consMM &&&&&& \\ +% +%I & \consIC & \consIS & \consIT & \consIP & \consIA +%& \consIG & \consIN & \consID & \consIE & \consIQ +%& \consIH & \consIR & \consIK & \consIM & \consII +%&&&&& \\ +% +%L & \consLC & \consLS & \consLT & \consLP & \consLA +%& \consLG & \consLN & \consLD & \consLE & \consLQ +%& \consLH & \consLR & \consLK & \consLM & \consLI +%& \consLL &&&& \\ +% +%V & \consVC & \consVS & \consVT & \consVP & \consVA +%& \consVG & \consVN & \consVD & \consVE & \consVQ +%& \consVH & \consVR & \consVK & \consVM & \consVI +%& \consVL & \consVV &&& \\ +% +%F & \consFC & \consFS & \consFT & \consFP & \consFA +%& \consFG & \consFN & \consFD & \consFE & \consFQ +%& \consFH & \consFR & \consFK & \consFM & \consFI +%& \consFL & \consFV & \consFF && \\ +% +%Y & \consYC & \consYS & \consYT & \consYP & \consYA +%& \consYG & \consYN & \consYD & \consYE & \consYQ +%& \consYH & \consYR & \consYK & \consYM & \consYI +%& \consYL & \consYV & \consYF & \consYY & \\ +% +%W & \consWC & \consWS & \consWT & \consWP & \consWA +%& \consWG & \consWN & \consWD & \consWE & \consWQ +%& \consWH & \consWR & \consWK & \consWM & \consWI +%& \consWL & \consWV & \consWF & \consWY & \consWW \\[1.5ex] +% +%& C & S & T & P & A & G & N & D & E & Q & H & R & K & M & I & L & V & F & Y & W \\ +% +%\end{tabular} +%} +% \bigskip +% +% +% \newpage +% \section{Quick Reference} +% +% \textbf{The \TeXshade{} logo} +% \medskip +% +% \quad |\TeXshade| +% +% \vspace{1.5\baselineskip} +% +% \textbf{The \TeXshade{} environment} (\pageref{tsenvironment}\,ff.) +% \medskip +% +% \begin{quote} +% |\begin{texshade}[|\meta{parameterfile}|]| +% |{|\meta{alignmentfile}|}| +% +% \quad\emph{further \emph{\TeXshade} commands, if needed} +% +% |\end{texshade}| +% \end{quote} +% \bigskip +% +% \textbf{Predefined shading modes} +% \medskip +% +% \quad|\seqtype{|\meta{type}|}| +% \hfill(|P| -- peptide, |N| -- nucleotide) \hfill[\pageref{Lseqtype}] +% +% \medskip +% +% \quad|\shadingmode[|\meta{option}|]{|\meta{mode}|}| +% \hfill[\pageref{Lshadingmode}] +% +% \medskip +% +% \begin{center} +% \begin{tabular}{lll} +% \meta{mode} & \meta{option} &\\ \hline +% |identical| & |allmatchspecial/number| &\\ +% |similar| & |allmatchspecial/number| &\\ +% |T-Coffee| & \meta{filename} &\\ +% |diverse| & \meta{seqref} &\\ +% |functional|& \meta{type} & |charge| \\ +% & & |hydropathy| \\ +% & & |structure| \\ +% & & |chemical| \\ +% & & |rasmol| \\ +% & & |standard area| \\ +% & & |accessible area| \\ \hline +% \end{tabular} +% \end{center} +% \medskip +% +% \quad|\allmatchspecial[|\meta{percentage}|]| +% \hfill[\pageref{Lallmatchspecial}] +% +% \quad|\hideallmatchpositions| +% \hfill[\pageref{Lhideallmatchpositions}] +% +% \quad|\shadeallresidues| +% \hfill[\pageref{Lshadeallresidues}] +% +% \vspace{1.5\baselineskip} +% +% \textbf{Shading colors} (\pageref{Lshadingcolors}\,ff.) +% \medskip +% +% \quad|\shadingcolors{|\meta{scheme}|}| \,\, (|blues|, |reds|, +% |greens|, |grays|, |black|) +% +% \quad|\nomatchresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}| +% +% \quad|\similarresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}| +% +% \quad|\conservedresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}| +% +% \quad|\allmatchresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}| +% +% \quad|\defshadingcolors{|\meta{name}|}| +% \newpage +% +% \quad|\funcshadingstyle{|\meta{residue}|}{|\meta{res.col.}|}{|\meta{shad.color}|}| +% +% \hfill|{|\meta{case}|}{|\meta{style}|}| [\pageref{Lfuncshadingstyle}] +% +% \vspace{1.5\baselineskip} +% +% \textbf{Residue grouping} +% \medskip +% +% \quad|\pepsims{|\meta{residue}|}{|\meta{similars}|}| +% \hfill[\pageref{Lpepsims}] +% +% \quad|\pepgroups{|\meta{group1}|,|\meta{group2}|, ... , |\meta{groupn}|}| +% \hfill[\pageref{Lpepgroups}] +% +% \quad|\DNAsims{|\meta{residue}|}{|\meta{similars}|}| +% \hfill[\pageref{LDNAsims}] +% +% \quad|\DNAgroups{|\meta{group1}|,|\meta{group2}|, ... , |\meta{groupn}|}| +% \hfill[\pageref{LDNAgroups}] +% +% \vspace{1.5\baselineskip} +% +% \textbf{Definition of new functional shading modes} +% \medskip +% +% \quad|\clearfuncgroups| \hfill [\pageref{Lclearfuncgroups}] +% +% \quad|\funcgroup{|\meta{descr}|}{|\meta{residues}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}| +% +% \hfill|{|\meta{case}|}{|\meta{style}|}| +% \hfill[\pageref{Lfuncgroup}] +% +% \vspace{1.5\baselineskip} +% +% \textbf{Appearance of the consensus line} +% \medskip +% +% \quad|\threshold[|\meta{percentage}|]{|\meta{percentage}|}| +% \hfill[\pageref{Lthreshold}] +% +% \quad|\constosingleseq{|\meta{seqref}|}| +% \hfill[\pageref{Lconstosingleseq}] +% +% \quad|\showconsensus[|\meta{color/scale}|[,|\meta{color/scale}|]]{|\meta{top/bot.}|}| +% \hfill[\pageref{Lshowconsensus}] +% +% \quad|\exportconsensus[|\meta{filename}|]{|\meta{seqref}|}| +% \hfill[\pageref{Lexportconsensus}] +% +% \quad|\hideconsensus| +% \hfill[\pageref{Lhideconsensus}] +% +% \quad|\nameconsensus{|\meta{name}|}| +% \hfill[\pageref{Lnameconsensus}] +% +% \quad|\defconsensus{|\meta{symbol1}|}{|\meta{symbol2}|}{|\meta{symbol3}|}| +% \hfill[\pageref{Ldefconsensus}] +% +% \vspace*{-0.5\baselineskip} +% +% \begin{tabbing} +% \quad|\consensuscolors|\=|{|\meta{res.col.1}|}{|\meta{shad.col.1}|}|\\ +% +% \>|{|\meta{res.col.2}|}{|\meta{shad.col.2}|}|\\ +% +% \>|{|\meta{res.col.3}|}{|\meta{shad.col.3}|}| +% \hspace{1.2in}[\pageref{Lconsensuscolors}]\\ +% \end{tabbing} +% +% \quad|\weighttable{|\meta{table}|}| +% \hfill[\pageref{Lweighttable}] +% +% \quad|\setweight{|\meta{res.1}|}{|\meta{res.2}|}{|\meta{value}|}| +% \hfill[\pageref{Lsetweight}] +% +% \quad|\gappenalty{|\meta{value}|}| +% \hfill[\pageref{Lgappenalty}] +% +% \vspace{1.5\baselineskip} +% +% \textbf{Sequence logos} +% \medskip +% +% \quad|\showsequencelogo[|\meta{colorset}|]{|\meta{top/bottom}|}| +% \hfill[\pageref{Lshowsequencelogo}] +% +% \quad|\hidesequencelogo| +% \hfill[\pageref{Lhidesequencelogo}] +% +% \quad|\clearlogocolors[|\meta{color}|]| +% \hfill[\pageref{Lclearlogocolors}] +% +% \quad|\logocolor{|\meta{residues}|}{|\meta{color}|}| +% \hfill[\pageref{Llogocolor}] +% +% \quad|\showlogoscale[|\meta{color}|]{|\meta{left/right/leftright}|}| +% \hfill[\pageref{Lshowlogoscale}] +% +% \quad|\hidelogoscale| +% \hfill[\pageref{Lhidelogoscale}] +% +% \quad|\logostretch{|\meta{factor}|}| +% \hfill[\pageref{Llogostretch}] +% +% \quad|\namesequencelogo{|\meta{name}|}| +% \hfill[\pageref{Lnamesequencelogo}] +% +% \quad|\dofrequencycorrection| +% \hfill[\pageref{Ldofrequencycorrection}] +% +% \quad|\undofrequencycorrection| +% \hfill[\pageref{Lundofrequencycorrection}] +% +% \vspace{1.5\baselineskip} +% +% \textbf{Subfamily logos} +% \medskip +% +% \quad|\showsubfamilylogo[|\meta{colorset}|]{|\meta{top/bottom}|}| +% \hfill[\pageref{Lshowsubfamilylogo}] +% +% \quad|\hidesubfamilylogo| +% \hfill[\pageref{Lhidesubfamilylogo}] +% +% \quad|\setsubfamily{|\meta{seqrefs}|}| +% \hfill[\pageref{Lsetsubfamily}] +% +% \quad|\shownegatives[|\meta{weak, medium, strong}|]| +% \hfill[\pageref{Lshownegatives}] +% +% \quad|\hidenegatives| +% \hfill[\pageref{Lhidenegatives}] +% +% \quad|\namesubfamilylogo[|\meta{neg.name}|]{|\meta{name}|}| +% \hfill[\pageref{Lnamesubfamilylogo}] +% +% \quad|\relevance{|\meta{bit-value}|}| +% \hfill[\pageref{Lrelevance}] +% +% \quad|\showrelevance[|\meta{color}|]{|\meta{symbol}|}| +% \hfill[\pageref{Lshowrelevance}] +% +% \quad|\hiderelevance| +% \hfill[\pageref{Lhiderelevance}] +% +% +% \vspace{1.5\baselineskip} +% +% \textbf{Appearance of the sequence lines} +% \medskip +% +% \quad|\shownames[|\meta{color}|]{|\meta{left/right}|}| +% \hfill[\pageref{Lshownames}] +% +% \quad|\shownumbering[|\meta{color}|]{|\meta{left/right/leftright}|}| +% \hfill[\pageref{Lshownumbering}] +% +% \quad|\nameseq{|\meta{seqref}|}{|\meta{name}|}| +% \hfill[\pageref{Lnameseq}] +% +% \quad|\namescolor{|\meta{color}|}| +% \hfill[\pageref{Lnamescolor}] +% +% \quad|\namecolor{|\meta{seq1}|, ... ,|\meta{seq n}|}{|\meta{color}|}| +% \hfill[\pageref{Lnamecolor}] +% +% \quad|\hidenames| +% \hfill[\pageref{Lhidenames}] +% +% \quad|\hidename{|\meta{seq1}|, ... ,|\meta{seq n}|}| +% \hfill[\pageref{Lhidename}] +% +% \quad|\numberingcolor{|\meta{color}|}| +% \hfill[\pageref{Lnumberingcolor}] +% +% \quad|\numbercolor{|\meta{seq1}|, ... ,|\meta{seq n}|}{|\meta{color}|}| +% \hfill[\pageref{Lnumbercolor}] +% +% \quad|\hidenumbering| +% \hfill[\pageref{Lhidenumbering}] +% +% \quad|\hidenumber{|\meta{seq1}|, ... ,|\meta{seq n}|}| +% \hfill[\pageref{Lhidenumber}] +% +% \quad|\hideresidues| +% \hfill[\pageref{Lhideresidues}] +% +% \quad|\showresidues| +% \hfill[\pageref{Lshowresidues}] +% +% \quad|\startnumber[|\meta{start..stop}|]{|\meta{seqref}|}{|\meta{startnumber}|}| +% \hfill[\pageref{Lstartnumber}] +% +% \quad|\allowzero| +% \hfill[\pageref{Lallowzero}] +% +% \quad|\disallowzero| +% \hfill[\pageref{Lallowzero}] +% +% \quad|\seqlength{|\meta{seqref}|}{|\meta{length}|}| +% \hfill[\pageref{Lseqlength}] +% +% \quad|\showruler[|\meta{color}|]{|\meta{top/bottom}|}{|\meta{seqref}|}| +% \hfill[\pageref{Lshowruler}] +% +% \quad|\rulersteps{|\meta{number}|}| +% \hfill[\pageref{Lrulersteps}] +% +% \quad|\rulercolor{|\meta{color}|}| +% \hfill[\pageref{Lrulercolor}] +% +% \quad|\hideruler| +% \hfill[\pageref{Lhideruler}] +% +% \quad|\rotateruler| +% \hfill[\pageref{Lrotateruler}] +% +% \quad|\unrotateruler| +% \hfill[\pageref{Lunrotateruler}] +% +% \quad|\namerulerpos{|\meta{number}|}{|\meta{text}|[|\meta{color}|]}| +% \hfill[\pageref{Lnamerulerpos}] +% +% \quad|\rulerspace{|\meta{length}|}| +% \hfill[\pageref{Lrulerspace}] +% +% \quad|\gapchar{|\meta{symbol}|}| +% \qquad (incl. |rule|) \hfill [\pageref{Lgapchar}] +% +% \quad|\gapcolors{|\meta{symbol color}|}{|\meta{background color}|}| +% \hfill[\pageref{Lgapcolors}] +% +% \quad|\showleadinggaps| +% \hfill[\pageref{Lshowleadinggaps}] +% +% \quad|\hideleadinggaps| +% \hfill[\pageref{Lhideleadinggaps}] +% +% \quad|\stopchar{|\meta{symbol}|}| +% \hfill [\pageref{Lstopchar}] +% +% \quad|\fingerprint{|\meta{res. per line}|}| +% \hfill[\pageref{Lfingerprint}] +% +% \vspace{1.5\baselineskip} +% +% \textbf{Displaying selected residues in the alignment} +% \medskip +% +% \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}| +% \hfill[\pageref{Lsetends}] +% +% \quad|\setdomain{|\meta{seqref}|}{|\meta{selection}|}| (see |\shaderegion| p.\,\pageref{Lshaderegion}) +% \hfill[\pageref{Lsetdomain}] +% +% \quad|\domaingaprule{|\meta{thickness}|}| +% \hfill[\pageref{Lsetdomain}] +% +% \quad|\domaingapcolors{|\meta{foreground}|}{|\meta{background}|}| +% \hfill[\pageref{Lsetdomain}] +% +% \vspace{1.5\baselineskip} +% +% \textbf{Hiding, killing, separating and ordering} +% \medskip +% +% \quad|\hideseq{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}| +% \hfill[\pageref{Lhideseq}] +% +% \quad|\hideseqs| +% \hfill[\pageref{Lhideseqs}] +% +% \quad|\showseqs| +% \hfill[\pageref{Lshowseqs}] +% +% \quad|\killseq{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}| +% \hfill[\pageref{Lkillseq}] +% +% \quad|\donotshade{|\meta{seq1}|,|\meta{seq2},\ldots|,|\meta{seq n}|}| +% \hfill[\pageref{Ldonotshade}] +% +% \quad|\separationline{|\meta{seqref}|}| +% \hfill[\pageref{Lseparationline}] +% +% \quad|\smallsep| +% \hfill[\pageref{Lsmallsep}] +% +% \quad|\medsep| +% \hfill[\pageref{Lmedsep}] +% +% \quad|\bigsep| +% \hfill[\pageref{Lbigsep}] +% +% \quad|\vsepspace{|\meta{length}|}| +% \hfill[\pageref{Lvsepspace}] +% +% \quad|\orderseqs{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}| +% \hfill[\pageref{Lorderseqs}] +% +% \vspace{1.5\baselineskip} +% +% \textbf{Residues per line and further settings} +% \medskip +% +% \quad|\residuesperline{|\meta{number}|}| +% \hfill[\pageref{Lresiduesperline}] +% +% \quad|\residuesperline*{|\meta{number}|}| +% \hfill[\pageref{Lresiduesperline*}] +% +% \quad|\charstretch{|\meta{factor}|}| +% \hfill[\pageref{Lcharstretch}] +% +% \quad|\linestretch{|\meta{factor}|}| +% \hfill[\pageref{Llinestretch}] +% +% \quad|\numberingwidth{|\meta{n digits}|}| +% \hfill[\pageref{Lnumberingwidth}] +% +% \quad|\smallblockskip| +% \hfill[\pageref{Lsmallblockskip}] +% +% \quad|\medblockskip| +% \hfill[\pageref{Lmedblockskip}] +% +% \quad|\bigblockskip| +% \hfill[\pageref{Lbigblockskip}] +% +% \quad|\noblockskip| +% \hfill[\pageref{Lnoblockskip}] +% +% \quad|\vblockspace{|\meta{length}|}| +% \hfill[\pageref{Lvblockspace}] +% +% \quad|\flexblockspace| +% \hfill[\pageref{Lflexblockspace}] +% +% \quad|\fixblockspace| +% \hfill[\pageref{Lfixblockspace}] +% +% \quad|\alignment{|\meta{left/center/right}|}| +% \hfill[\pageref{Lalignment}] +% +% \vspace{1.5\baselineskip} +% +% +% +% +% \textbf{Individual shading and labeling of sequence stretches} +% \medskip +% +% \quad|\shaderegion{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}| +% \hfill[\pageref{Lshaderegion}] +% +% \medskip +% +% \quad |{|\meta{selection}|}| = +% \medskip% +% +% \quad\quad|{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,|\ldots|,|\meta{start n}..\meta{stop n}|}| +% \medskip +% +% \quad\quad|{point[|\meta{dist}|]:|\meta{file}|,|\meta{num}|[CA/side]}| +% \medskip +% +% \quad\quad|{line[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side]}| +% \medskip +% +% \quad\quad|{plane[|\meta{dist}|]:|\meta{file}|,|\meta{num1}|[CA/side],|\meta{num2}|[CA/side],| +% \medskip +% +% \hfill\meta{num3}|[CA/side]}| +% \medskip +% +% +% \quad|\printPDBlist{|\meta{selection}|}| \quad|\messagePDBlist{|\meta{selection}|}| +% \hfill[\pageref{LprintPDBlist}] +% +% \quad|\shadeblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}| +% \hfill[\pageref{Lshadeblock}] +% +% \quad|\changeshadingcolors{|\meta{seqref}|}{|\meta{selection}|}{|\meta{name}|}| +% \hfill[\pageref{Lchangeshadingcolors}] +% +% \quad|\emphregion{|\meta{seqref}|}{|\meta{selection}|}| +% \hfill[\pageref{Lemphregion}] +% +% \quad|\emphblock{|\meta{seqref}|}{|\meta{selection}|}| +% \hfill[\pageref{Lemphblock}] +% +% \quad|\emphdefault{|\meta{style}|}| +% \hfill[\pageref{Lemphdefault}] +% +% \quad|\tintregion{|\meta{seqref}|}{|\meta{selection}|}| +% \hfill[\pageref{Ltintregion}] +% +% \quad|\tintblock{|\meta{seqref}|}{|\meta{selection}|}| +% \hfill[\pageref{Ltintblock}] +% +% \quad|\tintdefault{|\meta{effect}|}| \qquad\qquad|weak, normal, strong| +% \hfill[\pageref{Ltintdefault}] +% +% \quad|\lowerregion{|\meta{seqref}|}{|\meta{selection}|}| +% \hfill[\pageref{Llowerregion}] +% +% \quad|\lowerblock{|\meta{seqref}|}{|\meta{selection}|}| +% \hfill[\pageref{Llowerblock}] +% +% \quad|\frameblock{|\meta{seqref}|}{|\meta{selection}|}{|\meta{color}|[|\meta{length}|]}| +% \hfill[\pageref{Lframeblock}] +% +% \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{selection}|}| +% +% \hfill |{|\meta{labelstyle}|}{|\meta{text}|}| [\pageref{Lfeature}] +% +% \begin{tabbing} +% \quad\quad\quad|{|\meta{labelstyle}|}|\ \= = |{brace[|\meta{color}|]}|\\ +% \> = |{fill:|\meta{symbol}|[|\meta{textcolor}|]}|\\ +% \> = |{restriction[|\meta{color}|]}|\\ +% \> = |{helix[|\meta{helixcolor}|]}|\\ +% \> = |{box[|\meta{framecolor,boxcolor}|][|\meta{length}|]:|\\ +% \hspace{8.7cm}\meta{text}|[|\meta{textcolor}|]}|\\ +% \> = |{S-S}|\\ +% \> = arrows and bars (|-=<',|$\vert$|o|)(|-=|)(|-=>',|$\vert$|o|)\\ +% \> = |{translate[|\meta{color}|]}|\\ +% \> = |{bar[|\meta{min}|,|\meta{max}|]:|\\ +% \hspace{5cm}\meta{properties/file/data}|[|\meta{color(,bgcolor)}|]}|\\ +% \> = |{color[|\meta{min}|,|\meta{max}|]:|\\ +% \hspace{5cm}\meta{properties/file/data}|[|\meta{scale}|]}|\\ +% \hspace{5cm}\meta{properties}: |hydrophobicity|, |charge|,\\ +% \hspace{7.4cm}|molweight|, |conservation|\\ +% \hspace{5cm}\meta{scale}: |Gray|, |BlueRed|, |RedBlue|,\\ +% \hspace{6.5cm}|GreenRed|, |RedGreen|, |ColdHot|,\\ +% \hspace{6.5cm}|HotCold|, |T-Coffee|\\ +% \end{tabbing} +% +% \quad|\ttopspace{|\meta{length}|}| +% \hfill[\pageref{Lttopspace}] +% +% \quad|\topspace{|\meta{length}|}| +% \hfill[\pageref{Ltopspace}] +% +% \quad|\bottomspace{|\meta{length}|}| +% \hfill[\pageref{Lbottomspace}] +% +% \quad|\bbottomspace{|\meta{length}|}| +% \hfill[\pageref{Lbottomspace}] +% +% \quad|\featurerule{|\meta{length}|}| +% \hfill[\pageref{Lfeaturerule}] +% +% \quad|\bargraphstretch{|\meta{factor}|}| +% \hfill[\pageref{Lbargraphstretch}] +% +% \quad|\colorscalestretch{|\meta{factor}|}| +% \hfill[\pageref{Lcolorscalestretch}] +% +% \quad|\codon{|\meta{amino acid}|}{|\meta{triplet1,\ldots, triplet n}|}| +% \hfill[\pageref{Lcodon}] +% +% \quad|\geneticcode{|\meta{filename}|}| +% \hfill[\pageref{Lgeneticcode}] +% +% \quad|\backtranslabel[|\meta{size}|]{|\meta{style}|}| +% \hfill[\pageref{Lbacktranslabel}] +% +% \quad|\backtranstext[|\meta{size}|]{|\meta{style}|}| +% \hfill[\pageref{Lbacktranstext}] +% +% \begin{tabbing} +% \quad\quad\quad|{|\meta{style}|}|\ \= = |{horizontal}|\\ +% \> = |{alternating}|\\ +% \> = |{zigzag}|\\ +% \> = |{oblique}|\\ +% \> = |{vertical}| +% \end{tabbing} +% +% \quad |\showfeaturename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}| +% \hfill[\pageref{Lshowfeaturename}] +% +% \quad |\showfeaturestylename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}| +% \hfill[\pageref{Lshowfeaturestylename}] +% +% \quad |\hidefeaturename{|\meta{ttttop...bbbbottom}|}| +% \hfill[\pageref{Lhidefeaturename}] +% +% \quad |\hidefeaturestylename{|\meta{ttttop...bbbbottom}|}| +% \hfill[\pageref{Lhidefeaturestylename}] +% +% \quad |\hidefeaturenames| +% \hfill[\pageref{Lhidefeaturenames}] +% +% \quad|\hidefeaturestylenames| +% \hfill[\pageref{Lhidefeaturestylenames}] +% +% \quad |\featurenamescolor{|\meta{color}|}| +% \hfill[\pageref{Lfeaturenamescolor}] +% +% \quad |\featurestylenamescolor{|\meta{color}|}| +% \hfill[\pageref{Lfeaturestylenamescolor}] +% +% \quad |\featurenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}| +% \hfill[\pageref{Lfeaturenamecolor}] +% +% \quad |\featurestylenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}| +% \hfill[\pageref{Lfeaturestylenamecolor}] +% +% \vspace{1.5\baselineskip} +% +% \newpage +% +% \textbf{Including secondary structure information} +% \medskip +% +% \quad|\includeDSSP[make new]{|\meta{seqref}|}{|\meta{filename}|}| +% \hfill[\pageref{LincludeDSSP}] +% +% \quad|\includeSTRIDE[make new]{|\meta{seqref}|}{|\meta{filename}|}| +% \hfill[\pageref{LincludeSTRIDE}] +% +% \quad|\includePHDsec[make new]{|\meta{seqref}|}{|\meta{filename}|}| +% \hfill[\pageref{LincludePHDsec}] +% +% \quad|\includePHDtopo[make new]{|\meta{seqref}|}{|\meta{filename}|}| +% \hfill[\pageref{LincludePHDtopo}] +% +% \quad|\includeHMMTOP[make new]{|\meta{seqref}|[|\meta{seqref}|]}{|\meta{filename}|}| +% \hfill[\pageref{LincludeHMMTOP}] +% +% \quad|\showonDSSP{|\meta{structures}|}| +% \hfill[\pageref{LshowonDSSP}] +% +% \quad|\showonSTRIDE{|\meta{structures}|}| +% \hfill[\pageref{LshowonSTRIDE}] +% +% \quad|\showonPHDsec{|\meta{structures}|}| +% \hfill[\pageref{LshowonPHDsec}] +% +% \quad|\showonPHDtopo{|\meta{structures}|}| +% \hfill[\pageref{LshowonPHDtopo}] +% +% \quad|\showonHMMTOP{|\meta{structures}|}| +% \hfill[\pageref{LshowonHMMTOP}] +% +% \quad|\hideonDSSP{|\meta{structures}|}| +% \hfill[\pageref{LhideonDSSP}] +% +% \quad|\hideonSTRIDE{|\meta{structures}|}| +% \hfill[\pageref{LhideonSTRIDE}] +% +% \quad|\hideonPHDsec{|\meta{structures}|}| +% \hfill[\pageref{LhideonPHDsec}] +% +% \quad|\hideonPHDtopo{|\meta{structures}|}| +% \hfill[\pageref{LhideonPHDtopo}] +% +% \quad|\hideonHMMTOP{|\meta{structures}|}| +% \hfill[\pageref{LhideonHMMTOP}] +% +% \quad|\appearance{|\meta{type}|}{|\meta{position}|}{|\meta{labelstyle}|}{|\meta{text}|}| +% \hfill[\pageref{Lappearance}] +% +% \quad|\numcount| +% \hfill[\pageref{Lnumcount}] +% +% \quad|\alphacount| +% \hfill[\pageref{Lalphacount}] +% +% \quad|\Alphacount| +% \hfill[\pageref{LAlphacount}] +% +% \quad|\romancount| +% \hfill[\pageref{Lromancount}] +% +% \quad|\Romancount| +% \hfill[\pageref{LRomancount}] +% +% \quad|\firstcolumnDSSP| +% \hfill[\pageref{LfirstcolumnDSSP}] +% +% \quad|\secondcolumnDSSP| +% \hfill[\pageref{LsecondcolumnDSSP}] +% +% \vspace{1.5\baselineskip} +% +% +% \textbf{Displaying and building legends} +% \medskip +% +% \quad|\showlegend| +% \hfill[\pageref{Lshowlegend}] +% +% \quad|\hidelegend| +% \hfill[\pageref{Lhidelegend}] +% +% \quad|\movelegend{|\meta{x-offset}|}{|\meta{y-offset}|}| +% \hfill[\pageref{Lmovelegend}] +% +% \quad|\germanlanguage|, |\spanishlanguage|, |\englishlanguage| +% \hfill[\pageref{Lgermanlanguage}] +% +% \quad|\legendcolor{|\meta{color}|}| +% \hfill[\pageref{Llegendcolor}] +% +% \quad|\shadebox{|\meta{color}|}| +% \hfill[\pageref{Lshadebox}] +% +% \vspace{1.5\baselineskip} +% +% +% \textbf{Adding captions to the alignment} +% \medskip +% +% \quad|\showcaption[|\meta{top/bottom}|]{|\meta{text}|}| +% \hfill[\pageref{Lshowcaption}] +% +% \quad|\shortcaption{|\meta{text}|}| +% \hfill[\pageref{Lshortcaption}] +% +% \vspace{1.5\baselineskip} +% +% \newpage +% +% \textbf{Font handling} +% \medskip +% +% \quad|\setfamily{|\meta{text}|}{|\meta{family}|}| +% \hfill[\pageref{Lsetfamily}] +% +% \quad|\setseries{|\meta{text}|}{|\meta{series}|}| +% \hfill[\pageref{Lsetseries}] +% +% \quad|\setshape{|\meta{text}|}{|\meta{shape}|}| +% \hfill[\pageref{Lsetshape}] +% +% \quad|\setsize{|\meta{text}|}{|\meta{size}|}| +% \hfill[\pageref{Lsetsize}] +% +% \quad|\setfont{|\meta{text}|}{|\meta{family}|}{|\meta{series}|}{|\meta{shape}|}{|\meta{size}|}| +% \hfill[\pageref{Lsetfont}] +% +% \medskip +% +% \quad |\featuresrm| \quad |\featurestiny| \hfill[\pageref{Lfeaturesrm}] +% +% \quad |\featuressf| \quad |\featuresscriptsize| +% +% \quad |\featurestt| \quad |\featuresfootnotesize| +% +% \quad |\featuresbf| \quad |\featuressmall| +% +% \quad |\featuresmd| \quad |\featuresnormalsize| +% +% \quad |\featuresit| \quad |\featureslarge| +% +% \quad |\featuressl| \quad |\featuresLarge| +% +% \quad |\featuressc| \quad |\featuresLARGE| +% +% \quad |\featuresup| \quad |\featureshuge| +% +% \quad | | \quad |\featuresHuge| +% \medskip +% +% Corresponding sets are provided for the +% numbering (|\numberingrm| etc.), +% featurestyles (|featurestylesrm| etc.), names (|\namesrm| etc.), +% featurenames (|\featurenamesrm| etc.), +% featurestylenames (|\featurestylenames| etc.), +% residues (|\residuesrm| etc.), +% hideblock labels (|hideblockrm| etc.), +% rulers (|\rulerrm| etc.), and +% legend texts (|legendrm| etc.). +% \bigskip +% +% +% \textbf{Goodies---molweight and charge} +% \medskip +% +% \quad|\molweight{|\meta{seqref}|}{|\meta{Da/kDa}|}| +% \hfill[\pageref{Lmolweight}] +% +% \quad|\charge{|\meta{seqref}|}{|\meta{i/o/N/C}|}| +% \hfill[\pageref{Lcharge}] +% +% \quad|\percentsimilarity{|\meta{seqref1}|}{|\meta{seqref2}|}| +% \hfill[\pageref{Lpercentsimilarity}] +% +% \quad|\percentidentity{|\meta{seqref1}|}{|\meta{seqref2}|}| +% \hfill[\pageref{Lpercentidentity}] +% +% \quad|\similaritytable| +% \hfill[\pageref{Lsimilaritytable}] +% +% \StopEventually{% +% \newpage +% \section{References} +% [1] \textsc{Carlisle, D.} The Standard \LaTeX{} `Graphics +% Bundle', |color.sty|. +% +% [2] \textsc{Karlin, S.; Ghandour, G.} (1985) Multiple-alphabet +% amino acid sequence comparisons of the immunoglobulin +% $\kappa$-chain constant domain. +% \newblock \textit{Proc. Natl. Acad. Sci. USA}: \textbf{82}, +% 8597--8601. +% +% [3] \textsc{Kyte, J.; Doolittle, R. F.} (1982) A simple +% method for displaying the hydropathic character of a +% protein. +% \newblock \textit{J. Mol. Biol.}: \textbf{157}, 105--132. +% +% [4] \textsc{Rose, G. D.; Geselowitz, A. R.; Lesser, G. J.; +% Lee, R. H.; Zehfus, M. H.} (1985) Hydrophobicity of amino +% acid residues in globular proteins. +% \newblock \textit{Science}: \textbf{229}, 835--838. +% +% [5] \textsc{Lesser, G. J.; Rose, G. D.} (1990) Hydrophobicity +% of amino acid subgroups in proteins. +% \newblock \textit{Proteins: structure, function and +% genetics}: \textbf{8}, 6--13. +% +% [6] \textsc{Fr\"ohlich, K.-U.} (1994) Sequence similarity +% presenter: a tool for the graphic display of similarities +% of long sequences for use in presentations. +% \newblock \textit{Comput. Applic. Biosci.}: +% \textbf{10}, 179--183. +% +% [7] \textsc{Schneider, T.D.; Stephens, R.M.} (1990) Sequence logos: +% a new way to display consensus +% \newblock \textit{Nucleic Acid Res.}: \textbf{18}, 6097--6100. +% +% [8] DeLano Scientific LLC `www.pymol.org' +% +% [9] \textsc{Kabsch, W.; Sander, C.} (1983) Dictionary of +% protein secondary structure: pattern recognition of +% hydrogen-bonded and geometrical features. +% \newblock \textit{Biopolymers}: \textbf{22}, 2577--2637. +% +% [10] \textsc{Frishman, D.; Argos, P.} (1995) Knowledge-based +% protein secondary structure assignment. +% \newblock \textit{Proteins: structure, function and +% genetics}: \textbf{23}, 566--579. +% +% [11] \textsc{Rost, B.; Sander, C.} (1994) +% Combining evolutionary information and neural networks to predict +% protein secondary structure. +% \newblock \textit{Proteins: structure, function and +% genetics}: \textbf{19}, 55--72. +% +% [12] \textsc{Tusnady, G.E.; Simon, I.} (2001) +% The HMMTOP transmembrane topology prediction server. +% \newblock \textit{Bioinformatics}: \textbf{17}, 849-850. +% +% [13] \textsc{Rokicki, T.} DVIPS: A \TeX{} driver. +% +% [14] \textsc{Beitz, E.} (2006) Subfamily logos: visualization of sequence +% deviations at alignment positions with high information content. +% \newblock \textit{BMC Bioinformatics}: \textbf{7}:313. +% +% } +% \section{Implementation} +% \subsection{Documentation Driver} +% \begin{macrocode} +%<*driver> +\documentclass[12pt,a4paper]{ltxdoc} +\usepackage[dvips]{texshade} +\openin\structurefile = hyperref.sty +\ifeof\structurefile + \else +% \usepackage[dvips,colorlinks]{hyperref} + \usepackage[pdftex,colorlinks]{hyperref} + \fi +\closein\structurefile +\DisableCrossrefs +\sloppy +\def\BioTeX{\textsc{Bio}\kern-0.5ex\TeX} +\def\TeXtopo{\mbox{\TeX\textsf{topo}}} +\begin{document} + \OnlyDescription + \DocInput{texshade.dtx} +\end{document} +%</driver> +% \end{macrocode} +% \subsection{\texttt{texshade.sty}---no comments} +% \begin{macrocode} +%<*texshade> +\NeedsTeXFormat{LaTeX2e} +\ProvidesPackage{texshade}[2018/01/17 LaTeX TeXshade (v1.25)] +\message{Package `texshade', Version 1.25 of 2018/01/17.} + +\PassOptionsToPackage{dvips}{color} +\PassOptionsToPackage{dvips}{graphicx} +\DeclareOption*{% + \PassOptionsToPackage{\CurrentOption}{color}% + \PassOptionsToPackage{\CurrentOption}{graphicx}% +} +\ProcessOptions +\RequirePackage{color,graphics} + +\expandafter\ifx\csname TeXshade\endcsname\relax \else \endinput \fi + +\expandafter\ifx\csname TeXtopo\endcsname\relax \else + \PackageError{TeXtopo} + {TeXtopo loaded before TeXshade} + {\MessageBreak + For the proper function of the TeXtopo/TeXshade combo the \MessageBreak + TeXshade package must be loaded before the TeXtopo package.\MessageBreak + Please change the order of the \noexpand\usepackage commands in your + \MessageBreak + document header section or use the `biotex.sty'.\MessageBreak\MessageBreak + Quit here by typing \space X <return>. \MessageBreak +} +\fi + +\catcode`\@11 + +\def\rotopo#1{% + \Grot@setangle{#1}% + \setbox\z@\hbox\bgroup\ignorespaces} +\def\endrotopo{% + \unskip\egroup + \Grot@x\z@ + \Grot@y\z@ + \wd0\z@\dp0\z@\ht0\z@ + \Grot@box +} + +\newread\structurefile \newwrite\featurefile +\newread\alignfile \newread\sublogofile +\newwrite\exp@rtfile + +\expandafter\ifx\csname blacktriangleright\endcsname\relax + \openin\structurefile = amssymb.sty + \ifeof\structurefile + \message{<AMS symbol style `amssymb.sty' not installed - using round heads>} + \def\blacktriangleright{% + \rule[\width@tmp]{0.65ex}{\temp@@length}\kern-0.55ex\ensuremath{\bullet}% + } + \def\blacktriangleleft{% + \ensuremath{\bullet}\kern-0.55ex\rule[\width@tmp]{0.65ex}{\temp@@length}% + } + \else \RequirePackage[]{amssymb} \fi + \closein\structurefile +\fi + +\DeclareSymbolFont{alphahelix}{OML}{cmm}{m}{it} +\DeclareMathSymbol{\helixhook}{\mathrel}{alphahelix}{"5E} + +\newcount\loopcount \newcount\innerloopcount \newcount\outerloopcount +\newcount\seq@count \newcount\killseq@count +\newcount\seq@percent \newcount\res@count +\newcount\seq@pointer \newcount\pos@count +\newcount\res@perline \newcount\end@count +\newcount\cons@count \newcount\total@count +\newcount\temp@count \newcount\triple@count +\newcount\temp@@count \newcount\pos@sum + +\newlength\box@width \newlength\name@width +\newlength\box@depth \newlength\width@tmp +\newlength\box@height \newlength\number@width +\newlength\line@stretch +\newlength\center@fill \newlength\arrow@width +\newlength\arrow@height \newlength\rule@thick +\newlength\arrow@thick \newlength\logo@height +\newlength\equal@width \newlength\equal@tmp +\newlength\equal@height \newlength\temp@@length +\newlength\vspace@legend +\newlength\hspace@legend +\newlength\bar@length + +\newif\ifletter \newif\ifnumber +\newif\ifnewres \newif\ifall@shade +\newif\ifnames@right +\newif\ifnumbers@left \newif\ifnumbers@right +\newif\ifhide@cons \newif\ifshow@cons +\newif\iffuncmode \newif\iflegend@ +\newif\ifT@coffee +\newif\ifnumbers@ \newif\ifnames@ +\newif\ifgerm@n \newif\ifsp@nish +\newif\ifrpl@fix +\newif\ifnosh@de \newif\ifregionalshade +\newif\ifstart@ \newif\ifstop@ +\newif\iftopfeature \newif\ifbottomfeature +\newif\ifttopfeature \newif\ifbbottomfeature +\newif\iftttopfeature \newif\ifbbbottomfeature +\newif\ifttttopfeature\newif\ifbbbbottomfeature +\newif\ifall@fshade \newif\ifregionalemph +\newif\ifregionallower +\newif\ifframe@ \newif\ifregionaltint +\newif\ifshading@ +\newif\ifshow@logo \newif\ifshow@sublogo +\newif\ifhidechar \newif\ifsh@wg@ps +\newif\ifsimmode +\newif\ifregionaltintnow +\newif\ifregionalemphnow +\newif\ifregionallowernow +\newif\ifregionalshadenow +\newif\iftopfeaturenow +\newif\ifttopfeaturenow +\newif\iftttopfeaturenow +\newif\ifttttopfeaturenow +\newif\ifbottomfeaturenow +\newif\ifbbottomfeaturenow +\newif\ifbbbottomfeaturenow +\newif\ifbbbbottomfeaturenow +\newif\ifframenow +\newif\ifshadingnow +\newif\iffix@ + +\expandafter\ifx\csname mdqon\endcsname\relax + \germ@nfalse \sp@nishfalse \def\cons@name{consensus} +\else \germ@ntrue \sp@nishfalse \def\cons@name{Konsensus} \fi + +\def\n@me{Name:} \def\@msf{MSF:} \def\he@derend{//} \def\ampers@nd{&} +\def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:} +\def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H} +\def\gap@char{.} \def\dom@char{{\dom@rule}} \def\yes{yes} \def\y@{y} \def\n@{n} +\def\o@{o} \def\d@t{.} \def\questi@n{?} \def\st@p@char{*} \def\semic@n{;} +\def\br@cket{[} \def\p@r@gr@ph{¤} +\def\@TOM{ATOM} \def\C@lpha{CA} \def\@point@{point} \def\@line@{line} \def\@plane@{plane} +\def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}} +\def\dom@rule{\vrule depth\box@depth height\box@height width\domgap@rulethick} +\def\fgroup@num{0} \def\max@seqnumber{0} \def\@lign@count{0} +\def\resn@m@tch{upper} \def\ressimm@tch{upper} +\def\resm@tch{upper} \def\res@llm@tch{upper} +\def\tr@ns{translate} \def\gr@ydef@ult{GrayDefault} +\xdef\par@{\expandafter\string\par} +\expandafter\def\csname fg@textcolor/\endcsname{White} +\expandafter\def\csname fg@color/\endcsname{White} +\expandafter\def\csname func@style/\endcsname{\csname textup\endcsname} +\expandafter\def\csname func@style*\endcsname{\csname textup\endcsname} +\expandafter\def\csname funcm@tch/\endcsname{upper} +\expandafter\def\csname funcm@tch*\endcsname{upper} + +\setlength\hspace@legend{0pt} \setlength\vspace@legend{0pt} + +\expandafter\xdef\csname log2@1\endcsname{0} +\expandafter\xdef\csname log2@2\endcsname{1000} +\expandafter\xdef\csname log2@3\endcsname{1585} +\expandafter\xdef\csname log2@4\endcsname{2000} +\expandafter\xdef\csname log2@5\endcsname{2322} +\expandafter\xdef\csname log2@6\endcsname{2585} +\expandafter\xdef\csname log2@7\endcsname{2807} +\expandafter\xdef\csname log2@8\endcsname{3000} +\expandafter\xdef\csname log2@9\endcsname{3170} +\expandafter\xdef\csname log2@10\endcsname{3322} +\expandafter\xdef\csname log2@11\endcsname{3459} 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+\expandafter\xdef\csname log2@92\endcsname{6524} +\expandafter\xdef\csname log2@93\endcsname{6539} +\expandafter\xdef\csname log2@94\endcsname{6555} +\expandafter\xdef\csname log2@95\endcsname{6570} +\expandafter\xdef\csname log2@96\endcsname{6585} +\expandafter\xdef\csname log2@97\endcsname{6600} +\expandafter\xdef\csname log2@98\endcsname{6615} +\expandafter\xdef\csname log2@99\endcsname{6629} +\expandafter\xdef\csname log2@100\endcsname{6644} +\expandafter\xdef\csname log2@101\endcsname{6658} +\expandafter\xdef\csname log2@102\endcsname{6672} +\expandafter\xdef\csname log2@103\endcsname{6687} +\expandafter\xdef\csname log2@104\endcsname{6700} +\expandafter\xdef\csname log2@105\endcsname{6714} +\expandafter\xdef\csname log2@106\endcsname{6728} +\expandafter\xdef\csname log2@107\endcsname{6741} +\expandafter\xdef\csname log2@108\endcsname{6755} +\expandafter\xdef\csname log2@109\endcsname{6768} +\expandafter\xdef\csname log2@110\endcsname{6781} +\expandafter\xdef\csname log2@111\endcsname{6794} +\expandafter\xdef\csname log2@112\endcsname{6807} +\expandafter\xdef\csname log2@113\endcsname{6820} +\expandafter\xdef\csname log2@114\endcsname{6833} +\expandafter\xdef\csname log2@115\endcsname{6845} +\expandafter\xdef\csname log2@116\endcsname{6858} +\expandafter\xdef\csname log2@117\endcsname{6870} +\expandafter\xdef\csname log2@118\endcsname{6883} +\expandafter\xdef\csname log2@119\endcsname{6895} +\expandafter\xdef\csname log2@120\endcsname{6907} +\expandafter\xdef\csname log2@121\endcsname{6919} +\expandafter\xdef\csname log2@122\endcsname{6931} +\expandafter\xdef\csname log2@123\endcsname{6943} +\expandafter\xdef\csname log2@124\endcsname{6954} +\expandafter\xdef\csname log2@125\endcsname{6966} +\expandafter\xdef\csname log2@126\endcsname{6977} +\expandafter\xdef\csname log2@127\endcsname{6989} +\expandafter\xdef\csname log2@128\endcsname{7000} +\expandafter\xdef\csname log2@129\endcsname{7011} +\expandafter\xdef\csname log2@130\endcsname{7022} +\expandafter\xdef\csname log2@131\endcsname{7033} +\expandafter\xdef\csname log2@132\endcsname{7044} +\expandafter\xdef\csname log2@133\endcsname{7055} +\expandafter\xdef\csname log2@134\endcsname{7066} +\expandafter\xdef\csname log2@135\endcsname{7077} +\expandafter\xdef\csname log2@136\endcsname{7088} +\expandafter\xdef\csname log2@137\endcsname{7098} +\expandafter\xdef\csname log2@138\endcsname{7108} +\expandafter\xdef\csname log2@139\endcsname{7119} +\expandafter\xdef\csname log2@140\endcsname{7129} +\expandafter\xdef\csname log2@141\endcsname{7140} +\expandafter\xdef\csname log2@142\endcsname{7150} +\expandafter\xdef\csname log2@143\endcsname{7160} +\expandafter\xdef\csname log2@144\endcsname{7170} +\expandafter\xdef\csname log2@145\endcsname{7180} +\expandafter\xdef\csname log2@146\endcsname{7190} +\expandafter\xdef\csname log2@147\endcsname{7200} +\expandafter\xdef\csname log2@148\endcsname{7209} +\expandafter\xdef\csname log2@149\endcsname{7219} +\expandafter\xdef\csname log2@150\endcsname{7229} +\expandafter\xdef\csname log2@151\endcsname{7238} +\expandafter\xdef\csname log2@152\endcsname{7248} +\expandafter\xdef\csname log2@153\endcsname{7257} +\expandafter\xdef\csname log2@154\endcsname{7267} +\expandafter\xdef\csname log2@155\endcsname{7276} +\expandafter\xdef\csname log2@156\endcsname{7285} +\expandafter\xdef\csname log2@157\endcsname{7295} +\expandafter\xdef\csname log2@158\endcsname{7304} +\expandafter\xdef\csname log2@159\endcsname{7313} +\expandafter\xdef\csname log2@160\endcsname{7323} +\expandafter\xdef\csname log2@161\endcsname{7331} +\expandafter\xdef\csname log2@162\endcsname{7340} +\expandafter\xdef\csname log2@163\endcsname{7349} +\expandafter\xdef\csname log2@164\endcsname{7358} +\expandafter\xdef\csname log2@165\endcsname{7366} +\expandafter\xdef\csname log2@166\endcsname{7375} +\expandafter\xdef\csname log2@167\endcsname{7374} +\expandafter\xdef\csname log2@168\endcsname{7392} +\expandafter\xdef\csname log2@169\endcsname{7401} +\expandafter\xdef\csname log2@170\endcsname{7409} +\expandafter\xdef\csname log2@171\endcsname{7418} +\expandafter\xdef\csname log2@172\endcsname{7463} +\expandafter\xdef\csname log2@173\endcsname{7435} +\expandafter\xdef\csname log2@174\endcsname{7443} +\expandafter\xdef\csname log2@175\endcsname{7451} +\expandafter\xdef\csname log2@176\endcsname{7460} +\expandafter\xdef\csname log2@177\endcsname{7468} +\expandafter\xdef\csname log2@178\endcsname{7476} +\expandafter\xdef\csname log2@179\endcsname{7484} +\expandafter\xdef\csname log2@180\endcsname{7492} +\expandafter\xdef\csname log2@181\endcsname{7500} +\expandafter\xdef\csname log2@182\endcsname{7508} +\expandafter\xdef\csname log2@183\endcsname{7516} +\expandafter\xdef\csname log2@184\endcsname{7524} +\expandafter\xdef\csname log2@185\endcsname{7531} +\expandafter\xdef\csname log2@186\endcsname{7539} +\expandafter\xdef\csname log2@187\endcsname{7547} +\expandafter\xdef\csname log2@188\endcsname{7555} +\expandafter\xdef\csname log2@189\endcsname{7562} +\expandafter\xdef\csname log2@190\endcsname{7570} +\expandafter\xdef\csname log2@191\endcsname{7577} +\expandafter\xdef\csname log2@192\endcsname{7585} +\expandafter\xdef\csname log2@193\endcsname{7592} +\expandafter\xdef\csname log2@194\endcsname{7600} +\expandafter\xdef\csname log2@195\endcsname{7607} +\expandafter\xdef\csname log2@196\endcsname{7615} +\expandafter\xdef\csname log2@197\endcsname{7622} +\expandafter\xdef\csname log2@198\endcsname{7629} +\expandafter\xdef\csname log2@199\endcsname{7637} +\expandafter\xdef\csname log2@200\endcsname{7644} +\expandafter\xdef\csname log2@201\endcsname{7651} +\expandafter\xdef\csname log2@202\endcsname{7658} +\expandafter\xdef\csname log2@203\endcsname{7665} +\expandafter\xdef\csname log2@204\endcsname{7672} +\expandafter\xdef\csname log2@205\endcsname{7679} +\expandafter\xdef\csname log2@206\endcsname{7687} +\expandafter\xdef\csname log2@207\endcsname{7693} +\expandafter\xdef\csname log2@208\endcsname{7700} +\expandafter\xdef\csname log2@209\endcsname{7707} +\expandafter\xdef\csname log2@210\endcsname{7714} +\expandafter\xdef\csname log2@211\endcsname{7721} +\expandafter\xdef\csname log2@212\endcsname{7728} +\expandafter\xdef\csname log2@213\endcsname{7735} +\expandafter\xdef\csname log2@214\endcsname{7741} +\expandafter\xdef\csname log2@215\endcsname{7748} +\expandafter\xdef\csname log2@216\endcsname{7755} +\expandafter\xdef\csname log2@217\endcsname{7761} +\expandafter\xdef\csname log2@218\endcsname{7768} +\expandafter\xdef\csname log2@219\endcsname{7775} +\expandafter\xdef\csname log2@220\endcsname{7781} + + +\expandafter\xdef\csname ch@r@65\endcsname{A} +\expandafter\xdef\csname ch@r@66\endcsname{B} +\expandafter\xdef\csname ch@r@67\endcsname{C} +\expandafter\xdef\csname ch@r@68\endcsname{D} +\expandafter\xdef\csname ch@r@69\endcsname{E} +\expandafter\xdef\csname ch@r@70\endcsname{F} +\expandafter\xdef\csname ch@r@71\endcsname{G} +\expandafter\xdef\csname ch@r@72\endcsname{H} +\expandafter\xdef\csname ch@r@73\endcsname{I} +\expandafter\xdef\csname ch@r@74\endcsname{J} +\expandafter\xdef\csname ch@r@75\endcsname{K} +\expandafter\xdef\csname ch@r@76\endcsname{L} +\expandafter\xdef\csname ch@r@77\endcsname{M} +\expandafter\xdef\csname ch@r@78\endcsname{N} +\expandafter\xdef\csname ch@r@79\endcsname{O} +\expandafter\xdef\csname ch@r@80\endcsname{P} +\expandafter\xdef\csname ch@r@81\endcsname{Q} +\expandafter\xdef\csname ch@r@82\endcsname{R} +\expandafter\xdef\csname ch@r@83\endcsname{S} +\expandafter\xdef\csname ch@r@84\endcsname{T} +\expandafter\xdef\csname ch@r@85\endcsname{U} +\expandafter\xdef\csname ch@r@86\endcsname{V} +\expandafter\xdef\csname ch@r@87\endcsname{W} +\expandafter\xdef\csname ch@r@88\endcsname{X} +\expandafter\xdef\csname ch@r@89\endcsname{Y} +\expandafter\xdef\csname ch@r@90\endcsname{Z} + +\def\clear@sims{% + \expandafter\xdef\csname \prfx simA\endcsname{(1)A} + \expandafter\xdef\csname \prfx simB\endcsname{(1)B} + \expandafter\xdef\csname \prfx simC\endcsname{(1)C} + \expandafter\xdef\csname \prfx simD\endcsname{(1)D} + \expandafter\xdef\csname \prfx simE\endcsname{(1)E} + \expandafter\xdef\csname \prfx simF\endcsname{(1)F} + \expandafter\xdef\csname \prfx simG\endcsname{(1)G} + \expandafter\xdef\csname \prfx simH\endcsname{(1)H} + \expandafter\xdef\csname \prfx simI\endcsname{(1)I} + \expandafter\xdef\csname \prfx simJ\endcsname{(1)J} + \expandafter\xdef\csname \prfx simK\endcsname{(1)K} + \expandafter\xdef\csname \prfx simL\endcsname{(1)L} + \expandafter\xdef\csname \prfx simM\endcsname{(1)M} + \expandafter\xdef\csname \prfx simN\endcsname{(1)N} + \expandafter\xdef\csname \prfx simO\endcsname{(1)O} + \expandafter\xdef\csname \prfx simP\endcsname{(1)P} + \expandafter\xdef\csname \prfx simQ\endcsname{(1)Q} + \expandafter\xdef\csname \prfx simR\endcsname{(1)R} + \expandafter\xdef\csname \prfx simS\endcsname{(1)S} + \expandafter\xdef\csname \prfx simT\endcsname{(1)T} + \expandafter\xdef\csname \prfx simU\endcsname{(1)U} + \expandafter\xdef\csname \prfx simV\endcsname{(1)V} + \expandafter\xdef\csname \prfx simW\endcsname{(1)W} + \expandafter\xdef\csname \prfx simX\endcsname{(1)X} + \expandafter\xdef\csname \prfx simY\endcsname{(1)Y} + \expandafter\xdef\csname \prfx simZ\endcsname{(1)Z} +} + +\def\clear@simpairs{% +\xdef\simpairCC{1} \xdef\simpairCS{0} \xdef\simpairCT{0} \xdef\simpairCP{0} \xdef\simpairCA{0} +\xdef\simpairCG{0} \xdef\simpairCN{0} \xdef\simpairCD{0} \xdef\simpairCE{0} \xdef\simpairCQ{0} +\xdef\simpairCH{0} \xdef\simpairCR{0} \xdef\simpairCK{0} \xdef\simpairCM{0} \xdef\simpairCI{0} +\xdef\simpairCL{0} \xdef\simpairCV{0} \xdef\simpairCF{0} \xdef\simpairCY{0} \xdef\simpairCW{0} +\xdef\simpairCB{0} \xdef\simpairCJ{0} \xdef\simpairCO{0} \xdef\simpairCU{0} \xdef\simpairCX{0} \xdef\simpairCZ{0} + +\xdef\simpairSC{0} \xdef\simpairSS{1} \xdef\simpairST{0} \xdef\simpairSP{0} \xdef\simpairSA{0} +\xdef\simpairSG{0} \xdef\simpairSN{0} \xdef\simpairSD{0} \xdef\simpairSE{0} \xdef\simpairSQ{0} +\xdef\simpairSH{0} \xdef\simpairSR{0} \xdef\simpairSK{0} \xdef\simpairSM{0} \xdef\simpairSI{0} +\xdef\simpairSL{0} \xdef\simpairSV{0} \xdef\simpairSF{0} \xdef\simpairSY{0} \xdef\simpairSW{0} +\xdef\simpairSB{0} \xdef\simpairSJ{0} \xdef\simpairSO{0} \xdef\simpairSU{0} \xdef\simpairSX{0} \xdef\simpairSZ{0} + +\xdef\simpairTC{0} \xdef\simpairTS{0} \xdef\simpairTT{1} \xdef\simpairTP{0} \xdef\simpairTA{0} +\xdef\simpairTG{0} \xdef\simpairTN{0} \xdef\simpairTD{0} \xdef\simpairTE{0} \xdef\simpairTQ{0} +\xdef\simpairTH{0} \xdef\simpairTR{0} \xdef\simpairTK{0} \xdef\simpairTM{0} \xdef\simpairTI{0} +\xdef\simpairTL{0} \xdef\simpairTV{0} \xdef\simpairTF{0} \xdef\simpairTY{0} \xdef\simpairTW{0} +\xdef\simpairTB{0} \xdef\simpairTJ{0} \xdef\simpairTO{0} \xdef\simpairTU{0} \xdef\simpairTX{0} \xdef\simpairTZ{0} + +\xdef\simpairPC{0} \xdef\simpairPS{0} \xdef\simpairPT{0} \xdef\simpairPP{1} \xdef\simpairPA{0} +\xdef\simpairPG{0} \xdef\simpairPN{0} \xdef\simpairPD{0} \xdef\simpairPE{0} \xdef\simpairPQ{0} +\xdef\simpairPH{0} \xdef\simpairPR{0} \xdef\simpairPK{0} \xdef\simpairPM{0} \xdef\simpairPI{0} +\xdef\simpairPL{0} \xdef\simpairPV{0} \xdef\simpairPF{0} \xdef\simpairPY{0} \xdef\simpairPW{0} +\xdef\simpairPB{0} \xdef\simpairPJ{0} \xdef\simpairPO{0} \xdef\simpairPU{0} \xdef\simpairPX{0} \xdef\simpairPZ{0} + +\xdef\simpairAC{0} \xdef\simpairAS{0} \xdef\simpairAT{0} \xdef\simpairAP{0} \xdef\simpairAA{1} +\xdef\simpairAG{0} \xdef\simpairAN{0} \xdef\simpairAD{0} \xdef\simpairAE{0} \xdef\simpairAQ{0} +\xdef\simpairAH{0} \xdef\simpairAR{0} \xdef\simpairAK{0} \xdef\simpairAM{0} \xdef\simpairAI{0} +\xdef\simpairAL{0} \xdef\simpairAV{0} \xdef\simpairAF{0} \xdef\simpairAY{0} \xdef\simpairAW{0} +\xdef\simpairAB{0} \xdef\simpairAJ{0} \xdef\simpairAO{0} \xdef\simpairAU{0} \xdef\simpairAX{0} \xdef\simpairAZ{0} + +\xdef\simpairGC{0} \xdef\simpairGS{0} \xdef\simpairGT{0} \xdef\simpairGP{0} \xdef\simpairGA{0} +\xdef\simpairGG{1} \xdef\simpairGN{0} \xdef\simpairGD{0} \xdef\simpairGE{0} \xdef\simpairGQ{0} +\xdef\simpairGH{0} \xdef\simpairGR{0} \xdef\simpairGK{0} \xdef\simpairGM{0} \xdef\simpairGI{0} +\xdef\simpairGL{0} \xdef\simpairGV{0} \xdef\simpairGF{0} \xdef\simpairGY{0} \xdef\simpairGW{0} +\xdef\simpairGB{0} \xdef\simpairGJ{0} \xdef\simpairGO{0} \xdef\simpairGU{0} \xdef\simpairGX{0} \xdef\simpairGZ{0} + +\xdef\simpairNC{0} \xdef\simpairNS{0} \xdef\simpairNT{0} \xdef\simpairNP{0} \xdef\simpairNA{0} +\xdef\simpairNG{0} \xdef\simpairNN{1} \xdef\simpairND{0} \xdef\simpairNE{0} \xdef\simpairNQ{0} +\xdef\simpairNH{0} \xdef\simpairNR{0} \xdef\simpairNK{0} \xdef\simpairNM{0} \xdef\simpairNI{0} +\xdef\simpairNL{0} \xdef\simpairNV{0} \xdef\simpairNF{0} \xdef\simpairNY{0} \xdef\simpairNW{0} +\xdef\simpairNB{0} \xdef\simpairNJ{0} \xdef\simpairNO{0} \xdef\simpairNU{0} \xdef\simpairNX{0} \xdef\simpairNZ{0} + +\xdef\simpairDC{0} \xdef\simpairDS{0} \xdef\simpairDT{0} \xdef\simpairDP{0} \xdef\simpairDA{0} +\xdef\simpairDG{0} \xdef\simpairDN{0} \xdef\simpairDD{1} \xdef\simpairDE{0} \xdef\simpairDQ{0} +\xdef\simpairDH{0} \xdef\simpairDR{0} \xdef\simpairDK{0} \xdef\simpairDM{0} \xdef\simpairDI{0} +\xdef\simpairDL{0} \xdef\simpairDV{0} \xdef\simpairDF{0} \xdef\simpairDY{0} \xdef\simpairDW{0} +\xdef\simpairDB{0} \xdef\simpairDJ{0} \xdef\simpairDO{0} \xdef\simpairDU{0} \xdef\simpairDX{0} \xdef\simpairDZ{0} + +\xdef\simpairEC{0} \xdef\simpairES{0} \xdef\simpairET{0} \xdef\simpairEP{0} \xdef\simpairEA{0} +\xdef\simpairEG{0} \xdef\simpairEN{0} \xdef\simpairED{0} \xdef\simpairEE{1} \xdef\simpairEQ{0} +\xdef\simpairEH{0} \xdef\simpairER{0} \xdef\simpairEK{0} \xdef\simpairEM{0} \xdef\simpairEI{0} +\xdef\simpairEL{0} \xdef\simpairEV{0} \xdef\simpairEF{0} \xdef\simpairEY{0} \xdef\simpairEW{0} +\xdef\simpairEB{0} \xdef\simpairEJ{0} \xdef\simpairEO{0} \xdef\simpairEU{0} \xdef\simpairEX{0} \xdef\simpairEZ{0} + +\xdef\simpairQC{0} \xdef\simpairQS{0} \xdef\simpairQT{0} \xdef\simpairQP{0} \xdef\simpairQA{0} +\xdef\simpairQG{0} \xdef\simpairQN{0} \xdef\simpairQD{0} \xdef\simpairQE{0} \xdef\simpairQQ{1} +\xdef\simpairQH{0} \xdef\simpairQR{0} \xdef\simpairQK{0} \xdef\simpairQM{0} \xdef\simpairQI{0} +\xdef\simpairQL{0} \xdef\simpairQV{0} \xdef\simpairQF{0} \xdef\simpairQY{0} \xdef\simpairQW{0} +\xdef\simpairQB{0} \xdef\simpairQJ{0} \xdef\simpairQO{0} \xdef\simpairQU{0} \xdef\simpairQX{0} \xdef\simpairQZ{0} + +\xdef\simpairHC{0} \xdef\simpairHS{0} \xdef\simpairHT{0} \xdef\simpairHP{0} \xdef\simpairHA{0} +\xdef\simpairHG{0} \xdef\simpairHN{0} \xdef\simpairHD{0} \xdef\simpairHE{0} \xdef\simpairHQ{0} +\xdef\simpairHH{1} \xdef\simpairHR{0} \xdef\simpairHK{0} \xdef\simpairHM{0} \xdef\simpairHI{0} +\xdef\simpairHL{0} \xdef\simpairHV{0} \xdef\simpairHF{0} \xdef\simpairHY{0} \xdef\simpairHW{0} +\xdef\simpairHB{0} \xdef\simpairHJ{0} \xdef\simpairHO{0} \xdef\simpairHU{0} \xdef\simpairHX{0} \xdef\simpairHZ{0} + +\xdef\simpairRC{0} \xdef\simpairRS{0} \xdef\simpairRT{0} \xdef\simpairRP{0} \xdef\simpairRA{0} +\xdef\simpairRG{0} \xdef\simpairRN{0} \xdef\simpairRD{0} \xdef\simpairRE{0} \xdef\simpairRQ{0} +\xdef\simpairRH{0} \xdef\simpairRR{1} \xdef\simpairRK{0} \xdef\simpairRM{0} \xdef\simpairRI{0} +\xdef\simpairRL{0} \xdef\simpairRV{0} \xdef\simpairRF{0} \xdef\simpairRY{0} \xdef\simpairRW{0} +\xdef\simpairRB{0} \xdef\simpairRJ{0} \xdef\simpairRO{0} \xdef\simpairRU{0} \xdef\simpairRX{0} \xdef\simpairRZ{0} + +\xdef\simpairKC{0} \xdef\simpairKS{0} \xdef\simpairKT{0} \xdef\simpairKP{0} \xdef\simpairKA{0} +\xdef\simpairKG{0} \xdef\simpairKN{0} \xdef\simpairKD{0} \xdef\simpairKE{0} \xdef\simpairKQ{0} +\xdef\simpairKH{0} \xdef\simpairKR{0} \xdef\simpairKK{1} \xdef\simpairKM{0} \xdef\simpairKI{0} +\xdef\simpairKL{0} \xdef\simpairKV{0} \xdef\simpairKF{0} \xdef\simpairKY{0} \xdef\simpairKW{0} +\xdef\simpairKB{0} \xdef\simpairKJ{0} \xdef\simpairKO{0} \xdef\simpairKU{0} \xdef\simpairKX{0} \xdef\simpairKZ{0} + +\xdef\simpairMC{0} \xdef\simpairMS{0} \xdef\simpairMT{0} \xdef\simpairMP{0} \xdef\simpairMA{0} +\xdef\simpairMG{0} \xdef\simpairMN{0} \xdef\simpairMD{0} \xdef\simpairME{0} \xdef\simpairMQ{0} +\xdef\simpairMH{0} \xdef\simpairMR{0} \xdef\simpairMK{0} \xdef\simpairMM{1} \xdef\simpairMI{0} +\xdef\simpairML{0} \xdef\simpairMV{0} \xdef\simpairMF{0} \xdef\simpairMY{0} \xdef\simpairMW{0} +\xdef\simpairMB{0} \xdef\simpairMJ{0} \xdef\simpairMO{0} \xdef\simpairMU{0} \xdef\simpairMX{0} \xdef\simpairMZ{0} + +\xdef\simpairIC{0} \xdef\simpairIS{0} \xdef\simpairIT{0} \xdef\simpairIP{0} \xdef\simpairIA{0} +\xdef\simpairIG{0} \xdef\simpairIN{0} \xdef\simpairID{0} \xdef\simpairIE{0} \xdef\simpairIQ{0} +\xdef\simpairIH{0} \xdef\simpairIR{0} \xdef\simpairIK{0} \xdef\simpairIM{0} \xdef\simpairII{1} +\xdef\simpairIL{0} \xdef\simpairIV{0} \xdef\simpairIF{0} \xdef\simpairIY{0} \xdef\simpairIW{0} +\xdef\simpairIB{0} \xdef\simpairIJ{0} \xdef\simpairIO{0} \xdef\simpairIU{0} \xdef\simpairIX{0} \xdef\simpairIZ{0} + +\xdef\simpairLC{0} \xdef\simpairLS{0} \xdef\simpairLT{0} \xdef\simpairLP{0} \xdef\simpairLA{0} +\xdef\simpairLG{0} \xdef\simpairLN{0} \xdef\simpairLD{0} \xdef\simpairLE{0} \xdef\simpairLQ{0} +\xdef\simpairLH{0} \xdef\simpairLR{0} \xdef\simpairLK{0} \xdef\simpairLM{0} \xdef\simpairLI{0} +\xdef\simpairLL{1} \xdef\simpairLV{0} \xdef\simpairLF{0} \xdef\simpairLY{0} \xdef\simpairLW{0} +\xdef\simpairLB{0} \xdef\simpairLJ{0} \xdef\simpairLO{0} \xdef\simpairLU{0} \xdef\simpairLX{0} \xdef\simpairLZ{0} + +\xdef\simpairVC{0} \xdef\simpairVS{0} \xdef\simpairVT{0} \xdef\simpairVP{0} \xdef\simpairVA{0} +\xdef\simpairVG{0} \xdef\simpairVN{0} \xdef\simpairVD{0} \xdef\simpairVE{0} \xdef\simpairVQ{0} +\xdef\simpairVH{0} \xdef\simpairVR{0} \xdef\simpairVK{0} \xdef\simpairVM{0} \xdef\simpairVI{0} +\xdef\simpairVL{0} \xdef\simpairVV{1} \xdef\simpairVF{0} \xdef\simpairVY{0} \xdef\simpairVW{0} +\xdef\simpairVB{0} \xdef\simpairVJ{0} \xdef\simpairVO{0} \xdef\simpairVU{0} \xdef\simpairVX{0} \xdef\simpairVZ{0} + +\xdef\simpairFC{0} \xdef\simpairFS{0} \xdef\simpairFT{0} \xdef\simpairFP{0} \xdef\simpairFA{0} +\xdef\simpairFG{0} \xdef\simpairFN{0} \xdef\simpairFD{0} \xdef\simpairFE{0} \xdef\simpairFQ{0} +\xdef\simpairFH{0} \xdef\simpairFR{0} \xdef\simpairFK{0} \xdef\simpairFM{0} \xdef\simpairFI{0} +\xdef\simpairFL{0} \xdef\simpairFV{0} \xdef\simpairFF{1} \xdef\simpairFY{0} \xdef\simpairFW{0} +\xdef\simpairFB{0} \xdef\simpairFJ{0} \xdef\simpairFO{0} \xdef\simpairFU{0} \xdef\simpairFX{0} \xdef\simpairFZ{0} + +\xdef\simpairYC{0} \xdef\simpairYS{0} \xdef\simpairYT{0} \xdef\simpairYP{0} \xdef\simpairYA{0} +\xdef\simpairYG{0} \xdef\simpairYN{0} \xdef\simpairYD{0} \xdef\simpairYE{0} \xdef\simpairYQ{0} +\xdef\simpairYH{0} \xdef\simpairYR{0} \xdef\simpairYK{0} \xdef\simpairYM{0} \xdef\simpairYI{0} +\xdef\simpairYL{0} \xdef\simpairYV{0} \xdef\simpairYF{0} \xdef\simpairYY{1} \xdef\simpairYW{0} +\xdef\simpairYB{0} \xdef\simpairYJ{0} \xdef\simpairYO{0} \xdef\simpairYU{0} \xdef\simpairYX{0} \xdef\simpairYZ{0} + +\xdef\simpairWC{0} \xdef\simpairWS{0} \xdef\simpairWT{0} \xdef\simpairWP{0} \xdef\simpairWA{0} +\xdef\simpairWG{0} \xdef\simpairWN{0} \xdef\simpairWD{0} \xdef\simpairWE{0} \xdef\simpairWQ{0} +\xdef\simpairWH{0} \xdef\simpairWR{0} \xdef\simpairWK{0} \xdef\simpairWM{0} \xdef\simpairWI{0} +\xdef\simpairWL{0} \xdef\simpairWV{0} \xdef\simpairWF{0} \xdef\simpairWY{0} \xdef\simpairWW{1} +\xdef\simpairWB{0} \xdef\simpairWJ{0} \xdef\simpairWO{0} \xdef\simpairWU{0} \xdef\simpairWX{0} \xdef\simpairWZ{0} + +\xdef\simpairBC{0} \xdef\simpairBS{0} \xdef\simpairBT{0} \xdef\simpairBP{0} \xdef\simpairBA{0} +\xdef\simpairBG{0} \xdef\simpairBN{0} \xdef\simpairBD{0} \xdef\simpairBE{0} \xdef\simpairBQ{0} +\xdef\simpairBH{0} \xdef\simpairBR{0} \xdef\simpairBK{0} \xdef\simpairBM{0} \xdef\simpairBI{0} +\xdef\simpairBL{0} \xdef\simpairBV{0} \xdef\simpairBF{0} \xdef\simpairBY{0} \xdef\simpairBW{0} +\xdef\simpairBB{1} \xdef\simpairBJ{0} \xdef\simpairBO{0} \xdef\simpairBU{0} \xdef\simpairBX{0} \xdef\simpairBZ{0} + +\xdef\simpairJC{0} \xdef\simpairJS{0} \xdef\simpairJT{0} \xdef\simpairJP{0} \xdef\simpairJA{0} +\xdef\simpairJG{0} \xdef\simpairJN{0} \xdef\simpairJD{0} \xdef\simpairJE{0} \xdef\simpairJQ{0} +\xdef\simpairJH{0} \xdef\simpairJR{0} \xdef\simpairJK{0} \xdef\simpairJM{0} \xdef\simpairJI{0} +\xdef\simpairJL{0} \xdef\simpairJV{0} \xdef\simpairJF{0} \xdef\simpairJY{0} \xdef\simpairJW{0} +\xdef\simpairJB{0} \xdef\simpairJJ{1} \xdef\simpairJO{0} \xdef\simpairJU{0} \xdef\simpairJX{0} \xdef\simpairJZ{0} + +\xdef\simpairOC{0} \xdef\simpairOS{0} \xdef\simpairOT{0} \xdef\simpairOP{0} \xdef\simpairOA{0} +\xdef\simpairOG{0} \xdef\simpairON{0} \xdef\simpairOD{0} \xdef\simpairOE{0} \xdef\simpairOQ{0} +\xdef\simpairOH{0} \xdef\simpairOR{0} \xdef\simpairOK{0} \xdef\simpairOM{0} \xdef\simpairOI{0} +\xdef\simpairOL{0} \xdef\simpairOV{0} \xdef\simpairOF{0} \xdef\simpairOY{0} \xdef\simpairOW{0} +\xdef\simpairOB{0} \xdef\simpairOJ{0} \xdef\simpairOO{1} \xdef\simpairOU{0} \xdef\simpairOX{0} \xdef\simpairOZ{0} + +\xdef\simpairUC{0} \xdef\simpairUS{0} \xdef\simpairUT{0} \xdef\simpairUP{0} \xdef\simpairUA{0} +\xdef\simpairUG{0} \xdef\simpairUN{0} \xdef\simpairUD{0} \xdef\simpairUE{0} \xdef\simpairUQ{0} +\xdef\simpairUH{0} \xdef\simpairUR{0} \xdef\simpairUK{0} \xdef\simpairUM{0} \xdef\simpairUI{0} +\xdef\simpairUL{0} \xdef\simpairUV{0} \xdef\simpairUF{0} \xdef\simpairUY{0} \xdef\simpairUW{0} +\xdef\simpairUB{0} \xdef\simpairUJ{0} \xdef\simpairUO{0} \xdef\simpairUU{1} \xdef\simpairUX{0} \xdef\simpairUZ{0} + +\xdef\simpairXC{0} \xdef\simpairXS{0} \xdef\simpairXT{0} \xdef\simpairXP{0} \xdef\simpairXA{0} +\xdef\simpairXG{0} \xdef\simpairXN{0} \xdef\simpairXD{0} \xdef\simpairXE{0} \xdef\simpairXQ{0} +\xdef\simpairXH{0} \xdef\simpairXR{0} \xdef\simpairXK{0} \xdef\simpairXM{0} \xdef\simpairXI{0} +\xdef\simpairXL{0} \xdef\simpairXV{0} \xdef\simpairXF{0} \xdef\simpairXY{0} \xdef\simpairXW{0} +\xdef\simpairXB{0} \xdef\simpairXJ{0} \xdef\simpairXO{0} \xdef\simpairXU{0} \xdef\simpairXX{1} \xdef\simpairXZ{0} + +\xdef\simpairZC{0} \xdef\simpairZS{0} \xdef\simpairZT{0} \xdef\simpairZP{0} \xdef\simpairZA{0} +\xdef\simpairZG{0} \xdef\simpairZN{0} \xdef\simpairZD{0} \xdef\simpairZE{0} \xdef\simpairZQ{0} +\xdef\simpairZH{0} \xdef\simpairZR{0} \xdef\simpairZK{0} \xdef\simpairZM{0} \xdef\simpairZI{0} +\xdef\simpairZL{0} \xdef\simpairZV{0} \xdef\simpairZF{0} \xdef\simpairZY{0} \xdef\simpairZW{0} +\xdef\simpairZB{0} \xdef\simpairZJ{0} \xdef\simpairZO{0} \xdef\simpairZU{0} \xdef\simpairZX{0} \xdef\simpairZZ{1} + +} + +\def\clear@sim@count{ + \def\clear@sim@nums{% + \advance\innerloopcount by 1 + \ifnum\innerloopcount>\seq@count + \else + \expandafter\xdef\csname poscount\the\outerloopcount @\the\innerloopcount\endcsname{0} + \expandafter\xdef\csname identcount\the\outerloopcount @\the\innerloopcount\endcsname{0} + \expandafter\xdef\csname simcount\the\outerloopcount @\the\innerloopcount\endcsname{0} + \clear@sim@nums + \fi + } + + \outerloopcount=1 + \loop + \innerloopcount=\outerloopcount + \clear@sim@nums + \advance\outerloopcount by 1 + \ifnum\outerloopcount<\seq@count \repeat +} + +\xdef\pepmwA{711} \xdef\pepmwB{1146} \xdef\pepmwC{1032} +\xdef\pepmwD{1151} \xdef\pepmwE{1291} \xdef\pepmwF{1472} +\xdef\pepmwG{571} \xdef\pepmwH{1372} \xdef\pepmwI{1132} +\xdef\pepmwJ{0} \xdef\pepmwK{1282} \xdef\pepmwL{1132} +\xdef\pepmwM{1312} \xdef\pepmwN{1141} \xdef\pepmwO{0} +\xdef\pepmwP{971} \xdef\pepmwQ{1281} \xdef\pepmwR{1562} +\xdef\pepmwS{871} \xdef\pepmwT{1011} \xdef\pepmwU{0} +\xdef\pepmwV{991} \xdef\pepmwW{1862} \xdef\pepmwX{1282} +\xdef\pepmwY{1632} \xdef\pepmwZ{1286} + +\xdef\DNAmwA{3462} \xdef\DNAmwB{0} \xdef\DNAmwC{3222} +\xdef\DNAmwD{0} \xdef\DNAmwE{0} \xdef\DNAmwF{0} +\xdef\DNAmwG{3622} \xdef\DNAmwH{0} \xdef\DNAmwI{0} +\xdef\DNAmwJ{0} \xdef\DNAmwK{0} \xdef\DNAmwL{0} +\xdef\DNAmwM{0} \xdef\DNAmwN{0} \xdef\DNAmwO{0} +\xdef\DNAmwP{0} \xdef\DNAmwQ{0} \xdef\DNAmwR{0} +\xdef\DNAmwS{0} \xdef\DNAmwT{3372} \xdef\DNAmwU{3232} +\xdef\DNAmwV{0} \xdef\DNAmwW{0} \xdef\DNAmwX{0} +\xdef\DNAmwY{0} \xdef\DNAmwZ{0} + +\xdef\pepchargeA{0} \xdef\pepchargeB{0} \xdef\pepchargeC{-30} +\xdef\pepchargeD{-1000} \xdef\pepchargeE{-1000} \xdef\pepchargeF{0} +\xdef\pepchargeG{0} \xdef\pepchargeH{165} \xdef\pepchargeI{0} +\xdef\pepchargeJ{0} \xdef\pepchargeK{1000} \xdef\pepchargeL{0} +\xdef\pepchargeM{0} \xdef\pepchargeN{0} \xdef\pepchargeO{0} +\xdef\pepchargeP{0} \xdef\pepchargeQ{0} \xdef\pepchargeR{1000} +\xdef\pepchargeS{0} \xdef\pepchargeT{0} \xdef\pepchargeU{0} +\xdef\pepchargeV{0} \xdef\pepchargeW{0} \xdef\pepchargeX{0} +\xdef\pepchargeY{0} \xdef\pepchargeZ{0} +\xdef\chargeNterm{910} \xdef\chargeCterm{-1000} + +\xdef\chargeA{0} \xdef\chargeB{0} \xdef\chargeC{0} +\xdef\chargeD{-50} \xdef\chargeE{-50} \xdef\chargeF{0} +\xdef\chargeG{0} \xdef\chargeH{30} \xdef\chargeI{0} +\xdef\chargeJ{0} \xdef\chargeK{50} \xdef\chargeL{0} +\xdef\chargeM{0} \xdef\chargeN{0} \xdef\chargeO{0} +\xdef\chargeP{0} \xdef\chargeQ{0} \xdef\chargeR{50} +\xdef\chargeS{0} \xdef\chargeT{0} \xdef\chargeU{0} +\xdef\chargeV{0} \xdef\chargeW{0} \xdef\chargeX{0} +\xdef\chargeY{0} \xdef\chargeZ{0} + +\xdef\molwA{11} \xdef\molwB{45} \xdef\molwC{36} +\xdef\molwD{45} \xdef\molwE{66} \xdef\molwF{70} +\xdef\molwG{1} \xdef\molwH{62} \xdef\molwI{44} +\xdef\molwJ{N} \xdef\molwK{55} \xdef\molwL{44} +\xdef\molwM{58} \xdef\molwN{44} \xdef\molwO{N} +\xdef\molwP{31} \xdef\molwQ{55} \xdef\molwR{77} +\xdef\molwS{19} \xdef\molwT{34} \xdef\molwU{N} +\xdef\molwV{33} \xdef\molwW{100} \xdef\molwX{55} +\xdef\molwY{82} \xdef\molwZ{66} + +\xdef\HydroA{21} \xdef\HydroB{N} \xdef\HydroC{10} +\xdef\HydroD{-31} \xdef\HydroE{-25} \xdef\HydroF{41} +\xdef\HydroG{16} \xdef\HydroH{-14} \xdef\HydroI{47} +\xdef\HydroJ{N} \xdef\HydroK{-52} \xdef\HydroL{36} +\xdef\HydroM{22} \xdef\HydroN{-27} \xdef\HydroO{N} +\xdef\HydroP{4} \xdef\HydroQ{-29} \xdef\HydroR{-53} +\xdef\HydroS{-6} \xdef\HydroT{-2} \xdef\HydroU{N} +\xdef\HydroV{37} \xdef\HydroW{28} \xdef\HydroX{N} +\xdef\HydroY{9} \xdef\HydroZ{N} + + + +\xdef\consCB{0} \xdef\consCJ{0} \xdef\consCO{0} \xdef\consCU{0} \xdef\consCX{0} \xdef\consCZ{0} +\expandafter\xdef\csname consC?\endcsname{0} + +\xdef\consSB{0} \xdef\consSJ{0} \xdef\consSO{0} \xdef\consSU{0} \xdef\consSX{0} \xdef\consSZ{0} +\expandafter\xdef\csname consS?\endcsname{0} + +\xdef\consTB{0} \xdef\consTJ{0} \xdef\consTO{0} \xdef\consTU{0} \xdef\consTX{0} \xdef\consTZ{0} +\expandafter\xdef\csname consT?\endcsname{0} + +\xdef\consPB{0} \xdef\consPJ{0} \xdef\consPO{0} \xdef\consPU{0} \xdef\consPX{0} \xdef\consPZ{0} +\expandafter\xdef\csname consP?\endcsname{0} + +\xdef\consAB{0} \xdef\consAJ{0} \xdef\consAO{0} \xdef\consAU{0} \xdef\consAX{0} \xdef\consAZ{0} +\expandafter\xdef\csname consA?\endcsname{0} + +\xdef\consGB{0} \xdef\consGJ{0} \xdef\consGO{0} \xdef\consGU{0} \xdef\consGX{0} \xdef\consGZ{0} +\expandafter\xdef\csname consG?\endcsname{0} + +\xdef\consNB{0} \xdef\consNJ{0} \xdef\consNO{0} \xdef\consNU{0} \xdef\consNX{0} \xdef\consNZ{0} +\expandafter\xdef\csname consN?\endcsname{0} + +\xdef\consDB{0} \xdef\consDJ{0} \xdef\consDO{0} \xdef\consDU{0} \xdef\consDX{0} \xdef\consDZ{0} +\expandafter\xdef\csname consD?\endcsname{0} + +\xdef\consEB{0} \xdef\consEJ{0} \xdef\consEO{0} \xdef\consEU{0} \xdef\consEX{0} \xdef\consEZ{0} +\expandafter\xdef\csname consE?\endcsname{0} + +\xdef\consQB{0} \xdef\consQJ{0} \xdef\consQO{0} \xdef\consQU{0} \xdef\consQX{0} \xdef\consQZ{0} +\expandafter\xdef\csname consQ?\endcsname{0} + +\xdef\consHB{0} \xdef\consHJ{0} \xdef\consHO{0} \xdef\consHU{0} \xdef\consHX{0} \xdef\consHZ{0} +\expandafter\xdef\csname consH?\endcsname{0} + +\xdef\consRB{0} \xdef\consRJ{0} \xdef\consRO{0} \xdef\consRU{0} \xdef\consRX{0} \xdef\consRZ{0} +\expandafter\xdef\csname consR?\endcsname{0} + +\xdef\consKB{0} \xdef\consKJ{0} \xdef\consKO{0} \xdef\consKU{0} \xdef\consKX{0} \xdef\consKZ{0} +\expandafter\xdef\csname consK?\endcsname{0} + +\xdef\consMB{0} \xdef\consMJ{0} \xdef\consMO{0} \xdef\consMU{0} \xdef\consMX{0} \xdef\consMZ{0} +\expandafter\xdef\csname consM?\endcsname{0} + +\xdef\consIB{0} \xdef\consIJ{0} \xdef\consIO{0} \xdef\consIU{0} \xdef\consIX{0} \xdef\consIZ{0} +\expandafter\xdef\csname consI?\endcsname{0} + +\xdef\consLB{0} \xdef\consLJ{0} \xdef\consLO{0} \xdef\consLU{0} \xdef\consLX{0} \xdef\consLZ{0} +\expandafter\xdef\csname consL?\endcsname{0} + +\xdef\consVB{0} \xdef\consVJ{0} \xdef\consVO{0} \xdef\consVU{0} \xdef\consVX{0} \xdef\consVZ{0} +\expandafter\xdef\csname consV?\endcsname{0} + +\xdef\consFB{0} \xdef\consFJ{0} \xdef\consFO{0} \xdef\consFU{0} \xdef\consFX{0} \xdef\consFZ{0} +\expandafter\xdef\csname consF?\endcsname{0} + +\xdef\consYB{0} \xdef\consYJ{0} \xdef\consYO{0} \xdef\consYU{0} \xdef\consYX{0} \xdef\consYZ{0} +\expandafter\xdef\csname consY?\endcsname{0} + +\xdef\consWB{0} \xdef\consWJ{0} \xdef\consWO{0} \xdef\consWU{0} \xdef\consWX{0} \xdef\consWZ{0} +\expandafter\xdef\csname consW?\endcsname{0} + +\xdef\consBC{0} \xdef\consBS{0} \xdef\consBT{0} \xdef\consBP{0} \xdef\consBA{0} +\xdef\consBG{0} \xdef\consBN{0} \xdef\consBD{0} \xdef\consBE{0} \xdef\consBQ{0} +\xdef\consBH{0} \xdef\consBR{0} \xdef\consBK{0} \xdef\consBM{0} \xdef\consBI{0} +\xdef\consBL{0} \xdef\consBV{0} \xdef\consBF{0} \xdef\consBY{0} \xdef\consBW{0} +\xdef\consBB{10} \xdef\consBJ{0} \xdef\consBO{0} \xdef\consBU{0} \xdef\consBX{0} \xdef\consBZ{0} +\expandafter\xdef\csname consB.\endcsname{0} +\expandafter\xdef\csname consB?\endcsname{0} + +\xdef\consJC{0} \xdef\consJS{0} \xdef\consJT{0} \xdef\consJP{0} \xdef\consJA{0} +\xdef\consJG{0} \xdef\consJN{0} \xdef\consJD{0} \xdef\consJE{0} \xdef\consJQ{0} +\xdef\consJH{0} \xdef\consJR{0} \xdef\consJK{0} \xdef\consJM{0} \xdef\consJI{0} +\xdef\consJL{0} \xdef\consJV{0} \xdef\consJF{0} \xdef\consJY{0} \xdef\consJW{0} +\xdef\consJB{0} \xdef\consJJ{10} \xdef\consJO{0} \xdef\consJU{0} \xdef\consJX{0} \xdef\consJZ{0} +\expandafter\xdef\csname consJ.\endcsname{0} +\expandafter\xdef\csname consJ?\endcsname{0} + +\xdef\consOC{0} \xdef\consOS{0} \xdef\consOT{0} \xdef\consOP{0} \xdef\consOA{0} +\xdef\consOG{0} \xdef\consON{0} \xdef\consOD{0} \xdef\consOE{0} \xdef\consOQ{0} +\xdef\consOH{0} \xdef\consOR{0} \xdef\consOK{0} \xdef\consOM{0} \xdef\consOI{0} +\xdef\consOL{0} \xdef\consOV{0} \xdef\consOF{0} \xdef\consOY{0} \xdef\consOW{0} +\xdef\consOB{0} \xdef\consOJ{0} \xdef\consOO{10} \xdef\consOU{0} \xdef\consOX{0} \xdef\consOZ{0} +\expandafter\xdef\csname consO.\endcsname{0} +\expandafter\xdef\csname consO?\endcsname{0} + +\xdef\consUC{0} \xdef\consUS{0} \xdef\consUT{0} \xdef\consUP{0} \xdef\consUA{0} +\xdef\consUG{0} \xdef\consUN{0} \xdef\consUD{0} \xdef\consUE{0} \xdef\consUQ{0} +\xdef\consUH{0} \xdef\consUR{0} \xdef\consUK{0} \xdef\consUM{0} \xdef\consUI{0} +\xdef\consUL{0} \xdef\consUV{0} \xdef\consUF{0} \xdef\consUY{0} \xdef\consUW{0} +\xdef\consUB{0} \xdef\consUJ{0} \xdef\consUO{0} \xdef\consUU{10} \xdef\consUX{0} \xdef\consUZ{0} +\expandafter\xdef\csname consU.\endcsname{0} +\expandafter\xdef\csname consU?\endcsname{0} + +\xdef\consXC{0} \xdef\consXS{0} \xdef\consXT{0} \xdef\consXP{0} \xdef\consXA{0} +\xdef\consXG{0} \xdef\consXN{0} \xdef\consXD{0} \xdef\consXE{0} \xdef\consXQ{0} +\xdef\consXH{0} \xdef\consXR{0} \xdef\consXK{0} \xdef\consXM{0} \xdef\consXI{0} +\xdef\consXL{0} \xdef\consXV{0} \xdef\consXF{0} \xdef\consXY{0} \xdef\consXW{0} +\xdef\consXB{0} \xdef\consXJ{0} \xdef\consXO{0} \xdef\consXU{0} \xdef\consXX{10} \xdef\consXZ{0} +\expandafter\xdef\csname consX.\endcsname{0} +\expandafter\xdef\csname consX?\endcsname{0} + +\xdef\consZC{0} \xdef\consZS{0} \xdef\consZT{0} \xdef\consZP{0} \xdef\consZA{0} +\xdef\consZG{0} \xdef\consZN{0} \xdef\consZD{0} \xdef\consZE{0} \xdef\consZQ{0} +\xdef\consZH{0} \xdef\consZR{0} \xdef\consZK{0} \xdef\consZM{0} \xdef\consZI{0} +\xdef\consZL{0} \xdef\consZV{0} \xdef\consZF{0} \xdef\consZY{0} \xdef\consZW{0} +\xdef\consZB{0} \xdef\consZJ{0} \xdef\consZO{0} \xdef\consZU{0} \xdef\consZX{0} \xdef\consZZ{10} +\expandafter\xdef\csname consZ.\endcsname{0} +\expandafter\xdef\csname consZ?\endcsname{0} + +\expandafter\xdef\csname cons..\endcsname{0} +\expandafter\xdef\csname cons.?\endcsname{0} + +\expandafter\xdef\csname cons?C\endcsname{0} +\expandafter\xdef\csname cons?S\endcsname{0} +\expandafter\xdef\csname cons?T\endcsname{0} +\expandafter\xdef\csname cons?P\endcsname{0} +\expandafter\xdef\csname cons?A\endcsname{0} +\expandafter\xdef\csname cons?G\endcsname{0} +\expandafter\xdef\csname cons?N\endcsname{0} +\expandafter\xdef\csname cons?D\endcsname{0} +\expandafter\xdef\csname cons?E\endcsname{0} +\expandafter\xdef\csname cons?Q\endcsname{0} +\expandafter\xdef\csname cons?H\endcsname{0} +\expandafter\xdef\csname cons?R\endcsname{0} +\expandafter\xdef\csname cons?K\endcsname{0} +\expandafter\xdef\csname cons?M\endcsname{0} +\expandafter\xdef\csname cons?I\endcsname{0} +\expandafter\xdef\csname cons?L\endcsname{0} +\expandafter\xdef\csname cons?V\endcsname{0} +\expandafter\xdef\csname cons?F\endcsname{0} +\expandafter\xdef\csname cons?Y\endcsname{0} +\expandafter\xdef\csname cons?W\endcsname{0} +\expandafter\xdef\csname cons?B\endcsname{0} +\expandafter\xdef\csname cons?J\endcsname{0} +\expandafter\xdef\csname cons?O\endcsname{0} +\expandafter\xdef\csname cons?U\endcsname{0} +\expandafter\xdef\csname cons?X\endcsname{0} +\expandafter\xdef\csname cons?Z\endcsname{0} +\expandafter\xdef\csname cons?.\endcsname{0} +\expandafter\xdef\csname cons??\endcsname{0} + +\expandafter\xdef\csname cons==\endcsname{0} + + +\def\gappenalty#1{% +\expandafter\xdef\csname cons.C\endcsname{#1} \expandafter\xdef\csname consC.\endcsname{#1} +\expandafter\xdef\csname cons.S\endcsname{#1} \expandafter\xdef\csname consS.\endcsname{#1} +\expandafter\xdef\csname cons.T\endcsname{#1} \expandafter\xdef\csname consT.\endcsname{#1} +\expandafter\xdef\csname cons.P\endcsname{#1} \expandafter\xdef\csname consP.\endcsname{#1} +\expandafter\xdef\csname cons.A\endcsname{#1} \expandafter\xdef\csname consA.\endcsname{#1} +\expandafter\xdef\csname cons.G\endcsname{#1} \expandafter\xdef\csname consG.\endcsname{#1} +\expandafter\xdef\csname cons.N\endcsname{#1} \expandafter\xdef\csname consN.\endcsname{#1} +\expandafter\xdef\csname cons.D\endcsname{#1} \expandafter\xdef\csname consD.\endcsname{#1} +\expandafter\xdef\csname cons.E\endcsname{#1} \expandafter\xdef\csname consE.\endcsname{#1} +\expandafter\xdef\csname cons.Q\endcsname{#1} \expandafter\xdef\csname consQ.\endcsname{#1} +\expandafter\xdef\csname cons.H\endcsname{#1} \expandafter\xdef\csname consH.\endcsname{#1} +\expandafter\xdef\csname cons.R\endcsname{#1} \expandafter\xdef\csname consR.\endcsname{#1} +\expandafter\xdef\csname cons.K\endcsname{#1} \expandafter\xdef\csname consK.\endcsname{#1} +\expandafter\xdef\csname cons.M\endcsname{#1} \expandafter\xdef\csname consM.\endcsname{#1} +\expandafter\xdef\csname cons.I\endcsname{#1} \expandafter\xdef\csname consI.\endcsname{#1} +\expandafter\xdef\csname cons.L\endcsname{#1} \expandafter\xdef\csname consL.\endcsname{#1} +\expandafter\xdef\csname cons.V\endcsname{#1} \expandafter\xdef\csname consV.\endcsname{#1} +\expandafter\xdef\csname cons.F\endcsname{#1} \expandafter\xdef\csname consF.\endcsname{#1} +\expandafter\xdef\csname cons.Y\endcsname{#1} \expandafter\xdef\csname consY.\endcsname{#1} +\expandafter\xdef\csname cons.W\endcsname{#1} \expandafter\xdef\csname consW.\endcsname{#1} +\expandafter\xdef\csname cons.B\endcsname{#1} \expandafter\xdef\csname consB.\endcsname{#1} +\expandafter\xdef\csname cons.J\endcsname{#1} \expandafter\xdef\csname consJ.\endcsname{#1} +\expandafter\xdef\csname cons.O\endcsname{#1} \expandafter\xdef\csname consO.\endcsname{#1} +\expandafter\xdef\csname cons.U\endcsname{#1} \expandafter\xdef\csname consU.\endcsname{#1} +\expandafter\xdef\csname cons.X\endcsname{#1} \expandafter\xdef\csname consX.\endcsname{#1} +\expandafter\xdef\csname cons.Z\endcsname{#1} \expandafter\xdef\csname consZ.\endcsname{#1} +} + +\def\weighttable#1{% +\xdef\first@{#1} + +\xdef\temp@{identity} +\ifx\first@\temp@ + + +%%%% identity matrix + +\xdef\consCC{10} \xdef\consCS{0} \xdef\consCT{0} \xdef\consCP{0} \xdef\consCA{0} +\xdef\consCG{0} \xdef\consCN{0} \xdef\consCD{0} \xdef\consCE{0} \xdef\consCQ{0} +\xdef\consCH{0} \xdef\consCR{0} \xdef\consCK{0} \xdef\consCM{0} \xdef\consCI{0} +\xdef\consCL{0} \xdef\consCV{0} \xdef\consCF{0} \xdef\consCY{0} \xdef\consCW{0} + +\xdef\consSC{0} \xdef\consSS{10} \xdef\consST{0} \xdef\consSP{0} \xdef\consSA{0} +\xdef\consSG{0} \xdef\consSN{0} \xdef\consSD{0} \xdef\consSE{0} \xdef\consSQ{0} +\xdef\consSH{0} \xdef\consSR{0} \xdef\consSK{0} \xdef\consSM{0} \xdef\consSI{0} +\xdef\consSL{0} \xdef\consSV{0} \xdef\consSF{0} \xdef\consSY{0} \xdef\consSW{0} + +\xdef\consTC{0} \xdef\consTS{0} \xdef\consTT{10} \xdef\consTP{0} \xdef\consTA{0} +\xdef\consTG{0} \xdef\consTN{0} \xdef\consTD{0} \xdef\consTE{0} \xdef\consTQ{0} +\xdef\consTH{0} \xdef\consTR{0} \xdef\consTK{0} \xdef\consTM{0} \xdef\consTI{0} +\xdef\consTL{0} \xdef\consTV{0} \xdef\consTF{0} \xdef\consTY{0} \xdef\consTW{0} + +\xdef\consPC{0} \xdef\consPS{0} \xdef\consPT{0} \xdef\consPP{10} \xdef\consPA{0} +\xdef\consPG{0} \xdef\consPN{0} \xdef\consPD{0} \xdef\consPE{0} \xdef\consPQ{0} +\xdef\consPH{0} \xdef\consPR{0} \xdef\consPK{0} \xdef\consPM{0} \xdef\consPI{0} +\xdef\consPL{0} \xdef\consPV{0} \xdef\consPF{0} \xdef\consPY{0} \xdef\consPW{0} + +\xdef\consAC{0} \xdef\consAS{0} \xdef\consAT{0} \xdef\consAP{0} \xdef\consAA{10} +\xdef\consAG{0} \xdef\consAN{0} \xdef\consAD{0} \xdef\consAE{0} \xdef\consAQ{0} +\xdef\consAH{0} \xdef\consAR{0} \xdef\consAK{0} \xdef\consAM{0} \xdef\consAI{0} +\xdef\consAL{0} \xdef\consAV{0} \xdef\consAF{0} \xdef\consAY{0} \xdef\consAW{0} + +\xdef\consGC{0} \xdef\consGS{0} \xdef\consGT{0} \xdef\consGP{0} \xdef\consGA{0} +\xdef\consGG{10} \xdef\consGN{0} \xdef\consGD{0} \xdef\consGE{0} \xdef\consGQ{0} +\xdef\consGH{0} \xdef\consGR{0} \xdef\consGK{0} \xdef\consGM{0} \xdef\consGI{0} +\xdef\consGL{0} \xdef\consGV{0} \xdef\consGF{0} \xdef\consGY{0} \xdef\consGW{0} + +\xdef\consNC{0} \xdef\consNS{0} \xdef\consNT{0} \xdef\consNP{0} \xdef\consNA{0} +\xdef\consNG{0} \xdef\consNN{10} \xdef\consND{0} \xdef\consNE{0} \xdef\consNQ{0} +\xdef\consNH{0} \xdef\consNR{0} \xdef\consNK{0} \xdef\consNM{0} \xdef\consNI{0} +\xdef\consNL{0} \xdef\consNV{0} \xdef\consNF{0} \xdef\consNY{0} \xdef\consNW{0} + +\xdef\consDC{0} \xdef\consDS{0} \xdef\consDT{0} \xdef\consDP{0} \xdef\consDA{0} +\xdef\consDG{0} \xdef\consDN{0} \xdef\consDD{10} \xdef\consDE{0} \xdef\consDQ{0} +\xdef\consDH{0} \xdef\consDR{0} \xdef\consDK{0} \xdef\consDM{0} \xdef\consDI{0} +\xdef\consDL{0} \xdef\consDV{0} \xdef\consDF{0} \xdef\consDY{0} \xdef\consDW{0} + +\xdef\consEC{0} \xdef\consES{0} \xdef\consET{0} \xdef\consEP{0} \xdef\consEA{0} +\xdef\consEG{0} \xdef\consEN{0} \xdef\consED{0} \xdef\consEE{10} \xdef\consEQ{0} +\xdef\consEH{0} \xdef\consER{0} \xdef\consEK{0} \xdef\consEM{0} \xdef\consEI{0} +\xdef\consEL{0} \xdef\consEV{0} \xdef\consEF{0} \xdef\consEY{0} \xdef\consEW{0} + +\xdef\consQC{0} \xdef\consQS{0} \xdef\consQT{0} \xdef\consQP{0} \xdef\consQA{0} +\xdef\consQG{0} \xdef\consQN{0} \xdef\consQD{0} \xdef\consQE{0} \xdef\consQQ{10} +\xdef\consQH{0} \xdef\consQR{0} \xdef\consQK{0} \xdef\consQM{0} \xdef\consQI{0} +\xdef\consQL{0} \xdef\consQV{0} \xdef\consQF{0} \xdef\consQY{0} \xdef\consQW{0} + +\xdef\consHC{0} \xdef\consHS{0} \xdef\consHT{0} \xdef\consHP{0} \xdef\consHA{0} +\xdef\consHG{0} \xdef\consHN{0} \xdef\consHD{0} \xdef\consHE{0} \xdef\consHQ{0} +\xdef\consHH{10} \xdef\consHR{0} \xdef\consHK{0} \xdef\consHM{0} \xdef\consHI{0} +\xdef\consHL{0} \xdef\consHV{0} \xdef\consHF{0} \xdef\consHY{0} \xdef\consHW{0} + +\xdef\consRC{0} \xdef\consRS{0} \xdef\consRT{0} \xdef\consRP{0} \xdef\consRA{0} +\xdef\consRG{0} \xdef\consRN{0} \xdef\consRD{0} \xdef\consRE{0} \xdef\consRQ{0} +\xdef\consRH{0} \xdef\consRR{10} \xdef\consRK{0} \xdef\consRM{0} \xdef\consRI{0} +\xdef\consRL{0} \xdef\consRV{0} \xdef\consRF{0} \xdef\consRY{0} \xdef\consRW{0} + +\xdef\consKC{0} \xdef\consKS{0} \xdef\consKT{0} \xdef\consKP{0} \xdef\consKA{0} +\xdef\consKG{0} \xdef\consKN{0} \xdef\consKD{0} \xdef\consKE{0} \xdef\consKQ{0} +\xdef\consKH{0} \xdef\consKR{0} \xdef\consKK{10} \xdef\consKM{0} \xdef\consKI{0} +\xdef\consKL{0} \xdef\consKV{0} \xdef\consKF{0} \xdef\consKY{0} \xdef\consKW{0} + +\xdef\consMC{0} \xdef\consMS{0} \xdef\consMT{0} \xdef\consMP{0} \xdef\consMA{0} +\xdef\consMG{0} \xdef\consMN{0} \xdef\consMD{0} \xdef\consME{0} \xdef\consMQ{0} +\xdef\consMH{0} \xdef\consMR{0} \xdef\consMK{0} \xdef\consMM{10} \xdef\consMI{0} +\xdef\consML{0} \xdef\consMV{0} \xdef\consMF{0} \xdef\consMY{0} \xdef\consMW{0} + +\xdef\consIC{0} \xdef\consIS{0} \xdef\consIT{0} \xdef\consIP{0} \xdef\consIA{0} +\xdef\consIG{0} \xdef\consIN{0} \xdef\consID{0} \xdef\consIE{0} \xdef\consIQ{0} +\xdef\consIH{0} \xdef\consIR{0} \xdef\consIK{0} \xdef\consIM{0} \xdef\consII{10} +\xdef\consIL{0} \xdef\consIV{0} \xdef\consIF{0} \xdef\consIY{0} \xdef\consIW{0} + +\xdef\consLC{0} \xdef\consLS{0} \xdef\consLT{0} \xdef\consLP{0} \xdef\consLA{0} +\xdef\consLG{0} \xdef\consLN{0} \xdef\consLD{0} \xdef\consLE{0} \xdef\consLQ{0} +\xdef\consLH{0} \xdef\consLR{0} \xdef\consLK{0} \xdef\consLM{0} \xdef\consLI{0} +\xdef\consLL{10} \xdef\consLV{0} \xdef\consLF{0} \xdef\consLY{0} \xdef\consLW{0} + +\xdef\consVC{0} \xdef\consVS{0} \xdef\consVT{0} \xdef\consVP{0} \xdef\consVA{0} +\xdef\consVG{0} \xdef\consVN{0} \xdef\consVD{0} \xdef\consVE{0} \xdef\consVQ{0} +\xdef\consVH{0} \xdef\consVR{0} \xdef\consVK{0} \xdef\consVM{0} \xdef\consVI{0} +\xdef\consVL{0} \xdef\consVV{10} \xdef\consVF{0} \xdef\consVY{0} \xdef\consVW{0} + +\xdef\consFC{0} \xdef\consFS{0} \xdef\consFT{0} \xdef\consFP{0} \xdef\consFA{0} +\xdef\consFG{0} \xdef\consFN{0} \xdef\consFD{0} \xdef\consFE{0} \xdef\consFQ{0} +\xdef\consFH{0} \xdef\consFR{0} \xdef\consFK{0} \xdef\consFM{0} \xdef\consFI{0} +\xdef\consFL{0} \xdef\consFV{0} \xdef\consFF{10} \xdef\consFY{0} \xdef\consFW{0} + +\xdef\consYC{0} \xdef\consYS{0} \xdef\consYT{0} \xdef\consYP{0} \xdef\consYA{0} +\xdef\consYG{0} \xdef\consYN{0} \xdef\consYD{0} \xdef\consYE{0} \xdef\consYQ{0} +\xdef\consYH{0} \xdef\consYR{0} \xdef\consYK{0} \xdef\consYM{0} \xdef\consYI{0} +\xdef\consYL{0} \xdef\consYV{0} \xdef\consYF{0} \xdef\consYY{10} \xdef\consYW{0} + +\xdef\consWC{0} \xdef\consWS{0} \xdef\consWT{0} \xdef\consWP{0} \xdef\consWA{0} +\xdef\consWG{0} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{0} \xdef\consWQ{0} +\xdef\consWH{0} \xdef\consWR{0} \xdef\consWK{0} \xdef\consWM{0} \xdef\consWI{0} +\xdef\consWL{0} \xdef\consWV{0} \xdef\consWF{0} \xdef\consWY{0} \xdef\consWW{10} + +\gappenalty{0} \xdef\m@trixf@ctor{10} + +\else + +\xdef\temp@{structural} +\ifx\first@\temp@ + + +%%%% structural + +\xdef\consCC{10} \xdef\consCS{6} \xdef\consCT{3} \xdef\consCP{3} \xdef\consCA{3} +\xdef\consCG{5} \xdef\consCN{3} \xdef\consCD{1} \xdef\consCE{0} \xdef\consCQ{1} +\xdef\consCH{3} \xdef\consCR{3} \xdef\consCK{0} \xdef\consCM{3} \xdef\consCI{3} +\xdef\consCL{3} \xdef\consCV{3} \xdef\consCF{5} \xdef\consCY{5} \xdef\consCW{5} + +\xdef\consSC{6} \xdef\consSS{10} \xdef\consST{8} \xdef\consSP{6} \xdef\consSA{8} +\xdef\consSG{8} \xdef\consSN{8} \xdef\consSD{6} \xdef\consSE{5} \xdef\consSQ{5} +\xdef\consSH{5} \xdef\consSR{5} \xdef\consSK{5} \xdef\consSM{3} \xdef\consSI{3} +\xdef\consSL{3} \xdef\consSV{6} \xdef\consSF{5} \xdef\consSY{5} \xdef\consSW{3} + +\xdef\consTC{3} \xdef\consTS{8} \xdef\consTT{10} \xdef\consTP{6} \xdef\consTA{8} +\xdef\consTG{6} \xdef\consTN{6} \xdef\consTD{5} \xdef\consTE{5} \xdef\consTQ{5} +\xdef\consTH{3} \xdef\consTR{5} \xdef\consTK{6} \xdef\consTM{5} \xdef\consTI{5} +\xdef\consTL{3} \xdef\consTV{6} \xdef\consTF{3} \xdef\consTY{3} \xdef\consTW{1} + +\xdef\consPC{3} \xdef\consPS{6} \xdef\consPT{6} \xdef\consPP{10} \xdef\consPA{8} +\xdef\consPG{6} \xdef\consPN{3} \xdef\consPD{5} \xdef\consPE{5} \xdef\consPQ{5} +\xdef\consPH{5} \xdef\consPR{5} \xdef\consPK{3} \xdef\consPM{3} \xdef\consPI{3} +\xdef\consPL{5} \xdef\consPV{6} \xdef\consPF{5} \xdef\consPY{3} \xdef\consPW{3} + +\xdef\consAC{3} \xdef\consAS{8} \xdef\consAT{8} \xdef\consAP{8} \xdef\consAA{10} +\xdef\consAG{8} \xdef\consAN{5} \xdef\consAD{6} \xdef\consAE{6} \xdef\consAQ{5} +\xdef\consAH{3} \xdef\consAR{3} \xdef\consAK{5} \xdef\consAM{5} \xdef\consAI{3} +\xdef\consAL{3} \xdef\consAV{8} \xdef\consAF{5} \xdef\consAY{3} \xdef\consAW{3} + +\xdef\consGC{5} \xdef\consGS{8} \xdef\consGT{6} \xdef\consGP{6} \xdef\consGA{8} +\xdef\consGG{10} \xdef\consGN{5} \xdef\consGD{6} \xdef\consGE{6} \xdef\consGQ{3} +\xdef\consGH{1} \xdef\consGR{5} \xdef\consGK{3} \xdef\consGM{1} \xdef\consGI{3} +\xdef\consGL{3} \xdef\consGV{6} \xdef\consGF{3} \xdef\consGY{3} \xdef\consGW{5} + +\xdef\consNC{3} \xdef\consNS{8} \xdef\consNT{6} \xdef\consNP{3} \xdef\consNA{5} +\xdef\consNG{5} \xdef\consNN{10} \xdef\consND{8} \xdef\consNE{6} \xdef\consNQ{5} +\xdef\consNH{6} \xdef\consNR{5} \xdef\consNK{6} \xdef\consNM{1} \xdef\consNI{3} +\xdef\consNL{1} \xdef\consNV{3} \xdef\consNF{3} \xdef\consNY{5} \xdef\consNW{0} + +\xdef\consDC{1} \xdef\consDS{6} \xdef\consDT{5} \xdef\consDP{5} \xdef\consDA{6} +\xdef\consDG{6} \xdef\consDN{8} \xdef\consDD{10} \xdef\consDE{8} \xdef\consDQ{6} +\xdef\consDH{5} \xdef\consDR{3} \xdef\consDK{5} \xdef\consDM{3} \xdef\consDI{1} +\xdef\consDL{1} \xdef\consDV{5} \xdef\consDF{1} \xdef\consDY{3} \xdef\consDW{0} + +\xdef\consEC{0} \xdef\consES{5} \xdef\consET{5} \xdef\consEP{5} \xdef\consEA{6} +\xdef\consEG{6} \xdef\consEN{6} \xdef\consED{8} \xdef\consEE{10} \xdef\consEQ{6} +\xdef\consEH{3} \xdef\consER{5} \xdef\consEK{6} \xdef\consEM{3} \xdef\consEI{1} +\xdef\consEL{1} \xdef\consEV{6} \xdef\consEF{3} \xdef\consEY{1} \xdef\consEW{1} + +\xdef\consQC{1} \xdef\consQS{5} \xdef\consQT{5} \xdef\consQP{5} \xdef\consQA{5} +\xdef\consQG{3} \xdef\consQN{5} \xdef\consQD{6} \xdef\consQE{6} \xdef\consQQ{10} +\xdef\consQH{6} \xdef\consQR{5} \xdef\consQK{6} \xdef\consQM{3} \xdef\consQI{1} +\xdef\consQL{3} \xdef\consQV{3} \xdef\consQF{1} \xdef\consQY{3} \xdef\consQW{1} + +\xdef\consHC{3} \xdef\consHS{5} \xdef\consHT{3} \xdef\consHP{5} \xdef\consHA{3} +\xdef\consHG{1} \xdef\consHN{6} \xdef\consHD{5} \xdef\consHE{3} \xdef\consHQ{6} +\xdef\consHH{10} \xdef\consHR{6} \xdef\consHK{5} \xdef\consHM{3} \xdef\consHI{3} +\xdef\consHL{5} \xdef\consHV{1} \xdef\consHF{3} \xdef\consHY{5} \xdef\consHW{1} + +\xdef\consRC{3} \xdef\consRS{5} \xdef\consRT{5} \xdef\consRP{5} \xdef\consRA{3} +\xdef\consRG{5} \xdef\consRN{5} \xdef\consRD{3} \xdef\consRE{5} \xdef\consRQ{5} +\xdef\consRH{6} \xdef\consRR{10} \xdef\consRK{8} \xdef\consRM{3} \xdef\consRI{3} +\xdef\consRL{3} \xdef\consRV{3} \xdef\consRF{1} \xdef\consRY{1} \xdef\consRW{3} + +\xdef\consKC{0} \xdef\consKS{5} \xdef\consKT{6} \xdef\consKP{3} \xdef\consKA{5} +\xdef\consKG{3} \xdef\consKN{6} \xdef\consKD{5} \xdef\consKE{6} \xdef\consKQ{6} +\xdef\consKH{5} \xdef\consKR{8} \xdef\consKK{10} \xdef\consKM{3} \xdef\consKI{3} +\xdef\consKL{3} \xdef\consKV{5} \xdef\consKF{1} \xdef\consKY{1} \xdef\consKW{1} + +\xdef\consMC{3} \xdef\consMS{5} \xdef\consMT{5} \xdef\consMP{3} \xdef\consMA{5} +\xdef\consMG{1} \xdef\consMN{1} \xdef\consMD{3} \xdef\consME{3} \xdef\consMQ{3} +\xdef\consMH{3} \xdef\consMR{3} \xdef\consMK{3} \xdef\consMM{10} \xdef\consMI{6} +\xdef\consML{8} \xdef\consMV{6} \xdef\consMF{5} \xdef\consMY{3} \xdef\consMW{5} + +\xdef\consIC{3} \xdef\consIS{3} \xdef\consIT{5} \xdef\consIP{3} \xdef\consIA{3} +\xdef\consIG{3} \xdef\consIN{3} \xdef\consID{1} \xdef\consIE{1} \xdef\consIQ{1} +\xdef\consIH{3} \xdef\consIR{3} \xdef\consIK{3} \xdef\consIM{6} \xdef\consII{10} +\xdef\consIL{8} \xdef\consIV{3} \xdef\consIF{6} \xdef\consIY{5} \xdef\consIW{5} + +\xdef\consLC{3} \xdef\consLS{3} \xdef\consLT{3} \xdef\consLP{5} \xdef\consLA{3} +\xdef\consLG{3} \xdef\consLN{1} \xdef\consLD{1} \xdef\consLE{1} \xdef\consLQ{3} +\xdef\consLH{5} \xdef\consLR{3} \xdef\consLK{3} \xdef\consLM{8} \xdef\consLI{8} +\xdef\consLL{10} \xdef\consLV{3} \xdef\consLF{6} \xdef\consLY{5} \xdef\consLW{6} + +\xdef\consVC{3} \xdef\consVS{6} \xdef\consVT{6} \xdef\consVP{6} \xdef\consVA{8} +\xdef\consVG{6} \xdef\consVN{3} \xdef\consVD{5} \xdef\consVE{6} \xdef\consVQ{3} +\xdef\consVH{1} \xdef\consVR{3} \xdef\consVK{5} \xdef\consVM{6} \xdef\consVI{3} +\xdef\consVL{3} \xdef\consVV{10} \xdef\consVF{6} \xdef\consVY{5} \xdef\consVW{5} + +\xdef\consFC{5} \xdef\consFS{5} \xdef\consFT{3} \xdef\consFP{5} \xdef\consFA{5} +\xdef\consFG{3} \xdef\consFN{3} \xdef\consFD{1} \xdef\consFE{3} \xdef\consFQ{1} +\xdef\consFH{3} \xdef\consFR{1} \xdef\consFK{1} \xdef\consFM{5} \xdef\consFI{6} +\xdef\consFL{6} \xdef\consFV{6} \xdef\consFF{10} \xdef\consFY{8} \xdef\consFW{5} + +\xdef\consYC{5} \xdef\consYS{5} \xdef\consYT{3} \xdef\consYP{3} \xdef\consYA{3} +\xdef\consYG{3} \xdef\consYN{5} \xdef\consYD{3} \xdef\consYE{1} \xdef\consYQ{3} +\xdef\consYH{5} \xdef\consYR{1} \xdef\consYK{1} \xdef\consYM{3} \xdef\consYI{5} +\xdef\consYL{5} \xdef\consYV{5} \xdef\consYF{8} \xdef\consYY{10} \xdef\consYW{5} + +\xdef\consWC{5} \xdef\consWS{3} \xdef\consWT{1} \xdef\consWP{3} \xdef\consWA{3} +\xdef\consWG{5} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{1} \xdef\consWQ{1} +\xdef\consWH{1} \xdef\consWR{3} \xdef\consWK{1} \xdef\consWM{5} \xdef\consWI{5} +\xdef\consWL{6} \xdef\consWV{5} \xdef\consWF{5} \xdef\consWY{5} \xdef\consWW{10} + +\gappenalty{0} \xdef\m@trixf@ctor{10} + +\else + +\xdef\temp@{PAM250} +\ifx\first@\temp@ + +%%%% PAM250 + +\xdef\consCC{4} \xdef\consCS{0} \xdef\consCT{-2} \xdef\consCP{-3} \xdef\consCA{-2} +\xdef\consCG{-3} \xdef\consCN{-4} \xdef\consCD{2} \xdef\consCE{-5} \xdef\consCQ{-5} +\xdef\consCH{-3} \xdef\consCR{-4} \xdef\consCK{-5} \xdef\consCM{-5} \xdef\consCI{-2} +\xdef\consCL{-6} \xdef\consCV{-2} \xdef\consCF{-4} \xdef\consCY{0} \xdef\consCW{-8} +\xdef\consCB{-4} \xdef\consCZ{-5} \xdef\consCX{-3} + +\xdef\consSC{0} \xdef\consSS{3} \xdef\consST{1} \xdef\consSP{1} \xdef\consSA{1} +\xdef\consSG{1} \xdef\consSN{1} \xdef\consSD{0} \xdef\consSE{0} \xdef\consSQ{-1} +\xdef\consSH{-1} \xdef\consSR{0} \xdef\consSK{0} \xdef\consSM{-2} \xdef\consSI{-1} +\xdef\consSL{-3} \xdef\consSV{-1} \xdef\consSF{-3} \xdef\consSY{-3} \xdef\consSW{-2} +\xdef\consSB{0} \xdef\consSZ{0} \xdef\consSX{0} + +\xdef\consTC{-2} \xdef\consTS{1} \xdef\consTT{3} \xdef\consTP{0} \xdef\consTA{1} +\xdef\consTG{0} \xdef\consTN{0} \xdef\consTD{0} \xdef\consTE{0} \xdef\consTQ{-1} +\xdef\consTH{-1} \xdef\consTR{-1} \xdef\consTK{0} \xdef\consTM{-1} \xdef\consTI{0} +\xdef\consTL{-2} \xdef\consTV{0} \xdef\consTF{-2} \xdef\consTY{-3} \xdef\consTW{-5} +\xdef\consTB{0} \xdef\consTZ{-1} \xdef\consTX{0} + +\xdef\consPC{-3} \xdef\consPS{1} \xdef\consPT{0} \xdef\consPP{6} \xdef\consPA{1} +\xdef\consPG{-1} \xdef\consPN{-1} \xdef\consPD{-1} \xdef\consPE{-1} \xdef\consPQ{0} +\xdef\consPH{0} \xdef\consPR{0} \xdef\consPK{-1} \xdef\consPM{-2} \xdef\consPI{-2} +\xdef\consPL{-3} \xdef\consPV{-1} \xdef\consPF{-5} \xdef\consPY{-5} \xdef\consPW{-6} +\xdef\consPB{-1} \xdef\consPZ{0} \xdef\consPX{-1} + +\xdef\consAC{-2} \xdef\consAS{1} \xdef\consAT{1} \xdef\consAP{1} \xdef\consAA{2} +\xdef\consAG{1} \xdef\consAN{0} \xdef\consAD{0} \xdef\consAE{0} \xdef\consAQ{0} +\xdef\consAH{-1} \xdef\consAR{-2} \xdef\consAK{-1} \xdef\consAM{-1} \xdef\consAI{-1} +\xdef\consAL{-2} \xdef\consAV{0} \xdef\consAF{-4} \xdef\consAY{-3} \xdef\consAW{-6} +\xdef\consAB{0} \xdef\consAZ{0} \xdef\consAX{0} + +\xdef\consGC{-3} \xdef\consGS{1} \xdef\consGT{0} \xdef\consGP{-1} \xdef\consGA{1} +\xdef\consGG{5} \xdef\consGN{0} \xdef\consGD{1} \xdef\consGE{0} \xdef\consGQ{-1} +\xdef\consGH{-2} \xdef\consGR{-3} \xdef\consGK{-2} \xdef\consGM{-3} \xdef\consGI{-3} +\xdef\consGL{-4} \xdef\consGV{-1} \xdef\consGF{-5} \xdef\consGY{-5} \xdef\consGW{-7} +\xdef\consGB{0} \xdef\consGZ{0} \xdef\consGX{-1} + +\xdef\consNC{-4} \xdef\consNS{1} \xdef\consNT{0} \xdef\consNP{-1} \xdef\consNA{0} +\xdef\consNG{0} \xdef\consNN{2} \xdef\consND{2} \xdef\consNE{1} \xdef\consNQ{1} +\xdef\consNH{2} \xdef\consNR{0} \xdef\consNK{1} \xdef\consNM{-2} \xdef\consNI{-2} +\xdef\consNL{-3} \xdef\consNV{-2} \xdef\consNF{-4} \xdef\consNY{-2} \xdef\consNW{-4} +\xdef\consNB{2} \xdef\consNZ{1} \xdef\consNX{0} + +\xdef\consDC{-5} \xdef\consDS{0} \xdef\consDT{0} \xdef\consDP{-1} \xdef\consDA{0} +\xdef\consDG{1} \xdef\consDN{2} \xdef\consDD{4} \xdef\consDE{3} \xdef\consDQ{2} +\xdef\consDH{1} \xdef\consDR{-1} \xdef\consDK{0} \xdef\consDM{-3} \xdef\consDI{-2} +\xdef\consDL{-4} \xdef\consDV{-2} \xdef\consDF{-6} \xdef\consDY{-4} \xdef\consDW{-7} +\xdef\consDB{3} \xdef\consDZ{3} \xdef\consDX{-1} + +\xdef\consEC{-5} \xdef\consES{0} \xdef\consET{0} \xdef\consEP{-1} \xdef\consEA{0} +\xdef\consEG{0} \xdef\consEN{1} \xdef\consED{3} \xdef\consEE{4} \xdef\consEQ{2} +\xdef\consEH{1} \xdef\consER{-1} \xdef\consEK{0} \xdef\consEM{-2} \xdef\consEI{-2} +\xdef\consEL{-3} \xdef\consEV{-2} \xdef\consEF{-5} \xdef\consEY{-4} \xdef\consEW{-7} +\xdef\consEB{3} \xdef\consEZ{3} \xdef\consEX{-1} + +\xdef\consQC{-5} \xdef\consQS{-1} \xdef\consQT{-1} \xdef\consQP{0} \xdef\consQA{0} +\xdef\consQG{-1} \xdef\consQN{1} \xdef\consQD{2} \xdef\consQE{2} \xdef\consQQ{4} +\xdef\consQH{3} \xdef\consQR{1} \xdef\consQK{1} \xdef\consQM{-1} \xdef\consQI{-2} +\xdef\consQL{-2} \xdef\consQV{-2} \xdef\consQF{-5} \xdef\consQY{-4} \xdef\consQW{-5} +\xdef\consQB{1} \xdef\consQZ{3} \xdef\consQX{-1} + +\xdef\consHC{-3} \xdef\consHS{-1} \xdef\consHT{-1} \xdef\consHP{0} \xdef\consHA{-1} +\xdef\consHG{-2} \xdef\consHN{2} \xdef\consHD{1} \xdef\consHE{1} \xdef\consHQ{3} +\xdef\consHH{6} \xdef\consHR{2} \xdef\consHK{0} \xdef\consHM{-2} \xdef\consHI{-2} +\xdef\consHL{-2} \xdef\consHV{-2} \xdef\consHF{-2} \xdef\consHY{-5} \xdef\consHW{-7} +\xdef\consHB{1} \xdef\consHZ{2} \xdef\consHX{-1} + +\xdef\consRC{-4} \xdef\consRS{0} \xdef\consRT{-1} \xdef\consRP{0} \xdef\consRA{-2} +\xdef\consRG{-3} \xdef\consRN{0} \xdef\consRD{-1} \xdef\consRE{-1} \xdef\consRQ{1} +\xdef\consRH{2} \xdef\consRR{6} \xdef\consRK{3} \xdef\consRM{0} \xdef\consRI{-2} +\xdef\consRL{-3} \xdef\consRV{-2} \xdef\consRF{-4} \xdef\consRY{-4} \xdef\consRW{2} +\xdef\consRB{-1} \xdef\consRZ{0} \xdef\consRX{-1} + +\xdef\consKC{-5} \xdef\consKS{0} \xdef\consKT{0} \xdef\consKP{-1} \xdef\consKA{-1} +\xdef\consKG{-2} \xdef\consKN{1} \xdef\consKD{0} \xdef\consKE{0} \xdef\consKQ{1} +\xdef\consKH{0} \xdef\consKR{3} \xdef\consKK{5} \xdef\consKM{0} \xdef\consKI{-2} +\xdef\consKL{-3} \xdef\consKV{-2} \xdef\consKF{-5} \xdef\consKY{-4} \xdef\consKW{-3} +\xdef\consKB{1} \xdef\consKZ{-2} \xdef\consKX{-1} + +\xdef\consMC{-5} \xdef\consMS{-2} \xdef\consMT{-1} \xdef\consMP{-2} \xdef\consMA{-1} +\xdef\consMG{-3} \xdef\consMN{-2} \xdef\consMD{-3} \xdef\consME{-2} \xdef\consMQ{-1} +\xdef\consMH{-2} \xdef\consMR{0} \xdef\consMK{0} \xdef\consMM{6} \xdef\consMI{2} +\xdef\consML{4} \xdef\consMV{2} \xdef\consMF{0} \xdef\consMY{-2} \xdef\consMW{-4} +\xdef\consMB{-2} \xdef\consMZ{-2} \xdef\consMX{-1} + +\xdef\consIC{-2} \xdef\consIS{-1} \xdef\consIT{0} \xdef\consIP{-2} \xdef\consIA{-1} +\xdef\consIG{-3} \xdef\consIN{-2} \xdef\consID{-2} \xdef\consIE{-2} \xdef\consIQ{-2} +\xdef\consIH{-2} \xdef\consIR{-2} \xdef\consIK{-2} \xdef\consIM{2} \xdef\consII{5} +\xdef\consIL{2} \xdef\consIV{4} \xdef\consIF{1} \xdef\consIY{-1} \xdef\consIW{-5} +\xdef\consIB{-2} \xdef\consIZ{-2} \xdef\consIX{-1} + +\xdef\consLC{-6} \xdef\consLS{-3} \xdef\consLT{-2} \xdef\consLP{-3} \xdef\consLA{-2} +\xdef\consLG{-4} \xdef\consLN{-3} \xdef\consLD{-4} \xdef\consLE{-3} \xdef\consLQ{-2} +\xdef\consLH{-2} \xdef\consLR{-3} \xdef\consLK{-3} \xdef\consLM{4} \xdef\consLI{2} +\xdef\consLL{6} \xdef\consLV{2} \xdef\consLF{2} \xdef\consLY{-1} \xdef\consLW{-2} +\xdef\consLB{-3} \xdef\consLZ{-3} \xdef\consLX{-1} + +\xdef\consVC{-2} \xdef\consVS{-1} \xdef\consVT{0} \xdef\consVP{-1} \xdef\consVA{0} +\xdef\consVG{-1} \xdef\consVN{-2} \xdef\consVD{-2} \xdef\consVE{-2} \xdef\consVQ{-2} +\xdef\consVH{-2} \xdef\consVR{-2} \xdef\consVK{-2} \xdef\consVM{2} \xdef\consVI{4} +\xdef\consVL{2} \xdef\consVV{4} \xdef\consVF{-1} \xdef\consVY{-2} \xdef\consVW{-6} +\xdef\consVB{-2} \xdef\consVZ{-2} \xdef\consVX{-1} + +\xdef\consFC{-4} \xdef\consFS{-3} \xdef\consFT{-2} \xdef\consFP{-5} \xdef\consFA{-4} +\xdef\consFG{-5} \xdef\consFN{-4} \xdef\consFD{-6} \xdef\consFE{-5} \xdef\consFQ{-5} +\xdef\consFH{-2} \xdef\consFR{-4} \xdef\consFK{-5} \xdef\consFM{0} \xdef\consFI{1} +\xdef\consFL{2} \xdef\consFV{-1} \xdef\consFF{9} \xdef\consFY{7} \xdef\consFW{0} +\xdef\consFB{-4} \xdef\consFZ{-5} \xdef\consFX{-2} + +\xdef\consYC{0} \xdef\consYS{-3} \xdef\consYT{-3} \xdef\consYP{-5} \xdef\consYA{-3} +\xdef\consYG{-5} \xdef\consYN{-2} \xdef\consYD{-4} \xdef\consYE{-4} \xdef\consYQ{-4} +\xdef\consYH{0} \xdef\consYR{-4} \xdef\consYK{-4} \xdef\consYM{-2} \xdef\consYI{-1} +\xdef\consYL{-1} \xdef\consYV{-2} \xdef\consYF{7} \xdef\consYY{10} \xdef\consYW{0} +\xdef\consYB{-3} \xdef\consYZ{-4} \xdef\consYX{-2} + +\xdef\consWC{-8} \xdef\consWS{-2} \xdef\consWT{-5} \xdef\consWP{-6} \xdef\consWA{-6} +\xdef\consWG{-7} \xdef\consWN{-4} \xdef\consWD{-7} \xdef\consWE{-7} \xdef\consWQ{-5} +\xdef\consWH{-3} \xdef\consWR{2} \xdef\consWK{-3} \xdef\consWM{-4} \xdef\consWI{-5} +\xdef\consWL{-2} \xdef\consWV{-6} \xdef\consWF{0} \xdef\consWY{0} \xdef\consWW{17} +\xdef\consWB{-5} \xdef\consWZ{-6} \xdef\consWX{-4} + +\xdef\consBC{-4} \xdef\consBS{0} \xdef\consBT{0} \xdef\consBP{-1} \xdef\consBA{0} +\xdef\consBG{0} \xdef\consBN{2} \xdef\consBD{3} \xdef\consBE{3} \xdef\consBQ{1} +\xdef\consBH{1} \xdef\consBR{-1} \xdef\consBK{1} \xdef\consBM{-2} \xdef\consBI{-2} +\xdef\consBL{-3} \xdef\consBV{-2} \xdef\consBF{-4} \xdef\consBY{-3} \xdef\consBW{-5} +\xdef\consBB{3} \xdef\consBZ{2} \xdef\consBX{-1} + +\xdef\consZC{-5} \xdef\consZS{0} \xdef\consZT{-1} \xdef\consZP{0} \xdef\consZA{0} +\xdef\consZG{0} \xdef\consZN{1} \xdef\consZD{3} \xdef\consZE{3} \xdef\consZQ{3} +\xdef\consZH{2} \xdef\consZR{0} \xdef\consZK{0} \xdef\consZM{-2} \xdef\consZI{-2} +\xdef\consZL{-3} \xdef\consZV{-2} \xdef\consZF{-5} \xdef\consZY{-4} \xdef\consZW{-6} +\xdef\consZB{2} \xdef\consZZ{3} \xdef\consZX{-1} + +\xdef\consXC{-3} \xdef\consXS{0} \xdef\consXT{0} \xdef\consXP{-1} \xdef\consXA{0} +\xdef\consXG{-1} \xdef\consXN{0} \xdef\consXD{-1} \xdef\consXE{-1} \xdef\consXQ{-1} +\xdef\consXH{-1} \xdef\consXR{-1} \xdef\consXK{-1} \xdef\consXM{-1} \xdef\consXI{-1} +\xdef\consXL{-1} \xdef\consXV{-1} \xdef\consXF{-2} \xdef\consXY{-2} \xdef\consXW{-4} +\xdef\consXB{-1} \xdef\consXZ{-1} \xdef\consXX{-1} + +\expandafter\xdef\csname cons..\endcsname{1} +\gappenalty{-8} \xdef\m@trixf@ctor{10} + +\else +\xdef\temp@{PAM100} \xdef\m@trixf@ctor{10} +\ifx\first@\temp@ + +%%%% PAM100 + +\xdef\consCC{14} \xdef\consCS{-1} \xdef\consCT{-5} \xdef\consCP{-6} \xdef\consCA{-5} +\xdef\consCG{-8} \xdef\consCN{-8} \xdef\consCD{-11} \xdef\consCE{-11} \xdef\consCQ{-11} +\xdef\consCH{-6} \xdef\consCR{-6} \xdef\consCK{-11} \xdef\consCM{-11} \xdef\consCI{-5} +\xdef\consCL{-12} \xdef\consCV{-4} \xdef\consCF{-10} \xdef\consCY{-2} \xdef\consCW{-13} +\xdef\consCB{-6} \xdef\consCZ{-8} \xdef\consCX{-5} + +\xdef\consSC{-1} \xdef\consSS{6} \xdef\consST{2} \xdef\consSP{1} \xdef\consSA{2} +\xdef\consSG{1} \xdef\consSN{2} \xdef\consSD{-1} \xdef\consSE{-2} \xdef\consSQ{-3} +\xdef\consSH{-4} \xdef\consSR{-1} \xdef\consSK{-2} \xdef\consSM{-4} \xdef\consSI{-4} +\xdef\consSL{-7} \xdef\consSV{-4} \xdef\consSF{-5} \xdef\consSY{-6} \xdef\consSW{-4} +\xdef\consSB{0} \xdef\consSZ{-2} \xdef\consSX{1} + +\xdef\consTC{-5} \xdef\consTS{2} \xdef\consTT{7} \xdef\consTP{-1} \xdef\consTA{2} +\xdef\consTG{-3} \xdef\consTN{0} \xdef\consTD{-2} \xdef\consTE{-3} \xdef\consTQ{-3} +\xdef\consTH{-5} \xdef\consTR{-4} \xdef\consTK{-1} \xdef\consTM{-2} \xdef\consTI{-1} +\xdef\consTL{-5} \xdef\consTV{-1} \xdef\consTF{-6} \xdef\consTY{-6} \xdef\consTW{-10} +\xdef\consTB{-1} \xdef\consTZ{-2} \xdef\consTX{-1} + +\xdef\consPC{-6} \xdef\consPS{1} \xdef\consPT{-1} \xdef\consPP{10} \xdef\consPA{1} +\xdef\consPG{-3} \xdef\consPN{-3} \xdef\consPD{-4} \xdef\consPE{-3} \xdef\consPQ{-1} +\xdef\consPH{-2} \xdef\consPR{-2} \xdef\consPK{-4} \xdef\consPM{-6} \xdef\consPI{-6} +\xdef\consPL{-5} \xdef\consPV{-4} \xdef\consPF{-9} \xdef\consPY{-11} \xdef\consPW{-11} +\xdef\consPB{-3} \xdef\consPZ{-1} \xdef\consPX{-2} + +\xdef\consAC{-5} \xdef\consAS{2} \xdef\consAT{2} \xdef\consAP{1} \xdef\consAA{6} +\xdef\consAG{1} \xdef\consAN{-1} \xdef\consAD{-1} \xdef\consAE{0} \xdef\consAQ{-2} +\xdef\consAH{-5} \xdef\consAR{-5} \xdef\consAK{-4} \xdef\consAM{-3} \xdef\consAI{-3} +\xdef\consAL{-5} \xdef\consAV{0} \xdef\consAF{-7} \xdef\consAY{-6} \xdef\consAW{-11} +\xdef\consAB{-1} \xdef\consAZ{-1} \xdef\consAX{-1} + +\xdef\consGC{-8} \xdef\consGS{1} \xdef\consGT{-3} \xdef\consGP{-3} \xdef\consGA{1} +\xdef\consGG{8} \xdef\consGN{-1} \xdef\consGD{-1} \xdef\consGE{-2} \xdef\consGQ{-5} +\xdef\consGH{-7} \xdef\consGR{-8} \xdef\consGK{-5} \xdef\consGM{-8} \xdef\consGI{-7} +\xdef\consGL{-8} \xdef\consGV{-4} \xdef\consGF{-8} \xdef\consGY{-11} \xdef\consGW{-13} +\xdef\consGB{-1} \xdef\consGZ{-2} \xdef\consGX{-2} + +\xdef\consNC{-8} \xdef\consNS{2} \xdef\consNT{0} \xdef\consNP{-3} \xdef\consNA{-1} +\xdef\consNG{-1} \xdef\consNN{7} \xdef\consND{4} \xdef\consNE{1} \xdef\consNQ{-1} +\xdef\consNH{2} \xdef\consNR{-3} \xdef\consNK{1} \xdef\consNM{-5} \xdef\consNI{-4} +\xdef\consNL{-6} \xdef\consNV{-5} \xdef\consNF{-6} \xdef\consNY{-3} \xdef\consNW{-8} +\xdef\consNB{4} \xdef\consNZ{0} \xdef\consNX{-1} + +\xdef\consDC{-11} \xdef\consDS{-1} \xdef\consDT{-2} \xdef\consDP{-4} \xdef\consDA{-1} +\xdef\consDG{-1} \xdef\consDN{4} \xdef\consDD{8} \xdef\consDE{5} \xdef\consDQ{1} +\xdef\consDH{-1} \xdef\consDR{-6} \xdef\consDK{-2} \xdef\consDM{-8} \xdef\consDI{-6} +\xdef\consDL{-9} \xdef\consDV{-6} \xdef\consDF{-11} \xdef\consDY{-9} \xdef\consDW{-13} +\xdef\consDB{4} \xdef\consDZ{3} \xdef\consDX{-2} + +\xdef\consEC{-11} \xdef\consES{-2} \xdef\consET{-3} \xdef\consEP{-3} \xdef\consEA{0} +\xdef\consEG{-2} \xdef\consEN{1} \xdef\consED{5} \xdef\consEE{8} \xdef\consEQ{4} +\xdef\consEH{-2} \xdef\consER{-5} \xdef\consEK{-2} \xdef\consEM{-6} \xdef\consEI{-5} +\xdef\consEL{-7} \xdef\consEV{-5} \xdef\consEF{-11} \xdef\consEY{-7} \xdef\consEW{-14} +\xdef\consEB{3} \xdef\consEZ{4} \xdef\consEX{-2} + +\xdef\consQC{-11} \xdef\consQS{-3} \xdef\consQT{-3} \xdef\consQP{-1} \xdef\consQA{-2} +\xdef\consQG{-5} \xdef\consQN{-1} \xdef\consQD{1} \xdef\consQE{4} \xdef\consQQ{9} +\xdef\consQH{4} \xdef\consQR{1} \xdef\consQK{-1} \xdef\consQM{-2} \xdef\consQI{-5} +\xdef\consQL{-3} \xdef\consQV{-5} \xdef\consQF{-10} \xdef\consQY{-9} \xdef\consQW{-11} +\xdef\consQB{0} \xdef\consQZ{5} \xdef\consQX{-2} + +\xdef\consHC{-6} \xdef\consHS{-4} \xdef\consHT{-5} \xdef\consHP{-2} \xdef\consHA{-5} +\xdef\consHG{-7} \xdef\consHN{2} \xdef\consHD{-1} \xdef\consHE{-2} \xdef\consHQ{4} +\xdef\consHH{11} \xdef\consHR{1} \xdef\consHK{-3} \xdef\consHM{-7} \xdef\consHI{-7} +\xdef\consHL{-5} \xdef\consHV{-6} \xdef\consHF{-4} \xdef\consHY{-1} \xdef\consHW{-7} +\xdef\consHB{1} \xdef\consHZ{1} \xdef\consHX{-2} + +\xdef\consRC{-6} \xdef\consRS{-1} \xdef\consRT{-4} \xdef\consRP{-2} \xdef\consRA{-5} +\xdef\consRG{-8} \xdef\consRN{-3} \xdef\consRD{-6} \xdef\consRE{-5} \xdef\consRQ{1} +\xdef\consRH{1} \xdef\consRR{10} \xdef\consRK{3} \xdef\consRM{-2} \xdef\consRI{-4} +\xdef\consRL{-7} \xdef\consRV{-6} \xdef\consRF{-7} \xdef\consRY{-10} \xdef\consRW{1} +\xdef\consRB{-3} \xdef\consRZ{-1} \xdef\consRX{-2} + +\xdef\consKC{-11} \xdef\consKS{-2} \xdef\consKT{-1} \xdef\consKP{-4} \xdef\consKA{-4} +\xdef\consKG{-5} \xdef\consKN{1} \xdef\consKD{-2} \xdef\consKE{-2} \xdef\consKQ{-1} +\xdef\consKH{-3} \xdef\consKR{3} \xdef\consKK{8} \xdef\consKM{1} \xdef\consKI{-4} +\xdef\consKL{-6} \xdef\consKV{-6} \xdef\consKF{-11} \xdef\consKY{-10} \xdef\consKW{-9} +\xdef\consKB{0} \xdef\consKZ{-1} \xdef\consKX{-2} + +\xdef\consMC{-11} \xdef\consMS{-4} \xdef\consMT{-2} \xdef\consMP{-6} \xdef\consMA{-3} +\xdef\consMG{-8} \xdef\consMN{-5} \xdef\consMD{-8} \xdef\consME{-6} \xdef\consMQ{-2} +\xdef\consMH{-7} \xdef\consMR{-2} \xdef\consMK{1} \xdef\consMM{13} \xdef\consMI{2} +\xdef\consML{4} \xdef\consMV{1} \xdef\consMF{-2} \xdef\consMY{-8} \xdef\consMW{-11} +\xdef\consMB{-4} \xdef\consMZ{-2} \xdef\consMX{-2} + +\xdef\consIC{-5} \xdef\consIS{-4} \xdef\consIT{-1} \xdef\consIP{-6} \xdef\consIA{-3} +\xdef\consIG{-7} \xdef\consIN{-4} \xdef\consID{-6} \xdef\consIE{-5} \xdef\consIQ{-5} +\xdef\consIH{-7} \xdef\consIR{-4} \xdef\consIK{-4} \xdef\consIM{2} \xdef\consII{9} +\xdef\consIL{2} \xdef\consIV{5} \xdef\consIF{0} \xdef\consIY{-4} \xdef\consIW{-12} +\xdef\consIB{-3} \xdef\consIZ{-3} \xdef\consIX{-2} + +\xdef\consLC{-12} \xdef\consLS{-7} \xdef\consLT{-5} \xdef\consLP{-5} \xdef\consLA{-5} +\xdef\consLG{-8} \xdef\consLN{-6} \xdef\consLD{-9} \xdef\consLE{-7} \xdef\consLQ{-3} +\xdef\consLH{-5} \xdef\consLR{-7} \xdef\consLK{-6} \xdef\consLM{4} \xdef\consLI{2} +\xdef\consLL{9} \xdef\consLV{1} \xdef\consLF{0} \xdef\consLY{-5} \xdef\consLW{-7} +\xdef\consLB{-5} \xdef\consLZ{-4} \xdef\consLX{-3} + +\xdef\consVC{-4} \xdef\consVS{-4} \xdef\consVT{-1} \xdef\consVP{-4} \xdef\consVA{0} +\xdef\consVG{-4} \xdef\consVN{-5} \xdef\consVD{-6} \xdef\consVE{-5} \xdef\consVQ{-5} +\xdef\consVH{-6} \xdef\consVR{-6} \xdef\consVK{-6} \xdef\consVM{1} \xdef\consVI{5} +\xdef\consVL{1} \xdef\consVV{8} \xdef\consVF{-5} \xdef\consVY{-6} \xdef\consVW{-14} +\xdef\consVB{-4} \xdef\consVZ{-3} \xdef\consVX{-2} + +\xdef\consFC{-10} \xdef\consFS{-5} \xdef\consFT{-6} \xdef\consFP{-9} \xdef\consFA{-7} +\xdef\consFG{-8} \xdef\consFN{-6} \xdef\consFD{-11} \xdef\consFE{-11} \xdef\consFQ{-10} +\xdef\consFH{-4} \xdef\consFR{-7} \xdef\consFK{-11} \xdef\consFM{-2} \xdef\consFI{0} +\xdef\consFL{0} \xdef\consFV{-5} \xdef\consFF{12} \xdef\consFY{6} \xdef\consFW{-2} +\xdef\consFB{-6} \xdef\consFZ{-7} \xdef\consFX{-4} + +\xdef\consYC{-2} \xdef\consYS{-6} \xdef\consYT{-6} \xdef\consYP{-11} \xdef\consYA{-6} +\xdef\consYG{-11} \xdef\consYN{-3} \xdef\consYD{-9} \xdef\consYE{-7} \xdef\consYQ{-9} +\xdef\consYH{-1} \xdef\consYR{-10} \xdef\consYK{-10} \xdef\consYM{-8} \xdef\consYI{-4} +\xdef\consYL{-5} \xdef\consYV{-6} \xdef\consYF{6} \xdef\consYY{13} \xdef\consYW{-2} +\xdef\consYB{-4} \xdef\consYZ{-6} \xdef\consYX{-4} + +\xdef\consWC{-13} \xdef\consWS{-4} \xdef\consWT{-10} \xdef\consWP{-11} \xdef\consWA{-11} +\xdef\consWG{-13} \xdef\consWN{-8} \xdef\consWD{-13} \xdef\consWE{-14} \xdef\consWQ{-11} +\xdef\consWH{-7} \xdef\consWR{1} \xdef\consWK{-9} \xdef\consWM{-11} \xdef\consWI{-12} +\xdef\consWL{-7} \xdef\consWV{-14} \xdef\consWF{-2} \xdef\consWY{-2} \xdef\consWW{19} +\xdef\consWB{-6} \xdef\consWZ{-8} \xdef\consWX{-6} + +\xdef\consBC{-6} \xdef\consBS{0} \xdef\consBT{-1} \xdef\consBP{-3} \xdef\consBA{-1} +\xdef\consBG{-1} \xdef\consBN{4} \xdef\consBD{4} \xdef\consBE{3} \xdef\consBQ{0} +\xdef\consBH{1} \xdef\consBR{-3} \xdef\consBK{0} \xdef\consBM{-4} \xdef\consBI{-3} +\xdef\consBL{-5} \xdef\consBV{-4} \xdef\consBF{-6} \xdef\consBY{-4} \xdef\consBW{-6} +\xdef\consBB{4} \xdef\consBZ{2} \xdef\consBX{-2} + +\xdef\consZC{-8} \xdef\consZS{-2} \xdef\consZT{-2} \xdef\consZP{-1} \xdef\consZA{-1} +\xdef\consZG{-2} \xdef\consZN{0} \xdef\consZD{3} \xdef\consZE{4} \xdef\consZQ{5} +\xdef\consZH{1} \xdef\consZR{-1} \xdef\consZK{-1} \xdef\consZM{-2} \xdef\consZI{-3} +\xdef\consZL{-4} \xdef\consZV{-3} \xdef\consZF{-7} \xdef\consZY{-6} \xdef\consZW{-8} +\xdef\consZB{2} \xdef\consZZ{5} \xdef\consZX{-2} + +\xdef\consXC{-5} \xdef\consXS{-1} \xdef\consXT{-1} \xdef\consXP{-2} \xdef\consXA{-1} +\xdef\consXG{-2} \xdef\consXN{-1} \xdef\consXD{-2} \xdef\consXE{-2} \xdef\consXQ{-2} +\xdef\consXH{-2} \xdef\consXR{-2} \xdef\consXK{-2} \xdef\consXM{-2} \xdef\consXI{-2} +\xdef\consXL{-3} \xdef\consXV{-2} \xdef\consXF{-4} \xdef\consXY{-4} \xdef\consXW{-6} +\xdef\consXB{-2} \xdef\consXZ{-2} \xdef\consXX{-2} + +\expandafter\xdef\csname cons..\endcsname{1} +\gappenalty{-9} \xdef\m@trixf@ctor{10} + +\else +\xdef\temp@{BLOSUM62} +\ifx\first@\temp@ + +%%%% BLOSUM62 + +\xdef\consCC{9} \xdef\consCS{-1} \xdef\consCT{-1} \xdef\consCP{-3} \xdef\consCA{0} +\xdef\consCG{-3} \xdef\consCN{-3} \xdef\consCD{-3} \xdef\consCE{-4} \xdef\consCQ{-3} +\xdef\consCH{-3} \xdef\consCR{-3} \xdef\consCK{-3} \xdef\consCM{-1} \xdef\consCI{-1} +\xdef\consCL{-1} \xdef\consCV{-1} \xdef\consCF{-2} \xdef\consCY{-2} \xdef\consCW{-2} + +\xdef\consSC{-1} \xdef\consSS{4} \xdef\consST{1} \xdef\consSP{-1} \xdef\consSA{1} +\xdef\consSG{0} \xdef\consSN{1} \xdef\consSD{0} \xdef\consSE{0} \xdef\consSQ{0} +\xdef\consSH{-1} \xdef\consSR{-1} \xdef\consSK{0} \xdef\consSM{-1} \xdef\consSI{-2} +\xdef\consSL{-2} \xdef\consSV{-2} \xdef\consSF{-2} \xdef\consSY{-2} \xdef\consSW{-3} + +\xdef\consTC{-1} \xdef\consTS{1} \xdef\consTT{4} \xdef\consTP{1} \xdef\consTA{-1} +\xdef\consTG{1} \xdef\consTN{0} \xdef\consTD{1} \xdef\consTE{0} \xdef\consTQ{0} +\xdef\consTH{0} \xdef\consTR{-1} \xdef\consTK{0} \xdef\consTM{-1} \xdef\consTI{-2} +\xdef\consTL{-2} \xdef\consTV{-2} \xdef\consTF{-2} \xdef\consTY{-2} \xdef\consTW{-3} + +\xdef\consPC{-3} \xdef\consPS{-1} \xdef\consPT{1} \xdef\consPP{7} \xdef\consPA{-1} +\xdef\consPG{-2} \xdef\consPN{-1} \xdef\consPD{-1} \xdef\consPE{-1} \xdef\consPQ{-1} +\xdef\consPH{-2} \xdef\consPR{-2} \xdef\consPK{-1} \xdef\consPM{-2} \xdef\consPI{-3} +\xdef\consPL{-3} \xdef\consPV{-2} \xdef\consPF{-4} \xdef\consPY{-3} \xdef\consPW{-4} + +\xdef\consAC{0} \xdef\consAS{1} \xdef\consAT{-1} \xdef\consAP{-1} \xdef\consAA{4} +\xdef\consAG{0} \xdef\consAN{-1} \xdef\consAD{-2} \xdef\consAE{-1} \xdef\consAQ{-1} +\xdef\consAH{-2} \xdef\consAR{-1} \xdef\consAK{-1} \xdef\consAM{-1} \xdef\consAI{-1} +\xdef\consAL{-1} \xdef\consAV{-2} \xdef\consAF{-2} \xdef\consAY{-2} \xdef\consAW{-3} + +\xdef\consGC{-3} \xdef\consGS{0} \xdef\consGT{1} \xdef\consGP{-2} \xdef\consGA{0} +\xdef\consGG{6} \xdef\consGN{-2} \xdef\consGD{-1} \xdef\consGE{-2} \xdef\consGQ{-2} +\xdef\consGH{-2} \xdef\consGR{-2} \xdef\consGK{-2} \xdef\consGM{-3} \xdef\consGI{-4} +\xdef\consGL{-4} \xdef\consGV{0} \xdef\consGF{-3} \xdef\consGY{-3} \xdef\consGW{-2} + +\xdef\consNC{-3} \xdef\consNS{1} \xdef\consNT{0} \xdef\consNP{-2} \xdef\consNA{-2} +\xdef\consNG{0} \xdef\consNN{6} \xdef\consND{1} \xdef\consNE{0} \xdef\consNQ{0} +\xdef\consNH{-1} \xdef\consNR{0} \xdef\consNK{0} \xdef\consNM{-2} \xdef\consNI{-3} +\xdef\consNL{-3} \xdef\consNV{-3} \xdef\consNF{-3} \xdef\consNY{-2} \xdef\consNW{-4} + +\xdef\consDC{-3} \xdef\consDS{0} \xdef\consDT{1} \xdef\consDP{-1} \xdef\consDA{-2} +\xdef\consDG{-1} \xdef\consDN{1} \xdef\consDD{6} \xdef\consDE{2} \xdef\consDQ{0} +\xdef\consDH{-1} \xdef\consDR{-2} \xdef\consDK{-1} \xdef\consDM{-3} \xdef\consDI{-3} +\xdef\consDL{-4} \xdef\consDV{-3} \xdef\consDF{-3} \xdef\consDY{-3} \xdef\consDW{-4} + +\xdef\consEC{-4} \xdef\consES{0} \xdef\consET{0} \xdef\consEP{-1} \xdef\consEA{-1} +\xdef\consEG{-2} \xdef\consEN{0} \xdef\consED{2} \xdef\consEE{5} \xdef\consEQ{2} +\xdef\consEH{0} \xdef\consER{0} \xdef\consEK{1} \xdef\consEM{-2} \xdef\consEI{-3} +\xdef\consEL{-3} \xdef\consEV{-3} \xdef\consEF{-3} \xdef\consEY{-2} \xdef\consEW{-3} + +\xdef\consQC{-3} \xdef\consQS{0} \xdef\consQT{0} \xdef\consQP{-1} \xdef\consQA{-1} +\xdef\consQG{-2} \xdef\consQN{0} \xdef\consQD{0} \xdef\consQE{2} \xdef\consQQ{5} +\xdef\consQH{0} \xdef\consQR{1} \xdef\consQK{1} \xdef\consQM{0} \xdef\consQI{-3} +\xdef\consQL{-2} \xdef\consQV{-2} \xdef\consQF{-3} \xdef\consQY{-1} \xdef\consQW{-2} + +\xdef\consHC{-3} \xdef\consHS{-1} \xdef\consHT{0} \xdef\consHP{-2} \xdef\consHA{-2} +\xdef\consHG{-2} \xdef\consHN{1} \xdef\consHD{1} \xdef\consHE{0} \xdef\consHQ{0} +\xdef\consHH{8} \xdef\consHR{0} \xdef\consHK{-1} \xdef\consHM{-2} \xdef\consHI{-3} +\xdef\consHL{-3} \xdef\consHV{-2} \xdef\consHF{-1} \xdef\consHY{2} \xdef\consHW{-2} + +\xdef\consRC{-3} \xdef\consRS{-1} \xdef\consRT{-1} \xdef\consRP{-2} \xdef\consRA{-1} +\xdef\consRG{-2} \xdef\consRN{0} \xdef\consRD{-2} \xdef\consRE{0} \xdef\consRQ{1} +\xdef\consRH{0} \xdef\consRR{5} \xdef\consRK{2} \xdef\consRM{-1} \xdef\consRI{-3} +\xdef\consRL{-2} \xdef\consRV{-3} \xdef\consRF{-3} \xdef\consRY{-2} \xdef\consRW{-3} + +\xdef\consKC{-3} \xdef\consKS{0} \xdef\consKT{0} \xdef\consKP{-1} \xdef\consKA{-1} +\xdef\consKG{-2} \xdef\consKN{0} \xdef\consKD{-1} \xdef\consKE{1} \xdef\consKQ{1} +\xdef\consKH{-1} \xdef\consKR{2} \xdef\consKK{5} \xdef\consKM{-1} \xdef\consKI{-3} +\xdef\consKL{-2} \xdef\consKV{-3} \xdef\consKF{-3} \xdef\consKY{-2} \xdef\consKW{-3} + +\xdef\consMC{-1} \xdef\consMS{-1} \xdef\consMT{-1} \xdef\consMP{-2} \xdef\consMA{-1} +\xdef\consMG{-3} \xdef\consMN{-2} \xdef\consMD{-3} \xdef\consME{-2} \xdef\consMQ{0} +\xdef\consMH{-2} \xdef\consMR{-1} \xdef\consMK{-1} \xdef\consMM{5} \xdef\consMI{1} +\xdef\consML{2} \xdef\consMV{-2} \xdef\consMF{0} \xdef\consMY{-1} \xdef\consMW{-1} + +\xdef\consIC{-1} \xdef\consIS{-2} \xdef\consIT{-2} \xdef\consIP{-3} \xdef\consIA{-1} +\xdef\consIG{-4} \xdef\consIN{-3} \xdef\consID{-3} \xdef\consIE{-3} \xdef\consIQ{-3} +\xdef\consIH{-3} \xdef\consIR{-3} \xdef\consIK{-3} \xdef\consIM{1} \xdef\consII{4} +\xdef\consIL{2} \xdef\consIV{1} \xdef\consIF{0} \xdef\consIY{-1} \xdef\consIW{-3} + +\xdef\consLC{-1} \xdef\consLS{-2} \xdef\consLT{-2} \xdef\consLP{-3} \xdef\consLA{-1} +\xdef\consLG{-4} \xdef\consLN{-3} \xdef\consLD{-4} \xdef\consLE{-3} \xdef\consLQ{-2} +\xdef\consLH{-3} \xdef\consLR{-2} \xdef\consLK{-2} \xdef\consLM{2} \xdef\consLI{2} +\xdef\consLL{4} \xdef\consLV{3} \xdef\consLF{0} \xdef\consLY{-1} \xdef\consLW{-2} + +\xdef\consVC{-1} \xdef\consVS{-2} \xdef\consVT{-2} \xdef\consVP{-2} \xdef\consVA{0} +\xdef\consVG{-3} \xdef\consVN{-3} \xdef\consVD{-3} \xdef\consVE{-2} \xdef\consVQ{-2} +\xdef\consVH{-3} \xdef\consVR{-3} \xdef\consVK{-2} \xdef\consVM{1} \xdef\consVI{3} +\xdef\consVL{1} \xdef\consVV{4} \xdef\consVF{-1} \xdef\consVY{-1} \xdef\consVW{-3} + +\xdef\consFC{-2} \xdef\consFS{-2} \xdef\consFT{-2} \xdef\consFP{-4} \xdef\consFA{-2} +\xdef\consFG{-3} \xdef\consFN{-3} \xdef\consFD{-3} \xdef\consFE{-3} \xdef\consFQ{-3} +\xdef\consFH{-1} \xdef\consFR{-3} \xdef\consFK{-3} \xdef\consFM{0} \xdef\consFI{0} +\xdef\consFL{0} \xdef\consFV{-1} \xdef\consFF{6} \xdef\consFY{3} \xdef\consFW{1} + +\xdef\consYC{-2} \xdef\consYS{-2} \xdef\consYT{-2} \xdef\consYP{-3} \xdef\consYA{-2} +\xdef\consYG{-3} \xdef\consYN{-2} \xdef\consYD{-3} \xdef\consYE{-2} \xdef\consYQ{-1} +\xdef\consYH{2} \xdef\consYR{-2} \xdef\consYK{-2} \xdef\consYM{-1} \xdef\consYI{-1} +\xdef\consYL{-1} \xdef\consYV{-1} \xdef\consYF{3} \xdef\consYY{7} \xdef\consYW{2} + +\xdef\consWC{-2} \xdef\consWS{-3} \xdef\consWT{-3} \xdef\consWP{-4} \xdef\consWA{-3} +\xdef\consWG{-2} \xdef\consWN{-4} \xdef\consWD{-4} \xdef\consWE{-3} \xdef\consWQ{-2} +\xdef\consWH{-2} \xdef\consWR{-3} \xdef\consWK{-3} \xdef\consWM{-1} \xdef\consWI{-3} +\xdef\consWL{-2} \xdef\consWV{-3} \xdef\consWF{1} \xdef\consWY{2} \xdef\consWW{11} + +\gappenalty{0} \xdef\m@trixf@ctor{10} + +\else + +\message{<Unknown residue weight matrix - using `identity'>} \weighttable{identity} + +\fi +\fi +\fi +\fi +\fi +} + + +\def\setweight#1#2#3{% + \expandafter\xdef\csname cons#1#2\endcsname{#3} + \expandafter\xdef\csname cons#2#1\endcsname{#3} +} + +\weighttable{identity} +\gappenalty{0} + + +\def\c@d@ns{% +\codon{A}{GCA,GCG,GCC,GCT,GCU,GCN} +\codon{B}{---} +\codon{C}{TGC,TGT,UGC,UGU,TGY} +\codon{D}{GAC,GAT,GAU,GAY} +\codon{E}{GAA,GAG,GAR} +\codon{F}{TTC,TTT,UUC,UUU,TTY} +\codon{G}{GGA,GGG,GGC,GGT,GGU,GGN} +\codon{H}{CAC,CAT,CAY} +\codon{I}{ATA,ATC,ATT,AUA,AUC,AUU,ATH} +\codon{J}{---} +\codon{K}{AAA,AAG,AAG,AAR} +\codon{L}{CTA,CTG,CTC,CTT,TTA,TTG,CUG,CUG,CUC,CUU,UUA,UUG,YTN} +\codon{M}{ATG,AUG,ATG} +\codon{N}{AAC,AAT,AAU,AAY} +\codon{O}{---} +\codon{P}{CCA,CCG,CCC,CCT,CCU,CCN} +\codon{Q}{CAA,CAG,CAR} +\codon{R}{AGA,AGG,CGA,CGG,CGC,CGT,CGU,MGN} +\codon{S}{TCT,TCC,TCG,TCA,AGT,AGC,UCU,UCC,UCG,UCA,AGU,WSN} +\codon{T}{ACT,ACC,ACG,ACA,ACU,ACN} +\codon{U}{---} +\codon{V}{GTA,GTG,GTC,GTT,GUA,GUG,GUC,GUU,GTN} +\codon{W}{TGG,UGG,TGG} +\codon{X}{---} +\codon{Y}{TAC,TAT,UAC,UAU,TAY} +\codon{Z}{---} +\codon{.}{TAA,TAG,TGA,UAA,UAG,UGA,TRR} +} + +\definecolor{GreenYellow} {cmyk}{0.15,0,0.69,0} +\definecolor{Yellow} {cmyk}{0,0,1,0} +\definecolor{Goldenrod} {cmyk}{0,0.10,0.84,0} +\definecolor{Dandelion} {cmyk}{0,0.29,0.84,0} +\definecolor{Apricot} {cmyk}{0,0.32,0.52,0} +\definecolor{Peach} {cmyk}{0,0.50,0.70,0} +\definecolor{Melon} {cmyk}{0,0.46,0.50,0} +\definecolor{YellowOrange} {cmyk}{0,0.42,1,0} +\definecolor{Orange} {cmyk}{0,0.61,0.87,0} +\definecolor{BurntOrange} {cmyk}{0,0.51,1,0} +\definecolor{Bittersweet} {cmyk}{0,0.75,1,0.24} +\definecolor{RedOrange} {cmyk}{0,0.77,0.87,0} +\definecolor{Mahagony} {cmyk}{0,0.85,0.87,0.35} +\definecolor{Maroon} {cmyk}{0,0.87,0.68,0.32} +\definecolor{BrickRed} {cmyk}{0,0.89,0.94,0.28} +\definecolor{Red} {cmyk}{0,1,1,0} +\definecolor{OrangeRed} {cmyk}{0,1,0.50,0} +\definecolor{RubineRed} {cmyk}{0,1,0.13,0} +\definecolor{WildStrawberry}{cmyk}{0,0.96,0.39,0} +\definecolor{Salmon} {cmyk}{0,0.53,0.38,0} +\definecolor{CarnationPink} {cmyk}{0,0.63,0,0} +\definecolor{Magenta} {cmyk}{0,1,0,0} +\definecolor{VioletRed} {cmyk}{0,0.81,0,0} +\definecolor{Rhodamine} {cmyk}{0,0.82,0,0} +\definecolor{Mulberry} {cmyk}{0.34,0.90,0,0.02} +\definecolor{RedViolet} {cmyk}{0.07,0.90,0,0.34} +\definecolor{Fuchsia} {cmyk}{0.47,0.91,0,0.08} +\definecolor{Lavender} {cmyk}{0,0.48,0,0} +\definecolor{Thistle} {cmyk}{0.12,0.59,0,0} +\definecolor{Orchid} {cmyk}{0.32,0.64,0,0} +\definecolor{DarkOrchid} {cmyk}{0.40,0.80,0.20,0} +\definecolor{Purple} {cmyk}{0.45,0.86,0,0} +\definecolor{Plum} {cmyk}{0.50,1,0,0} +\definecolor{Violet} {cmyk}{0.79,0.88,0,0} +\definecolor{RoyalPurple} {cmyk}{0.75,0.90,0,0} +\definecolor{BlueViolet} {cmyk}{0.86,0.91,0,0.04} +\definecolor{Periwinkle} {cmyk}{0.57,0.55,0,0} +\definecolor{CadetBlue} {cmyk}{0.62,0.57,0.23,0} +\definecolor{CornflowerBlue}{cmyk}{0.65,0.13,0,0} +\definecolor{MidnightBlue} {cmyk}{0.98,0.13,0,0.43} +\definecolor{NavyBlue} {cmyk}{0.94,0.54,0,0} +\definecolor{RoyalBlue} {cmyk}{1,0.50,0,0} +\definecolor{Blue} {cmyk}{1,1,0,0} +\definecolor{Cerulean} {cmyk}{0.94,0.11,0,0} +\definecolor{Cyan} {cmyk}{1,0,0,0} +\definecolor{ProcessBlue} {cmyk}{0.96,0,0,0} +\definecolor{SkyBlue} {cmyk}{0.62,0,0.12,0} +\definecolor{Turquoise} {cmyk}{0.85,0,0.20,0} +\definecolor{TealBlue} {cmyk}{0.86,0,0.34,0.02} +\definecolor{Aquamarine} {cmyk}{0.82,0,0.30,0} +\definecolor{BlueGreen} {cmyk}{0.85,0,0.33,0} +\definecolor{Emerald} {cmyk}{1,0,0.50,0} +\definecolor{JungleGreen} {cmyk}{0.99,0,0.52,0} +\definecolor{SeaGreen} {cmyk}{0.69,0,0.50,0} +\definecolor{Green} {cmyk}{1,0,1,0} +\definecolor{ForestGreen} {cmyk}{0.91,0,0.88,0.12} +\definecolor{PineGreen} {cmyk}{0.92,0,0.59,0.25} +\definecolor{LimeGreen} {cmyk}{0.50,0,1,0} +\definecolor{YellowGreen} {cmyk}{0.44,0,0.74,0} +\definecolor{SpringGreen} {cmyk}{0.26,0,0.76,0} +\definecolor{OliveGreen} {cmyk}{0.64,0,0.95,0.40} +\definecolor{RawSienna} {cmyk}{0,0.72,1,0.45} +\definecolor{Sepia} {cmyk}{0,0.83,1,0.70} +\definecolor{Brown} {cmyk}{0,0.81,1,0.60} +\definecolor{Tan} {cmyk}{0.14,0.42,0.56,0} +\definecolor{White} {cmyk}{0,0,0,0} +\definecolor{Gray0} {cmyk}{0,0,0,0} +\definecolor{Gray5} {cmyk}{0,0,0,0.05} +\definecolor{Gray10} {cmyk}{0,0,0,0.10} +\definecolor{Gray15} {cmyk}{0,0,0,0.15} +\definecolor{Gray20} {cmyk}{0,0,0,0.20} +\definecolor{Gray25} {cmyk}{0,0,0,0.25} +\definecolor{Gray30} {cmyk}{0,0,0,0.30} +\definecolor{LightGray} {cmyk}{0,0,0,0.33} +\definecolor{Gray35} {cmyk}{0,0,0,0.35} +\definecolor{Gray40} {cmyk}{0,0,0,0.40} +\definecolor{Gray45} {cmyk}{0,0,0,0.45} +\definecolor{Gray50} {cmyk}{0,0,0,0.50} +\definecolor{Gray} {cmyk}{0,0,0,0.50} +\definecolor{GrayDefault} {cmyk}{0,0,0,0.50} +\definecolor{Gray55} {cmyk}{0,0,0,0.55} +\definecolor{Gray60} {cmyk}{0,0,0,0.60} +\definecolor{Gray65} {cmyk}{0,0,0,0.65} +\definecolor{DarkGray} {cmyk}{0,0,0,0.66} +\definecolor{Gray70} {cmyk}{0,0,0,0.70} +\definecolor{Gray75} {cmyk}{0,0,0,0.75} +\definecolor{Gray80} {cmyk}{0,0,0,0.80} +\definecolor{Gray85} {cmyk}{0,0,0,0.85} +\definecolor{Gray90} {cmyk}{0,0,0,0.90} +\definecolor{Gray95} {cmyk}{0,0,0,0.95} +\definecolor{Black} {cmyk}{0,0,0,1} +\definecolor{Gray100} {cmyk}{0,0,0,1} +\definecolor{TC0} {cmyk}{0.4,0.4,0,0} +\definecolor{TC1} {cmyk}{0.6,0,0.7,0} +\definecolor{TC2} {cmyk}{0.4,0,0.7,0} +\definecolor{TC3} {cmyk}{0.2,0,1,0} +\definecolor{TC4} {cmyk}{0,0,1,0} +\definecolor{TC5} {cmyk}{0,0.2,1,0} +\definecolor{TC6} {cmyk}{0,0.4,1,0} +\definecolor{TC7} {cmyk}{0,0.6,1,0} +\definecolor{TC8} {cmyk}{0,0.8,1,0} +\definecolor{TC9} {cmyk}{0,0.875,1,0} +\definecolor{TC99} {cmyk}{0,0,0,0} +\definecolor{LightGreenYellow} {cmyk}{0.08,0,0.35,0} +\definecolor{LightYellow} {cmyk}{0,0,0.50,0} +\definecolor{LightGoldenrod} {cmyk}{0,0.05,0.42,0} +\definecolor{LightDandelion} {cmyk}{0,0.15,0.42,0} +\definecolor{LightApricot} {cmyk}{0,0.16,0.26,0} +\definecolor{LightPeach} {cmyk}{0,0.25,0.35,0} +\definecolor{LightMelon} {cmyk}{0,0.23,0.25,0} +\definecolor{LightYellowOrange} {cmyk}{0,0.21,0.50,0} +\definecolor{LightOrange} {cmyk}{0,0.31,0.44,0} +\definecolor{LightBurntOrange} {cmyk}{0,0.26,0.50,0} +\definecolor{LightBittersweet} {cmyk}{0,0.38,0.50,0.12} +\definecolor{LightRedOrange} {cmyk}{0,0.39,0.44,0} +\definecolor{LightMahagony} {cmyk}{0,0.43,0.44,0.18} +\definecolor{LightMaroon} {cmyk}{0,0.44,0.34,0.16} +\definecolor{LightBrickRed} {cmyk}{0,0.45,0.47,0.14} +\definecolor{LightRed} {cmyk}{0,0.50,0.50,0} +\definecolor{LightOrangeRed} {cmyk}{0,0.50,0.25,0} +\definecolor{LightRubineRed} {cmyk}{0,0.50,0.07,0} +\definecolor{LightWildStrawberry}{cmyk}{0,0.48,0.20,0} +\definecolor{LightSalmon} {cmyk}{0,0.27,0.19,0} +\definecolor{LightCarnationPink} {cmyk}{0,0.32,0,0} +\definecolor{LightMagenta} {cmyk}{0,0.50,0,0} +\definecolor{LightVioletRed} {cmyk}{0,0.40,0,0} +\definecolor{LightRhodamine} {cmyk}{0,0.41,0,0} +\definecolor{LightMulberry} {cmyk}{0.17,0.45,0,0.01} +\definecolor{LightRedViolet} {cmyk}{0.04,0.45,0,0.17} +\definecolor{LightFuchsia} {cmyk}{0.24,0.46,0,0.04} +\definecolor{LightLavender} {cmyk}{0,0.24,0,0} +\definecolor{LightThistle} {cmyk}{0.06,0.30,0,0} +\definecolor{LightOrchid} {cmyk}{0.16,0.32,0,0} +\definecolor{LightDarkOrchid} {cmyk}{0.20,0.40,0.10,0} +\definecolor{LightPurple} {cmyk}{0.23,0.43,0,0} +\definecolor{LightPlum} {cmyk}{0.25,0.50,0,0} +\definecolor{LightViolet} {cmyk}{0.40,0.44,0,0} +\definecolor{LightRoyalPurple} {cmyk}{0.38,0.45,0,0} +\definecolor{LightBlueViolet} {cmyk}{0.43,0.46,0,0.02} +\definecolor{LightPeriwinkle} {cmyk}{0.29,0.28,0,0} +\definecolor{LightCadetBlue} {cmyk}{0.31,0.29,0.12,0} +\definecolor{LightCornflowerBlue}{cmyk}{0.33,0.07,0,0} +\definecolor{LightMidnightBlue} {cmyk}{0.49,0.07,0,0.22} +\definecolor{LightNavyBlue} {cmyk}{0.47,0.27,0,0} +\definecolor{LightRoyalBlue} {cmyk}{0.50,0.25,0,0} +\definecolor{LightBlue} {cmyk}{0.50,0.50,0,0} +\definecolor{LightCerulean} {cmyk}{0.47,0.06,0,0} +\definecolor{LightCyan} {cmyk}{0.50,0,0,0} +\definecolor{LightProcessBlue} {cmyk}{0.48,0,0,0} +\definecolor{LightSkyBlue} {cmyk}{0.31,0,0.06,0} +\definecolor{LightTurquoise} {cmyk}{0.43,0,0.10,0} +\definecolor{LightTealBlue} {cmyk}{0.43,0,0.17,0.01} +\definecolor{LightAquamarine} {cmyk}{0.41,0,0.15,0} +\definecolor{LightBlueGreen} {cmyk}{0.43,0,0.17,0} +\definecolor{LightEmerald} {cmyk}{0.50,0,0.25,0} +\definecolor{LightJungleGreen} {cmyk}{0.50,0,0.26,0} +\definecolor{LightSeaGreen} {cmyk}{0.35,0,0.25,0} +\definecolor{LightGreen} {cmyk}{0.50,0,0.50,0} +\definecolor{LightForestGreen} {cmyk}{0.46,0,0.44,0.06} +\definecolor{LightPineGreen} {cmyk}{0.46,0,0.30,0.13} +\definecolor{LightLimeGreen} {cmyk}{0.25,0,0.50,0} +\definecolor{LightYellowGreen} {cmyk}{0.22,0,0.37,0} +\definecolor{LightSpringGreen} {cmyk}{0.13,0,0.38,0} +\definecolor{LightOliveGreen} {cmyk}{0.32,0,0.48,0.20} +\definecolor{LightRawSienna} {cmyk}{0,0.36,0.50,0.23} +\definecolor{LightSepia} {cmyk}{0,0.44,0.50,0.35} +\definecolor{LightBrown} {cmyk}{0,0.41,0.50,0.30} +\definecolor{LightTan} {cmyk}{0.07,0.21,0.28,0} +\definecolor{LightWhite} {cmyk}{0,0,0,0} +\definecolor{LightGray0} {cmyk}{0,0,0,0} +\definecolor{LightGray5} {cmyk}{0,0,0,0.02} +\definecolor{LightGray10} {cmyk}{0,0,0,0.05} +\definecolor{LightGray15} {cmyk}{0,0,0,0.07} +\definecolor{LightGray20} {cmyk}{0,0,0,0.10} +\definecolor{LightGray25} {cmyk}{0,0,0,0.12} +\definecolor{LightGray30} {cmyk}{0,0,0,0.15} +\definecolor{LightLightGray} {cmyk}{0,0,0,0.16} +\definecolor{LightGray35} {cmyk}{0,0,0,0.17} +\definecolor{LightGray40} {cmyk}{0,0,0,0.20} +\definecolor{LightGray45} {cmyk}{0,0,0,0.22} +\definecolor{LightGray50} {cmyk}{0,0,0,0.25} +\definecolor{LightGray} {cmyk}{0,0,0,0.25} +\definecolor{LightGray55} {cmyk}{0,0,0,0.27} +\definecolor{LightGray60} {cmyk}{0,0,0,0.30} +\definecolor{LightGray65} {cmyk}{0,0,0,0.32} +\definecolor{LightDarkGray} {cmyk}{0,0,0,0.33} +\definecolor{LightGray70} {cmyk}{0,0,0,0.35} +\definecolor{LightGray75} {cmyk}{0,0,0,0.37} +\definecolor{LightGray80} {cmyk}{0,0,0,0.40} +\definecolor{LightGray85} {cmyk}{0,0,0,0.42} +\definecolor{LightGray90} {cmyk}{0,0,0,0.45} +\definecolor{LightGray95} {cmyk}{0,0,0,0.47} +\definecolor{LightBlack} {cmyk}{0,0,0,0.50} +\definecolor{LightGray100} {cmyk}{0,0,0,0.50} +\definecolor{LightTC0} {cmyk}{0.2,0.2,0,0} +\definecolor{LightTC1} {cmyk}{0.3,0,0.35,0} +\definecolor{LightTC2} {cmyk}{0.2,0,0.35,0} +\definecolor{LightTC3} {cmyk}{0.1,0,0.5,0} +\definecolor{LightTC4} {cmyk}{0,0,0.5,0} +\definecolor{LightTC5} {cmyk}{0,0.1,0.5,0} +\definecolor{LightTC6} {cmyk}{0,0.2,0.5,0} +\definecolor{LightTC7} {cmyk}{0,0.3,0.5,0} +\definecolor{LightTC8} {cmyk}{0,0.4,0.5,0} +\definecolor{LightTC99} {cmyk}{0,0,0,0} +\definecolor{LightLightGreenYellow} {cmyk}{0.04,0,0.17,0} +\definecolor{LightLightYellow} {cmyk}{0,0,0.25,0} +\definecolor{LightLightGoldenrod} {cmyk}{0,0.02,0.21,0} +\definecolor{LightLightDandelion} {cmyk}{0,0.07,0.21,0} +\definecolor{LightLightApricot} {cmyk}{0,0.08,0.13,0} +\definecolor{LightLightPeach} {cmyk}{0,0.12,0.17,0} +\definecolor{LightLightMelon} {cmyk}{0,0.11,0.12,0} +\definecolor{LightLightYellowOrange} {cmyk}{0,0.10,0.25,0} +\definecolor{LightLightOrange} {cmyk}{0,0.15,0.22,0} +\definecolor{LightLightBurntOrange} {cmyk}{0,0.13,0.25,0} +\definecolor{LightLightBittersweet} {cmyk}{0,0.19,0.25,0.06} +\definecolor{LightLightRedOrange} {cmyk}{0,0.14,0.22,0} +\definecolor{LightLightMahagony} {cmyk}{0,0.21,0.22,0.09} +\definecolor{LightLightMaroon} {cmyk}{0,0.22,0.17,0.08} +\definecolor{LightLightBrickRed} {cmyk}{0,0.22,0.23,0.07} +\definecolor{LightLightRed} {cmyk}{0,0.25,0.25,0} +\definecolor{LightLightOrangeRed} {cmyk}{0,0.25,0.12,0} +\definecolor{LightLightRubineRed} {cmyk}{0,0.25,0.03,0} +\definecolor{LightLightWildStrawberry}{cmyk}{0,0.24,0.10,0} +\definecolor{LightLightSalmon} {cmyk}{0,0.13,0.09,0} +\definecolor{LightLightCarnationPink} {cmyk}{0,0.16,0,0} +\definecolor{LightLightMagenta} {cmyk}{0,0.25,0,0} +\definecolor{LightLightVioletRed} {cmyk}{0,0.20,0,0} +\definecolor{LightLightRhodamine} {cmyk}{0,0.20,0,0} +\definecolor{LightLightMulberry} {cmyk}{0.08,0.22,0,0.005} +\definecolor{LightLightRedViolet} {cmyk}{0.02,0.22,0,0.08} +\definecolor{LightLightFuchsia} {cmyk}{0.12,0.23,0,0.02} +\definecolor{LightLightLavender} {cmyk}{0,0.12,0,0} +\definecolor{LightLightThistle} {cmyk}{0.03,0.15,0,0} +\definecolor{LightLightOrchid} {cmyk}{0.08,0.16,0,0} +\definecolor{LightLightDarkOrchid} {cmyk}{0.10,0.20,0.05,0} +\definecolor{LightLightPurple} {cmyk}{0.11,0.21,0,0} +\definecolor{LightLightPlum} {cmyk}{0.12,0.25,0,0} +\definecolor{LightLightViolet} {cmyk}{0.20,0.22,0,0} +\definecolor{LightLightRoyalPurple} {cmyk}{0.19,0.22,0,0} +\definecolor{LightLightBlueViolet} {cmyk}{0.21,0.23,0,0.01} +\definecolor{LightLightPeriwinkle} {cmyk}{0.14,0.14,0,0} +\definecolor{LightLightCadetBlue} {cmyk}{0.15,0.14,0.06,0} +\definecolor{LightLightCornflowerBlue}{cmyk}{0.16,0.03,0,0} +\definecolor{LightLightMidnightBlue} {cmyk}{0.24,0.03,0,0.11} +\definecolor{LightLightNavyBlue} {cmyk}{0.23,0.13,0,0} +\definecolor{LightLightRoyalBlue} {cmyk}{0.25,0.12,0,0} +\definecolor{LightLightBlue} {cmyk}{0.25,0.25,0,0} +\definecolor{LightLightCerulean} {cmyk}{0.23,0.03,0,0} +\definecolor{LightLightCyan} {cmyk}{0.25,0,0,0} +\definecolor{LightLightProcessBlue} {cmyk}{0.24,0,0,0} +\definecolor{LightLightSkyBlue} {cmyk}{0.15,0,0.03,0} +\definecolor{LightLightTurquoise} {cmyk}{0.21,0,0.05,0} +\definecolor{LightLightTealBlue} {cmyk}{0.21,0,0.08,0.005} +\definecolor{LightLightAquamarine} {cmyk}{0.20,0,0.07,0} +\definecolor{LightLightBlueGreen} {cmyk}{0.21,0,0.08,0} +\definecolor{LightLightEmerald} {cmyk}{0.25,0,0.12,0} +\definecolor{LightLightJungleGreen} {cmyk}{0.25,0,0.13,0} +\definecolor{LightLightSeaGreen} {cmyk}{0.17,0,0.12,0} +\definecolor{LightLightGreen} {cmyk}{0.25,0,0.25,0} +\definecolor{LightLightForestGreen} {cmyk}{0.23,0,0.22,0.03} +\definecolor{LightLightPineGreen} {cmyk}{0.23,0,0.15,0.06} +\definecolor{LightLightLimeGreen} {cmyk}{0.12,0,0.25,0} +\definecolor{LightLightYellowGreen} {cmyk}{0.11,0,0.18,0} +\definecolor{LightLightSpringGreen} {cmyk}{0.06,0,0.19,0} +\definecolor{LightLightOliveGreen} {cmyk}{0.16,0,0.24,0.10} +\definecolor{LightLightRawSienna} {cmyk}{0,0.18,0.25,0.11} +\definecolor{LightLightSepia} {cmyk}{0,0.22,0.25,0.17} +\definecolor{LightLightBrown} {cmyk}{0,0.20,0.25,0.15} +\definecolor{LightLightTan} {cmyk}{0.03,0.10,0.14,0} +\definecolor{LightLightWhite} {cmyk}{0,0,0,0} +\definecolor{LightLightGray0} {cmyk}{0,0,0,0} +\definecolor{LightLightGray5} {cmyk}{0,0,0,0.01} +\definecolor{LightLightGray10} {cmyk}{0,0,0,0.02} +\definecolor{LightLightGray15} {cmyk}{0,0,0,0.03} +\definecolor{LightLightGray20} {cmyk}{0,0,0,0.05} +\definecolor{LightLightGray25} {cmyk}{0,0,0,0.06} +\definecolor{LightLightGray30} {cmyk}{0,0,0,0.07} +\definecolor{LightLightLightGray} {cmyk}{0,0,0,0.08} +\definecolor{LightLightGray35} {cmyk}{0,0,0,0.09} +\definecolor{LightLightGray40} {cmyk}{0,0,0,0.10} +\definecolor{LightLightGray45} {cmyk}{0,0,0,0.11} +\definecolor{LightLightGray50} {cmyk}{0,0,0,0.12} +\definecolor{LightLightGray} {cmyk}{0,0,0,0.13} +\definecolor{LightLightGray55} {cmyk}{0,0,0,0.14} +\definecolor{LightLightGray60} {cmyk}{0,0,0,0.15} +\definecolor{LightLightGray65} {cmyk}{0,0,0,0.16} +\definecolor{LightLightDarkGray} {cmyk}{0,0,0,0.17} +\definecolor{LightLightGray70} {cmyk}{0,0,0,0.18} +\definecolor{LightLightGray75} {cmyk}{0,0,0,0.19} +\definecolor{LightLightGray80} {cmyk}{0,0,0,0.20} +\definecolor{LightLightGray85} {cmyk}{0,0,0,0.21} +\definecolor{LightLightGray90} {cmyk}{0,0,0,0.22} +\definecolor{LightLightGray95} {cmyk}{0,0,0,0.23} +\definecolor{LightLightBlack} {cmyk}{0,0,0,0.25} +\definecolor{LightLightGray100} {cmyk}{0,0,0,0.25} +\definecolor{LightLightTC0} {cmyk}{0.1,0.1,0,0} +\definecolor{LightLightTC1} {cmyk}{0.15,0,0.175,0} +\definecolor{LightLightTC2} {cmyk}{0.1,0,0.175,0} +\definecolor{LightLightTC3} {cmyk}{0.05,0,0.25,0} +\definecolor{LightLightTC4} {cmyk}{0,0,0.25,0} +\definecolor{LightLightTC5} {cmyk}{0,0.05,0.25,0} +\definecolor{LightLightTC6} {cmyk}{0,0.1,0.25,0} +\definecolor{LightLightTC7} {cmyk}{0,0.15,0.25,0} +\definecolor{LightLightTC8} {cmyk}{0,0.2,0.25,0} +\definecolor{LightLightTC99} {cmyk}{0,0,0,0} +\definecolor{LightLightLightGreenYellow} {cmyk}{0.02,0,0.08,0} +\definecolor{LightLightLightYellow} {cmyk}{0,0,0.12,0} +\definecolor{LightLightLightGoldenrod} {cmyk}{0,0.01,0.10,0} +\definecolor{LightLightLightDandelion} {cmyk}{0,0.03,0.10,0} +\definecolor{LightLightLightApricot} {cmyk}{0,0.04,0.06,0} +\definecolor{LightLightLightPeach} {cmyk}{0,0.06,0.08,0} +\definecolor{LightLightLightMelon} {cmyk}{0,0.05,0.06,0} +\definecolor{LightLightLightYellowOrange} {cmyk}{0,0.05,0.12,0} +\definecolor{LightLightLightOrange} {cmyk}{0,0.07,0.11,0} +\definecolor{LightLightLightBurntOrange} {cmyk}{0,0.06,0.12,0} +\definecolor{LightLightLightBittersweet} {cmyk}{0,0.09,0.12,0.03} +\definecolor{LightLightLightRedOrange} {cmyk}{0,0.07,0.11,0} +\definecolor{LightLightLightMahagony} {cmyk}{0,0.10,0.11,0.04} +\definecolor{LightLightLightMaroon} {cmyk}{0,0.11,0.08,0.04} +\definecolor{LightLightLightBrickRed} {cmyk}{0,0.11,0.11,0.03} +\definecolor{LightLightLightRed} {cmyk}{0,0.12,0.12,0} +\definecolor{LightLightLightOrangeRed} {cmyk}{0,0.12,0.06,0} +\definecolor{LightLightLightRubineRed} {cmyk}{0,0.12,0.01,0} +\definecolor{LightLightLightWildStrawberry}{cmyk}{0,0.12,0.05,0} +\definecolor{LightLightLightSalmon} {cmyk}{0,0.06,0.04,0} +\definecolor{LightLightLightCarnationPink} {cmyk}{0,0.08,0,0} +\definecolor{LightLightLightMagenta} {cmyk}{0,0.12,0,0} +\definecolor{LightLightLightLightMagenta} {cmyk}{0,0.06,0,0} +\definecolor{LightLightLightVioletRed} {cmyk}{0,0.10,0,0} +\definecolor{LightLightLightRhodamine} {cmyk}{0,0.10,0,0} +\definecolor{LightLightLightMulberry} {cmyk}{0.04,0.11,0,0.002} +\definecolor{LightLightLightRedViolet} {cmyk}{0.01,0.11,0,0.04} +\definecolor{LightLightLightFuchsia} {cmyk}{0.06,0.11,0,0.01} +\definecolor{LightLightLightLavender} {cmyk}{0,0.06,0,0} +\definecolor{LightLightLightThistle} {cmyk}{0.01,0.07,0,0} +\definecolor{LightLightLightOrchid} {cmyk}{0.04,0.08,0,0} +\definecolor{LightLightLightDarkOrchid} {cmyk}{0.05,0.10,0.02,0} +\definecolor{LightLightLightPurple} {cmyk}{0.05,0.10,0,0} +\definecolor{LightLightLightPlum} {cmyk}{0.06,0.12,0,0} +\definecolor{LightLightLightViolet} {cmyk}{0.10,0.11,0,0} +\definecolor{LightLightLightRoyalPurple} {cmyk}{0.09,0.11,0,0} +\definecolor{LightLightLightBlueViolet} {cmyk}{0.10,0.11,0,0.005} +\definecolor{LightLightLightPeriwinkle} {cmyk}{0.07,0.07,0,0} +\definecolor{LightLightLightCadetBlue} {cmyk}{0.07,0.07,0.03,0} +\definecolor{LightLightLightCornflowerBlue}{cmyk}{0.08,0.01,0,0} +\definecolor{LightLightLightMidnightBlue} {cmyk}{0.12,0.01,0,0.05} +\definecolor{LightLightLightNavyBlue} {cmyk}{0.11,0.06,0,0} +\definecolor{LightLightLightRoyalBlue} {cmyk}{0.12,0.06,0,0} +\definecolor{LightLightLightBlue} {cmyk}{0.12,0.12,0,0} +\definecolor{LightLightLightCerulean} {cmyk}{0.11,0.01,0,0} +\definecolor{LightLightLightCyan} {cmyk}{0.12,0,0,0} +\definecolor{LightLightLightProcessBlue} {cmyk}{0.12,0,0,0} +\definecolor{LightLightLightSkyBlue} {cmyk}{0.07,0,0.01,0} +\definecolor{LightLightLightTurquoise} {cmyk}{0.10,0,0.02,0} +\definecolor{LightLightLightTealBlue} {cmyk}{0.10,0,0.04,0.002} +\definecolor{LightLightLightAquamarine} {cmyk}{0.10,0,0.03,0} +\definecolor{LightLightLightBlueGreen} {cmyk}{0.10,0,0.04,0} +\definecolor{LightLightLightEmerald} {cmyk}{0.12,0,0.06,0} +\definecolor{LightLightLightJungleGreen} {cmyk}{0.12,0,0.06,0} +\definecolor{LightLightLightSeaGreen} {cmyk}{0.08,0,0.06,0} +\definecolor{LightLightLightGreen} {cmyk}{0.12,0,0.12,0} +\definecolor{LightLightLightForestGreen} {cmyk}{0.11,0,0.11,0.01} +\definecolor{LightLightLightPineGreen} {cmyk}{0.11,0,0.07,0.03} +\definecolor{LightLightLightLimeGreen} {cmyk}{0.06,0,0.12,0} +\definecolor{LightLightLightYellowGreen} {cmyk}{0.05,0,0.09,0} +\definecolor{LightLightLightSpringGreen} {cmyk}{0.03,0,0.09,0} +\definecolor{LightLightLightOliveGreen} {cmyk}{0.08,0,0.12,0.05} +\definecolor{LightLightLightRawSienna} {cmyk}{0,0.09,0.12,0.05} +\definecolor{LightLightLightSepia} {cmyk}{0,0.11,0.12,0.06} +\definecolor{LightLightLightBrown} {cmyk}{0,0.10,0.12,0.07} +\definecolor{LightLightLightTan} {cmyk}{0.01,0.05,0.07,0} +\definecolor{LightLightLightWhite} {cmyk}{0,0,0,0} +\definecolor{LightLightLightGray0} {cmyk}{0,0,0,0} +\definecolor{LightLightLightGray5} {cmyk}{0,0,0,0.005} +\definecolor{LightLightLightGray10} {cmyk}{0,0,0,0.01} +\definecolor{LightLightLightGray15} {cmyk}{0,0,0,0.015} +\definecolor{LightLightLightGray20} {cmyk}{0,0,0,0.025} +\definecolor{LightLightLightGray25} {cmyk}{0,0,0,0.03} +\definecolor{LightLightLightGray30} {cmyk}{0,0,0,0.035} +\definecolor{LightLightLightLightGray} {cmyk}{0,0,0,0.04} +\definecolor{LightLightLightGray35} {cmyk}{0,0,0,0.045} +\definecolor{LightLightLightGray40} {cmyk}{0,0,0,0.05} +\definecolor{LightLightLightGray45} {cmyk}{0,0,0,0.055} +\definecolor{LightLightLightGray50} {cmyk}{0,0,0,0.06} +\definecolor{LightLightLightGray} {cmyk}{0,0,0,0.065} +\definecolor{LightLightLightGray55} {cmyk}{0,0,0,0.07} +\definecolor{LightLightLightGray60} {cmyk}{0,0,0,0.075} +\definecolor{LightLightLightGray65} {cmyk}{0,0,0,0.08} +\definecolor{LightLightLightDarkGray} {cmyk}{0,0,0,0.085} +\definecolor{LightLightLightGray70} {cmyk}{0,0,0,0.09} +\definecolor{LightLightLightGray75} {cmyk}{0,0,0,0.095} +\definecolor{LightLightLightGray80} {cmyk}{0,0,0,0.10} +\definecolor{LightLightLightGray85} {cmyk}{0,0,0,0.105} +\definecolor{LightLightLightGray90} {cmyk}{0,0,0,0.11} +\definecolor{LightLightLightGray95} {cmyk}{0,0,0,0.115} +\definecolor{LightLightLightBlack} {cmyk}{0,0,0,0.12} +\definecolor{LightLightLightGray100} {cmyk}{0,0,0,0.125} +\definecolor{LightLightLightTC0} {cmyk}{0.05,0.05,0,0} +\definecolor{LightLightLightTC1} {cmyk}{0.075,0,0.086,0} +\definecolor{LightLightLightTC2} {cmyk}{0.05,0,0.086,0} +\definecolor{LightLightLightTC3} {cmyk}{0.025,0,0.125,0} +\definecolor{LightLightLightTC4} {cmyk}{0,0,0.125,0} +\definecolor{LightLightLightTC5} {cmyk}{0,0.025,0.125,0} +\definecolor{LightLightLightTC6} {cmyk}{0,0.05,0.125,0} +\definecolor{LightLightLightTC7} {cmyk}{0,0.0175,0.125,0} +\definecolor{LightLightLightTC8} {cmyk}{0,0.1,0.125,0} +\definecolor{LightLightLightTC99} {cmyk}{0,0,0,0} +\definecolor{BlueRed5} {rgb} {0.15,0.17,0.55} +\definecolor{BlueRed10} {rgb} {0.20,0.23,0.57} +\definecolor{BlueRed15} {rgb} {0.24,0.29,0.60} +\definecolor{BlueRed20} {rgb} {0.33,0.35,0.64} +\definecolor{BlueRed25} {rgb} {0.43,0.43,0.68} +\definecolor{BlueRed30} {rgb} {0.52,0.52,0.73} +\definecolor{BlueRed35} {rgb} {0.60,0.60,0.78} +\definecolor{BlueRed40} {rgb} {0.70,0.70,0.84} +\definecolor{BlueRed45} {rgb} {0.80,0.80,0.85} +\definecolor{BlueRed50} {rgb} {0.86,0.82,0.82} +\definecolor{BlueRed55} {rgb} {0.87,0.73,0.73} +\definecolor{BlueRed60} {rgb} {0.89,0.64,0.64} +\definecolor{BlueRed65} {rgb} {0.90,0.55,0.55} +\definecolor{BlueRed70} {rgb} {0.91,0.47,0.46} +\definecolor{BlueRed75} {rgb} {0.91,0.39,0.37} +\definecolor{BlueRed80} {rgb} {0.90,0.33,0.28} +\definecolor{BlueRed85} {rgb} {0.89,0.25,0.20} +\definecolor{BlueRed90} {rgb} {0.88,0.23,0.14} +\definecolor{BlueRed95} {rgb} {0.87,0.21,0.09} +\definecolor{BlueRed100} {rgb} {0.87,0.16,0.04} +\definecolor{RedBlue100} {rgb} {0.15,0.17,0.55} +\definecolor{RedBlue95} {rgb} {0.15,0.17,0.55} +\definecolor{RedBlue90} {rgb} {0.20,0.23,0.57} +\definecolor{RedBlue85} {rgb} {0.24,0.29,0.60} +\definecolor{RedBlue80} {rgb} {0.33,0.35,0.64} +\definecolor{RedBlue75} {rgb} {0.43,0.43,0.68} +\definecolor{RedBlue70} {rgb} {0.52,0.52,0.73} +\definecolor{RedBlue65} {rgb} {0.60,0.60,0.78} +\definecolor{RedBlue60} {rgb} {0.70,0.70,0.84} +\definecolor{RedBlue55} {rgb} {0.80,0.80,0.85} +\definecolor{RedBlue50} {rgb} {0.86,0.82,0.82} +\definecolor{RedBlue45} {rgb} {0.87,0.73,0.73} +\definecolor{RedBlue40} {rgb} {0.89,0.64,0.64} +\definecolor{RedBlue35} {rgb} {0.90,0.55,0.55} +\definecolor{RedBlue30} {rgb} {0.91,0.47,0.46} +\definecolor{RedBlue25} {rgb} {0.91,0.39,0.37} +\definecolor{RedBlue20} {rgb} {0.90,0.33,0.28} +\definecolor{RedBlue15} {rgb} {0.89,0.25,0.20} +\definecolor{RedBlue10} {rgb} {0.88,0.23,0.14} +\definecolor{RedBlue5} {rgb} {0.87,0.21,0.09} +\definecolor{GreenRed5} {rgb} {0,1,0} +\definecolor{GreenRed10} {rgb} {0.05,0.95,0} +\definecolor{GreenRed15} {rgb} {0.10,0.90,0} +\definecolor{GreenRed20} {rgb} {0.15,0.85,0} +\definecolor{GreenRed25} {rgb} {0.20,0.80,0} +\definecolor{GreenRed30} {rgb} {0.25,0.75,0} +\definecolor{GreenRed35} {rgb} {0.30,0.70,0} +\definecolor{GreenRed40} {rgb} {0.35,0.65,0} +\definecolor{GreenRed45} {rgb} {0.40,0.60,0} +\definecolor{GreenRed50} {rgb} {0.45,0.55,0} +\definecolor{GreenRed55} {rgb} {0.50,0.50,0} +\definecolor{GreenRed60} {rgb} {0.55,0.45,0} +\definecolor{GreenRed65} {rgb} {0.60,0.40,0} +\definecolor{GreenRed70} {rgb} {0.65,0.35,0} +\definecolor{GreenRed75} {rgb} {0.70,0.30,0} +\definecolor{GreenRed80} {rgb} {0.75,0.25,0} +\definecolor{GreenRed85} {rgb} {0.80,0.20,0} +\definecolor{GreenRed90} {rgb} {0.85,0.15,0} +\definecolor{GreenRed95} {rgb} {0.90,0.10,0} +\definecolor{GreenRed100} {rgb} {0.95,0.05,0} +\definecolor{RedGreen100} {rgb} {0.05,0.95,0} +\definecolor{RedGreen95} {rgb} {0.10,0.90,0} +\definecolor{RedGreen90} {rgb} {0.15,0.85,0} +\definecolor{RedGreen85} {rgb} {0.20,0.80,0} +\definecolor{RedGreen80} {rgb} {0.25,0.75,0} +\definecolor{RedGreen75} {rgb} {0.30,0.70,0} +\definecolor{RedGreen70} {rgb} {0.35,0.65,0} +\definecolor{RedGreen65} {rgb} {0.40,0.60,0} +\definecolor{RedGreen60} {rgb} {0.45,0.55,0} +\definecolor{RedGreen55} {rgb} {0.50,0.50,0} +\definecolor{RedGreen50} {rgb} {0.55,0.45,0} +\definecolor{RedGreen45} {rgb} {0.60,0.40,0} +\definecolor{RedGreen40} {rgb} {0.65,0.35,0} +\definecolor{RedGreen35} {rgb} {0.70,0.30,0} +\definecolor{RedGreen30} {rgb} {0.75,0.25,0} +\definecolor{RedGreen25} {rgb} {0.80,0.20,0} +\definecolor{RedGreen20} {rgb} {0.85,0.15,0} +\definecolor{RedGreen15} {rgb} {0.90,0.10,0} +\definecolor{RedGreen10} {rgb} {0.95,0.05,0} +\definecolor{RedGreen5} {rgb} {1,0,0} +\definecolor{ColdHot5} {rgb} {0,0.08,1} +\definecolor{ColdHot10} {rgb} {0,0.29,1} +\definecolor{ColdHot15} {rgb} {0,0.49,1} +\definecolor{ColdHot20} {rgb} {0,0.70,1} +\definecolor{ColdHot25} {rgb} {0,0.90,1} +\definecolor{ColdHot30} {rgb} {0,1,0.87} +\definecolor{ColdHot35} {rgb} {0,1,0.68} +\definecolor{ColdHot40} {rgb} {0,1,0.46} +\definecolor{ColdHot45} {rgb} {0,1,0.25} +\definecolor{ColdHot50} {rgb} {0,1,0.04} +\definecolor{ColdHot55} {rgb} {0.16,1,0} +\definecolor{ColdHot60} {rgb} {0.35,1,0} +\definecolor{ColdHot65} {rgb} {0.56,1,0} +\definecolor{ColdHot70} {rgb} {0.79,1,0} +\definecolor{ColdHot75} {rgb} {0.98,1,0} +\definecolor{ColdHot80} {rgb} {1,0.82,0} +\definecolor{ColdHot85} {rgb} {1,0.60,0} +\definecolor{ColdHot90} {rgb} {1,0.40,0} +\definecolor{ColdHot95} {rgb} {1,0.20,0} +\definecolor{ColdHot100} {rgb} {0.91,0,0} +\definecolor{HotCold100} {rgb} {0,0.08,1} +\definecolor{HotCold95} {rgb} {0,0.29,1} +\definecolor{HotCold90} {rgb} {0,0.49,1} +\definecolor{HotCold85} {rgb} {0,0.70,1} +\definecolor{HotCold80} {rgb} {0,0.90,1} +\definecolor{HotCold75} {rgb} {0,1,0.87} +\definecolor{HotCold70} {rgb} {0,1,0.68} +\definecolor{HotCold65} {rgb} {0,1,0.46} +\definecolor{HotCold60} {rgb} {0,1,0.25} +\definecolor{HotCold55} {rgb} {0,1,0.04} +\definecolor{HotCold50} {rgb} {0.16,1,0} +\definecolor{HotCold45} {rgb} {0.35,1,0} +\definecolor{HotCold40} {rgb} {0.56,1,0} +\definecolor{HotCold35} {rgb} {0.79,1,0} +\definecolor{HotCold30} {rgb} {0.98,1,0} +\definecolor{HotCold25} {rgb} {1,0.82,0} +\definecolor{HotCold20} {rgb} {1,0.60,0} +\definecolor{HotCold15} {rgb} {1,0.40,0} +\definecolor{HotCold10} {rgb} {1,0.20,0} +\definecolor{HotCold5} {rgb} {0.91,0,0} +\expandafter\def\csname BlueRed5\endcsname{[0.15,0.17,0.55]} +\expandafter\def\csname BlueRed10\endcsname{[0.20,0.23,0.57]} +\expandafter\def\csname BlueRed15\endcsname{[0.24,0.29,0.60]} +\expandafter\def\csname BlueRed20\endcsname{[0.33,0.35,0.64]} +\expandafter\def\csname BlueRed25\endcsname{[0.43,0.43,0.68]} +\expandafter\def\csname BlueRed30\endcsname{[0.52,0.52,0.73]} +\expandafter\def\csname BlueRed35\endcsname{[0.60,0.60,0.78]} +\expandafter\def\csname BlueRed40\endcsname{[0.70,0.70,0.84]} +\expandafter\def\csname BlueRed45\endcsname{[0.80,0.80,0.85]} +\expandafter\def\csname BlueRed50\endcsname{[0.86,0.82,0.82]} +\expandafter\def\csname BlueRed55\endcsname{[0.87,0.73,0.73]} +\expandafter\def\csname BlueRed60\endcsname{[0.89,0.64,0.64]} +\expandafter\def\csname BlueRed65\endcsname{[0.90,0.55,0.55]} +\expandafter\def\csname BlueRed70\endcsname{[0.91,0.47,0.46]} +\expandafter\def\csname BlueRed75\endcsname{[0.91,0.39,0.37]} +\expandafter\def\csname BlueRed80\endcsname{[0.90,0.33,0.28]} +\expandafter\def\csname BlueRed85\endcsname{[0.89,0.25,0.20]} +\expandafter\def\csname BlueRed90\endcsname{[0.88,0.23,0.14]} +\expandafter\def\csname BlueRed95\endcsname{[0.87,0.21,0.09]} +\expandafter\def\csname BlueRed100\endcsname{[0.87,0.16,0.04]} +\expandafter\def\csname RedBlue100\endcsname{[0.15,0.17,0.55]} +\expandafter\def\csname RedBlue95\endcsname{[0.15,0.17,0.55]} +\expandafter\def\csname RedBlue90\endcsname{[0.20,0.23,0.57]} +\expandafter\def\csname RedBlue85\endcsname{[0.24,0.29,0.60]} +\expandafter\def\csname RedBlue80\endcsname{[0.33,0.35,0.64]} +\expandafter\def\csname RedBlue75\endcsname{[0.43,0.43,0.68]} +\expandafter\def\csname RedBlue70\endcsname{[0.52,0.52,0.73]} +\expandafter\def\csname RedBlue65\endcsname{[0.60,0.60,0.78]} +\expandafter\def\csname RedBlue60\endcsname{[0.70,0.70,0.84]} +\expandafter\def\csname RedBlue55\endcsname{[0.80,0.80,0.85]} +\expandafter\def\csname RedBlue50\endcsname{[0.86,0.82,0.82]} +\expandafter\def\csname RedBlue45\endcsname{[0.87,0.73,0.73]} +\expandafter\def\csname RedBlue40\endcsname{[0.89,0.64,0.64]} +\expandafter\def\csname RedBlue35\endcsname{[0.90,0.55,0.55]} +\expandafter\def\csname RedBlue30\endcsname{[0.91,0.47,0.46]} +\expandafter\def\csname RedBlue25\endcsname{[0.91,0.39,0.37]} +\expandafter\def\csname RedBlue20\endcsname{[0.90,0.33,0.28]} +\expandafter\def\csname RedBlue15\endcsname{[0.89,0.25,0.20]} +\expandafter\def\csname RedBlue10\endcsname{[0.88,0.23,0.14]} +\expandafter\def\csname RedBlue5\endcsname{[0.87,0.21,0.09]} +\expandafter\def\csname GreenRed5\endcsname{[0,1,0]} +\expandafter\def\csname GreenRed10\endcsname{[0.05,0.95,0]} +\expandafter\def\csname GreenRed15\endcsname{[0.10,0.90,0]} +\expandafter\def\csname GreenRed20\endcsname{[0.15,0.85,0]} +\expandafter\def\csname GreenRed25\endcsname{[0.20,0.80,0]} +\expandafter\def\csname GreenRed30\endcsname{[0.25,0.75,0]} +\expandafter\def\csname GreenRed35\endcsname{[0.30,0.70,0]} +\expandafter\def\csname GreenRed40\endcsname{[0.35,0.65,0]} +\expandafter\def\csname GreenRed45\endcsname{[0.40,0.60,0]} +\expandafter\def\csname GreenRed50\endcsname{[0.45,0.55,0]} +\expandafter\def\csname GreenRed55\endcsname{[0.50,0.50,0]} +\expandafter\def\csname GreenRed60\endcsname{[0.55,0.45,0]} +\expandafter\def\csname GreenRed65\endcsname{[0.60,0.40,0]} +\expandafter\def\csname GreenRed70\endcsname{[0.65,0.35,0]} +\expandafter\def\csname GreenRed75\endcsname{[0.70,0.30,0]} +\expandafter\def\csname GreenRed80\endcsname{[0.75,0.25,0]} +\expandafter\def\csname GreenRed85\endcsname{[0.80,0.20,0]} +\expandafter\def\csname GreenRed90\endcsname{[0.85,0.15,0]} +\expandafter\def\csname GreenRed95\endcsname{[0.90,0.10,0]} +\expandafter\def\csname GreenRed100\endcsname{[0.95,0.05,0]} +\expandafter\def\csname RedGreen100\endcsname{[0.05,0.95,0]} +\expandafter\def\csname RedGreen95\endcsname{[0.10,0.90,0]} +\expandafter\def\csname RedGreen90\endcsname{[0.15,0.85,0]} +\expandafter\def\csname RedGreen85\endcsname{[0.20,0.80,0]} +\expandafter\def\csname RedGreen80\endcsname{[0.25,0.75,0]} +\expandafter\def\csname RedGreen75\endcsname{[0.30,0.70,0]} +\expandafter\def\csname RedGreen70\endcsname{[0.35,0.65,0]} +\expandafter\def\csname RedGreen65\endcsname{[0.40,0.60,0]} +\expandafter\def\csname RedGreen60\endcsname{[0.45,0.55,0]} +\expandafter\def\csname RedGreen55\endcsname{[0.50,0.50,0]} +\expandafter\def\csname RedGreen50\endcsname{[0.55,0.45,0]} +\expandafter\def\csname RedGreen45\endcsname{[0.60,0.40,0]} +\expandafter\def\csname RedGreen40\endcsname{[0.65,0.35,0]} +\expandafter\def\csname RedGreen35\endcsname{[0.70,0.30,0]} +\expandafter\def\csname RedGreen30\endcsname{[0.75,0.25,0]} +\expandafter\def\csname RedGreen25\endcsname{[0.80,0.20,0]} +\expandafter\def\csname RedGreen20\endcsname{[0.85,0.15,0]} +\expandafter\def\csname RedGreen15\endcsname{[0.90,0.10,0]} +\expandafter\def\csname RedGreen10\endcsname{[0.95,0.05,0]} +\expandafter\def\csname RedGreen5\endcsname{[1,0,0]} +\expandafter\def\csname ColdHot5\endcsname{[0,0.08,1]} +\expandafter\def\csname ColdHot10\endcsname{[0,0.29,1]} +\expandafter\def\csname ColdHot15\endcsname{[0,0.49,1]} +\expandafter\def\csname ColdHot20\endcsname{[0,0.70,1]} +\expandafter\def\csname ColdHot25\endcsname{[0,0.90,1]} +\expandafter\def\csname ColdHot30\endcsname{[0,1,0.87]} +\expandafter\def\csname ColdHot35\endcsname{[0,1,0.68]} +\expandafter\def\csname ColdHot40\endcsname{[0,1,0.46]} +\expandafter\def\csname ColdHot45\endcsname{[0,1,0.25]} +\expandafter\def\csname ColdHot50\endcsname{[0,1,0.04]} +\expandafter\def\csname ColdHot55\endcsname{[0.16,1,0]} +\expandafter\def\csname ColdHot60\endcsname{[0.35,1,0]} +\expandafter\def\csname ColdHot65\endcsname{[0.56,1,0]} +\expandafter\def\csname ColdHot70\endcsname{[0.79,1,0]} +\expandafter\def\csname ColdHot75\endcsname{[0.98,1,0]} +\expandafter\def\csname ColdHot80\endcsname{[1,0.82,0]} +\expandafter\def\csname ColdHot85\endcsname{[1,0.60,0]} +\expandafter\def\csname ColdHot90\endcsname{[1,0.40,0]} +\expandafter\def\csname ColdHot95\endcsname{[1,0.20,0]} +\expandafter\def\csname ColdHot100\endcsname{[0.91,0,0]} +\expandafter\def\csname HotCold100\endcsname{[0,0.08,1]} +\expandafter\def\csname HotCold95\endcsname{[0,0.29,1]} +\expandafter\def\csname HotCold90\endcsname{[0,0.49,1]} +\expandafter\def\csname HotCold85\endcsname{[0,0.70,1]} +\expandafter\def\csname HotCold80\endcsname{[0,0.90,1]} +\expandafter\def\csname HotCold75\endcsname{[0,1,0.87]} +\expandafter\def\csname HotCold70\endcsname{[0,1,0.68]} +\expandafter\def\csname HotCold65\endcsname{[0,1,0.46]} +\expandafter\def\csname HotCold60\endcsname{[0,1,0.25]} +\expandafter\def\csname HotCold55\endcsname{[0,1,0.04]} +\expandafter\def\csname HotCold50\endcsname{[0.16,1,0]} +\expandafter\def\csname HotCold45\endcsname{[0.35,1,0]} +\expandafter\def\csname HotCold40\endcsname{[0.56,1,0]} +\expandafter\def\csname HotCold35\endcsname{[0.79,1,0]} +\expandafter\def\csname HotCold30\endcsname{[0.98,1,0]} +\expandafter\def\csname HotCold25\endcsname{[1,0.82,0]} +\expandafter\def\csname HotCold20\endcsname{[1,0.60,0]} +\expandafter\def\csname HotCold15\endcsname{[1,0.40,0]} +\expandafter\def\csname HotCold10\endcsname{[1,0.20,0]} +\expandafter\def\csname HotCold5\endcsname{[0.91,0,0]} + + +\def\make@lower{% +\if\first@ A\xdef\first@{a}\else \if\first@ B\xdef\first@{b}\else +\if\first@ C\xdef\first@{c}\else \if\first@ D\xdef\first@{d}\else +\if\first@ E\xdef\first@{e}\else \if\first@ F\xdef\first@{f}\else +\if\first@ G\xdef\first@{g}\else \if\first@ H\xdef\first@{h}\else +\if\first@ I\xdef\first@{i}\else \if\first@ J\xdef\first@{j}\else +\if\first@ K\xdef\first@{k}\else \if\first@ L\xdef\first@{l}\else +\if\first@ M\xdef\first@{m}\else \if\first@ N\xdef\first@{n}\else +\if\first@ O\xdef\first@{o}\else \if\first@ P\xdef\first@{p}\else +\if\first@ Q\xdef\first@{q}\else \if\first@ R\xdef\first@{r}\else +\if\first@ S\xdef\first@{s}\else \if\first@ T\xdef\first@{t}\else +\if\first@ U\xdef\first@{u}\else \if\first@ V\xdef\first@{v}\else +\if\first@ W\xdef\first@{w}\else \if\first@ X\xdef\first@{x}\else +\if\first@ Y\xdef\first@{y}\else \if\first@ Z\xdef\first@{z}\else +\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi} + +\def\make@upper{% +\if\first@ a\xdef\first@{A}\else \if\first@ b\xdef\first@{B}\else +\if\first@ c\xdef\first@{C}\else \if\first@ d\xdef\first@{D}\else +\if\first@ e\xdef\first@{E}\else \if\first@ f\xdef\first@{F}\else +\if\first@ g\xdef\first@{G}\else \if\first@ h\xdef\first@{H}\else +\if\first@ i\xdef\first@{I}\else \if\first@ j\xdef\first@{J}\else +\if\first@ k\xdef\first@{K}\else \if\first@ l\xdef\first@{L}\else +\if\first@ m\xdef\first@{M}\else \if\first@ n\xdef\first@{N}\else +\if\first@ o\xdef\first@{O}\else \if\first@ p\xdef\first@{P}\else +\if\first@ q\xdef\first@{Q}\else \if\first@ r\xdef\first@{R}\else +\if\first@ s\xdef\first@{S}\else \if\first@ t\xdef\first@{T}\else +\if\first@ u\xdef\first@{U}\else \if\first@ v\xdef\first@{V}\else +\if\first@ w\xdef\first@{W}\else \if\first@ x\xdef\first@{X}\else +\if\first@ y\xdef\first@{Y}\else \if\first@ z\xdef\first@{Z}\else +\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi} + +\def\type@get#1 MSF: #2 Type: #3 #4@{\seqtype{#3}} +\def\inf@@get#1 #2 #3 #4 #5 #6@{% + \def\first@{#1} + \def\second@{#2} + \def\third@{#3} + \xdef\fourth@{#4 @} + \expandafter\check@letter\fourth@ + \ifnumber + \def\fourth@{#4} + \else + \xdef\fourth@{#5 @} + \expandafter\check@letter\fourth@ + \ifnumber + \def\fourth@{#5} + \else + \def\fourth@{99999999} + \fi + \fi + \def\fifth@{#5} + \def\last@{#6}} +\def\check@char#1{\letterfalse \ifnum\catcode`#1=11 \lettertrue \fi + \numberfalse \ifnum\catcode`#1=12 \numbertrue \fi + \xdef\code@num{\the\catcode`#1} + \xdef\char@num{`#1}} +\def\check@letter#1#2@{\letterfalse\ifnum\catcode`#1=11 \lettertrue\fi% + \numberfalse\ifnum\catcode`#1=12 \numbertrue\fi} +\def\seq@get#1 #2@{\def\first@{#1} \def\seq@line{#2}} +\def\res@get#1#2@{\def\first@{#1} \def\seq@line{#2&@}} +\def\tot@get#1#2@{% + \xdef\first@{#1} + \expandafter\xdef\csname seq\the\triple@count\endcsname{#2&@}} +\def\dis@get#1#2@{% + \xdef\first@{#1} + \expandafter\xdef\csname res\the\triple@count\endcsname{#1} + \expandafter\xdef\csname seq\the\triple@count\endcsname{#2&@}} +\def\firstchar@get#1#2@{\def\first@{#1}\def\third@{#2@}} +\def\residue@get#1#2@{\xdef\first@{#1} + \xdef\char@num{`#1} + \expandafter\xdef\csname res\the\loopcount\endcsname{\first@} + \expandafter\xdef\csname sequence\the\loopcount\endcsname{#2@}} +\def\remove@fromseq#1@{\expandafter\xdef\csname sequence\the\loopcount\endcsname{#1}} +\def\get@temp#1@{\xdef\temp@{#1}} +\def\TC@get#1#2@{\xdef\char@num{`#1} + \ifnum\char@num=45 \xdef\TC@first@{*} + \else + \ifnum\char@num>57 \xdef\TC@first@{*} + \else + \xdef\TC@first@{#1} + \fi + \fi + \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\TC@first@} + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{#2@}} +\def\sublogo@get#1 @{\xdef\first@{#1}} +\def\re@write#1,#2@{% + \xdef\third@{#2,@} + \xdef\first@{\csname hide@@@seq#1\endcsname} + \ifx\first@\last@ + \else + \xdef\first@{#1&} + \ifx\first@\ampers@nd \else \advance\innerloopcount by 1 \fi + \if\second@ e \xdef\second@{\csname @rd#1\endcsname} + \else \xdef\second@{\second@,\csname @rd#1\endcsname}\fi + \fi + } +\def\order@set#1,#2@{% + \xdef\second@{#2,@} + \expandafter\xdef\csname @rd#1\endcsname{\the\loopcount} + \expandafter\xdef\csname res@count\the\loopcount\endcsname{% + \csname pos#1\endcsname} + \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{% + \csname hide@@seq#1\endcsname} + \expandafter\xdef\csname hide@name\the\loopcount\endcsname{% + \csname hide@@name#1\endcsname} + \expandafter\xdef\csname hide@number\the\loopcount\endcsname{% + \csname hide@@number#1\endcsname} + \expandafter\xdef\csname seq@start\the\loopcount\endcsname{% + \csname seq@@start#1\endcsname} + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{% + \csname seq@@len#1\endcsname} + \expandafter\xdef\csname seqname\the\loopcount\endcsname{% + \csname seq@name#1\endcsname} + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% + \csname newseq@name#1\endcsname} + \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{% + \csname seq@@gap#1\endcsname} + \expandafter\xdef\csname name@col\the\loopcount\endcsname{% + \csname name@@col#1\endcsname} + \expandafter\xdef\csname number@col\the\loopcount\endcsname{% + \csname number@@col#1\endcsname} + \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{% + \csname stack@@reg#1\endcsname} + \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% + \csname stack@@tintreg#1\endcsname} + \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% + \csname stack@@emphreg#1\endcsname} + \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{% + \csname stack@@lowerreg#1\endcsname} + \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% + \csname stack@@framereg#1\endcsname} + \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{% + \csname stack@@shadingreg#1\endcsname} + \expandafter\xdef\csname stack@top\the\loopcount\endcsname{% + \csname stack@@top#1\endcsname} + \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% + \csname stack@@ttop#1\endcsname} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% + \csname stack@@tttop#1\endcsname} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% + \csname stack@@ttttop#1\endcsname} + \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% + \csname stack@@bottom#1\endcsname} + \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% + \csname stack@@bbottom#1\endcsname} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% + \csname stack@@bbbottom#1\endcsname} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% + \csname stack@@bbbbottom#1\endcsname} +} +\def\reorder@seqs#1{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname pos\the\loopcount\endcsname{% + \csname res@count\the\loopcount\endcsname} + \expandafter\xdef\csname hide@@seq\the\loopcount\endcsname{% + \csname hide@seq\the\loopcount\endcsname} + \expandafter\xdef\csname hide@@name\the\loopcount\endcsname{% + \csname hide@name\the\loopcount\endcsname} + \expandafter\xdef\csname hide@@number\the\loopcount\endcsname{% + \csname hide@number\the\loopcount\endcsname} + \expandafter\xdef\csname seq@@start\the\loopcount\endcsname{% + \csname seq@start\the\loopcount\endcsname} + \expandafter\xdef\csname seq@@len\the\loopcount\endcsname{% + \csname seq@len\the\loopcount\endcsname} + \expandafter\xdef\csname seq@name\the\loopcount\endcsname{% + \csname seqname\the\loopcount\endcsname} + \expandafter\xdef\csname newseq@name\the\loopcount\endcsname{% + \csname newseqname\the\loopcount\endcsname} + \expandafter\xdef\csname seq@@gap\the\loopcount\endcsname{% + \csname seq@gap\the\loopcount\endcsname} + \expandafter\xdef\csname name@@col\the\loopcount\endcsname{% + \csname name@col\the\loopcount\endcsname} + \expandafter\xdef\csname number@@col\the\loopcount\endcsname{% + \csname number@col\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@reg\the\loopcount\endcsname{% + \csname stack@reg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{% + \csname stack@tintreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{% + \csname stack@emphreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@lowerreg\the\loopcount\endcsname{% + \csname stack@lowerreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{% + \csname stack@framereg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@shadingreg\the\loopcount\endcsname{% + \csname stack@shadingreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@top\the\loopcount\endcsname{% + \csname stack@top\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@ttop\the\loopcount\endcsname{% + \csname stack@ttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@tttop\the\loopcount\endcsname{% + \csname stack@tttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@ttttop\the\loopcount\endcsname{% + \csname stack@ttttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bottom\the\loopcount\endcsname{% + \csname stack@bottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbottom\the\loopcount\endcsname{% + \csname stack@bbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbbottom\the\loopcount\endcsname{% + \csname stack@bbbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbbbottom\the\loopcount\endcsname{% + \csname stack@bbbbottom\the\loopcount\endcsname} + \ifnum\loopcount<\killseq@count \repeat + \xdef\third@{#1} + \loopcount=0 \innerloopcount=0 \xdef\last@{kill} \xdef\second@{e} + \loop + \advance\loopcount by 1 + \expandafter\re@write\third@ + \ifnum\loopcount<\seq@count \repeat + \ifnum\innerloopcount<\killseq@count + \@latex@error{Not enough sequences specified in `orderseqs' + (\the\innerloopcount/\the\killseq@count)}\@ehc + \fi + \loopcount=0 \xdef\second@{\second@,@} + \loop + \advance\loopcount by 1 + \expandafter\order@set\second@ + \ifnum\loopcount<\killseq@count \repeat + \ifnum\cons@num>0 \xdef\cons@num{\csname @rd\cons@num\endcsname} \fi + \ifnum\rule@num>0 \xdef\rule@num{\csname @rd\rule@num\endcsname} \fi + \ifnum\divref@>0 \xdef\divref@{\csname @rd\divref@\endcsname} \fi + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname pos\the\loopcount\endcsname{0} + \ifnum\loopcount<\killseq@count \repeat +} +\def\group@get#1,#2@{% + \def\group@set{\expandafter\residue@get\second@ + \ifnum\char@num>96 \make@upper \fi + \ifx\first@\ampers@nd + \else \expandafter\xdef\csname \prfx grp\first@\endcsname{\the\loopcount} + \xdef\second@{\csname sequence\the\loopcount\endcsname} \group@set + \fi} + \xdef\second@{#1 &@} \xdef\third@{#2&,@} \group@set} +\def\get@item#1,#2@{\xdef\first@{#2@}\xdef\first@@{#2}\xdef\fourth@{#1}} +\def\get@first@@#1-#2@{\xdef\first@@{#1}} +\def\get@digit#1,#2@{% + \def\check@series##1-##2##3@{% + \xdef\first@@{##2}\xdef\fourth@{##1}\xdef\fourth@@{##3}} + \xdef\first@{#2@} + \xdef\fourth@{#1-&@} + \expandafter\check@series\fourth@ + \ifx\first@@\ampers@nd + \else + \xdef\first@@{\first@@\fourth@@-&@} + \expandafter\get@first@@\first@@ + \loopcount=\fourth@ + \ifnum\first@@>\fourth@ + \advance\loopcount by 1 + \xdef\first@{\the\loopcount-\first@@,#2@} + \else + \ifnum\first@@<\fourth@ + \advance\loopcount by -1 + \xdef\first@{\the\loopcount-\first@@,#2@} + \fi + \fi + \fi +} +\def\donot@shade{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\first@\endcsname{noshade} + \fi + \xdef\first@{\first@@ @} + \donot@shade + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\fourth@\endcsname{noshade} + \fi + \donot@shade + \fi + \fi} +\def\clear@res@nums#1{% + \temp@count=65 + \loop + \xdef\first@@{\csname ch@r@\the\temp@count\endcsname} + \expandafter\xdef\csname res@num\first@@ #1\endcsname{0} + \advance\temp@count by 1 + \ifnum\temp@count>90\else\repeat + \expandafter\xdef\csname res@num\d@t #1\endcsname{0} + \expandafter\xdef\csname res@num\questi@n #1\endcsname{0} +} +\def\setsubfamily@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \advance\res@count by 1 + \expandafter\xdef\csname subfamily@num\first@\endcsname{\subfamily@count} + \xdef\first@{\first@@ @} + \setsubfamily@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \advance\res@count by 1 + \expandafter\xdef\csname subfamily@num\fourth@\endcsname{\subfamily@count} + \setsubfamily@ + \fi + \fi +} +\def\hideseq@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\first@\endcsname{true} + \fi + \xdef\first@{\first@@ @} + \hideseq@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\fourth@\endcsname{true} + \fi + \hideseq@ + \fi + \fi} +\def\hidename@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \expandafter\xdef\csname hide@name\first@\endcsname{yes} + \xdef\first@{\first@@ @} + \hidename@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \expandafter\xdef\csname hide@name\fourth@\endcsname{yes} + \hidename@ + \fi + \fi} +\def\hidenumber@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \expandafter\xdef\csname hide@number\first@\endcsname{yes} + \xdef\first@{\first@@ @} + \hidenumber@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \expandafter\xdef\csname hide@number\fourth@\endcsname{yes} + \hidenumber@ + \fi + \fi} +\def\namecolor@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \expandafter\xdef\csname name@col\first@\endcsname{\third@} + \xdef\first@{\first@@ @} + \namecolor@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \expandafter\xdef\csname name@col\fourth@\endcsname{\third@} + \namecolor@ + \fi + \fi} +\def\numbercolor@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \expandafter\xdef\csname number@col\first@\endcsname{\third@} + \xdef\first@{\first@@ @} + \numbercolor@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \expandafter\xdef\csname number@col\fourth@\endcsname{\third@} + \numbercolor@ + \fi + \fi} +\def\killseq@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \ifnum\first@>\seq@count + \else + \ifnum\killseq@count>1 + \xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\first@\endcsname{kill} + \expandafter\xdef\csname hide@@@seq\first@\endcsname{kill} + \ifnum\first@=\cons@num \xdef\cons@num{0} \fi + \advance\killseq@count by -1 +% \seq@percent=100 \divide\seq@percent by \killseq@count + \fi + \fi\fi + \xdef\first@{\first@@ @} + \killseq@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \ifnum\fourth@>\seq@count + \else + \ifnum\killseq@count>1 + \xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\fourth@\endcsname{kill} + \expandafter\xdef\csname hide@@@seq\fourth@\endcsname{kill} + \ifnum\fourth@=\cons@num \xdef\cons@num{0} \fi + \advance\killseq@count by -1 +% \seq@percent=100 \divide\seq@percent by \killseq@count + \fi + \fi\fi + \killseq@ + \fi + \fi} +\def\kill@loop{% + \advance\innerloopcount by 1 + \xdef\first@{\csname hide@seq\the\innerloopcount\endcsname} + \ifx\first@\second@ \kill@loop \fi} +\def\kill@seqnow{% + \xdef\first@{\csname hide@seq\the\loopcount\endcsname} \xdef\second@{kill} + \innerloopcount=\loopcount + \ifx\first@\second@ + \kill@loop + \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{% + \csname hide@seq\the\innerloopcount\endcsname} + \expandafter\xdef\csname seqname\the\loopcount\endcsname{% + \csname seqname\the\innerloopcount\endcsname} + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% + \csname newseqname\the\innerloopcount\endcsname} + \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{% + \csname seq@gap\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{% + \csname stack@reg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% + \csname stack@tintreg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% + \csname stack@emphreg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{% + \csname stack@lowerreg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% + \csname stack@framereg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{% + \csname stack@shadingreg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@top\the\loopcount\endcsname{% + \csname stack@top\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% + \csname stack@ttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% + \csname stack@tttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% + \csname stack@ttttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% + \csname stack@bottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% + \csname stack@bbottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% + \csname stack@bbbottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% + \csname stack@bbbbottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname res@count\the\loopcount\endcsname{% + \csname res@count\the\innerloopcount\endcsname} + \expandafter\xdef\csname hide@seq\the\innerloopcount\endcsname{kill} + \ifnum\loopcount=\rule@num \hideruler \fi + \fi + \expandafter\xdef\csname @rd\the\innerloopcount\endcsname{\the\loopcount} + \advance\loopcount by 1 + \ifnum\loopcount>\killseq@count + \ifnum\rule@num>0\xdef\rule@num{\csname @rd\rule@num\endcsname}\fi + \ifnum\cons@num>0\xdef\cons@num{\csname @rd\cons@num\endcsname}\fi + \else + \kill@seqnow + \fi} +\def\get@sim#1#2@{\xdef\sim@char{#1} \xdef\last@{#2 &@}} +\def\getsim@char{% + \advance\innerloopcount by 1 + \ifnum\innerloopcount>\m@x + \else + \expandafter\get@sim\last@ + \ifx\second@\sim@char \xdef\third@{2} \innerloopcount=\m@x \fi + \getsim@char + \fi} +\def\get@count(#1)#2@{\xdef\last@{#2 &@} \xdef\m@x{#1}} +\def\get@nums#1..#2@{\xdef\first@{#1} \xdef\second@{#2}} +\def\func@shading#1{% + \clearfuncgroups + \xdef\temp@{#1} + \xdef\second@{charge} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{basisch ($+$)}{KRH}{White}{Blue}{upper}{up} + \else + \ifsp@nish + \funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up} + \else + \funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up} + \fi + \fi + \else + \xdef\second@{hydropathy} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{basisch ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{polar ungeladen}{YSTGNQC}{Black}{Yellow}{upper}{up} + \funcgroup{hydrophob unpolar}{AFPMWVIL}{White}{Green}{upper}{up} + \else + \ifsp@nish + \funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{polar sin carga}{YSTGNQC}{Black}{Yellow}{upper}{up} + \funcgroup{hidrof\'obico no polar}{AFPMWVIL}{White}{Green}{upper}{up} + \else + \funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{polar uncharged}{YSTGNQC}{Black}{Yellow}{upper}{up} + \funcgroup{hydrophobic nonpolar}{AFPMWVIL}{White}{Green}{upper}{up} + \fi + \fi + \else + \xdef\second@{chemical} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{aliphatisch}{AGVIL}{White}{Black}{upper}{up} + \funcgroup{aliphatisch (klein)}{AG}{White}{Gray}{upper}{up} + \funcgroup{Amid}{NQ}{White}{Green}{upper}{up} + \funcgroup{aromatisch}{FYW}{White}{Brown}{upper}{up} + \funcgroup{basisch (+)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{Hydroxyl}{ST}{Black}{Magenta}{upper}{up} + \funcgroup{Imin}{P}{Black}{Orange}{upper}{up} + \funcgroup{Schwefel}{CM}{Black}{Yellow}{upper}{up} + \else + \ifsp@nish + \funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{alif\'atico}{AGVIL}{White}{Black}{upper}{up} + \funcgroup{alif\'atico (parvo)}{AG}{White}{Gray}{upper}{up} + \funcgroup{amida}{NQ}{White}{Green}{upper}{up} + \funcgroup{arom\'atico}{FYW}{White}{Brown}{upper}{up} + \funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{hidr\'oxido}{ST}{Black}{Magenta}{upper}{up} + \funcgroup{imino}{P}{Black}{Orange}{upper}{up} + \funcgroup{azufre}{CM}{Black}{Yellow}{upper}{up} + \else + \funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{aliphatic}{AGVIL}{White}{Black}{upper}{up} + \funcgroup{aliphatic (small)}{AG}{White}{Gray}{upper}{up} + \funcgroup{amide}{NQ}{White}{Green}{upper}{up} + \funcgroup{aromatic}{FYW}{White}{Brown}{upper}{up} + \funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{hydroxyl}{ST}{Black}{Magenta}{upper}{up} + \funcgroup{imino}{P}{Black}{Orange}{upper}{up} + \funcgroup{sulfur}{CM}{Black}{Yellow}{upper}{up} + \fi + \fi + \else + \xdef\second@{structure} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{extern}{DEHKNQR}{Black}{Orange}{upper}{up} + \funcgroup{ambivalent}{ACGPSTWY}{Black}{Yellow}{upper}{up} + \funcgroup{intern}{FILMV}{White}{Green}{upper}{up} + \else + \ifsp@nish + \funcgroup{externo}{DEHKNQR}{Black}{Orange}{upper}{up} + \funcgroup{ambivalente}{ACGPSTWY}{Black}{Yellow}{upper}{up} + \funcgroup{interno}{FILMV}{White}{Green}{upper}{up} + \else + \funcgroup{external}{DEHKNQR}{Black}{Orange}{upper}{up} + \funcgroup{ambivalent}{ACGPSTWY}{Black}{Yellow}{upper}{up} + \funcgroup{internal}{FILMV}{White}{Green}{upper}{up} + \fi + \fi + \else + \xdef\second@{standard area} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{\ 88,1 (G); Standard Seitenkettenfl\"ache % + (\AA$^2$)}% + {G}{Black}{BrickRed}{upper}{up} + \funcgroup{118,2 (A); 129,8 (S)}{AS}{Black}{Orange}{upper}{up} + \funcgroup{146,1 (C); 146,8 (P)}% + {CP}{Black}{Yellow}{upper}{up} + \funcgroup{152,5 (T); 158,7 (D); 164,5 (V); 165,5 (N)}% + {TDVN}{Black}{YellowGreen}{upper}{up} + \funcgroup{181,0 (I); 186,2 (E)}{IE}{White}{PineGreen}{upper}{up} + \funcgroup{193,1 (L); 193,2 (Q); 202,5 (H); 203,3 (M)}% + {LQHM}{Black}{SkyBlue}{upper}{up} + \funcgroup{222,8 (F); 225,8 (K)}{FK}{White}{RoyalPurple}{upper}{up} + \funcgroup{238,8 (Y)}{Y}{White}{RedViolet}{upper}{up} + \funcgroup{256,0 (R); 266,2 (W)}{RW}{White}{Black}{upper}{up} + \else + \ifsp@nish + \funcgroup{\ 88.1 (G); Superficie est\'andar de la cadena lateral (\AA$^2$)}% + {G}{Black}{BrickRed}{upper}{up} + \funcgroup{118.2 (A); 129.8 (S)}{AS}{Black}{Orange}{upper}{up} + \funcgroup{146.1 (C); 146.8 (P)}% + {CP}{Black}{Yellow}{upper}{up} + \funcgroup{152.5 (T); 158.7 (D); 164.5 (V); 165.5 (N)}% + {TDVN}{Black}{YellowGreen}{upper}{up} + \funcgroup{181.0 (I); 186.2 (E)}{IE}{White}{PineGreen}{upper}{up} + \funcgroup{193.1 (L); 193.2 (Q); 202.5 (H); 203.3 (M)}% + {LQHM}{Black}{SkyBlue}{upper}{up} + \funcgroup{222.8 (F); 225.8 (K)}{FK}{White}{RoyalPurple}{upper}{up} + \funcgroup{238.8 (Y)}{Y}{White}{RedViolet}{upper}{up} + \funcgroup{256.0 (R); 266.2 (W)}{RW}{White}{Black}{upper}{up} + \else + \funcgroup{\ 88.1 (G); Standard sidechain area (\AA$^2$)}% + {G}{Black}{BrickRed}{upper}{up} + \funcgroup{118.2 (A); 129.8 (S)}{AS}{Black}{Orange}{upper}{up} + \funcgroup{146.1 (C); 146.8 (P)}% + {CP}{Black}{Yellow}{upper}{up} + \funcgroup{152.5 (T); 158.7 (D); 164.5 (V); 165.5 (N)}% + {TDVN}{Black}{YellowGreen}{upper}{up} + \funcgroup{181.0 (I); 186.2 (E)}{IE}{White}{PineGreen}{upper}{up} + \funcgroup{193.1 (L); 193.2 (Q); 202.5 (H); 203.3 (M)}% + {LQHM}{Black}{SkyBlue}{upper}{up} + \funcgroup{222.8 (F); 225.8 (K)}{FK}{White}{RoyalPurple}{upper}{up} + \funcgroup{238.8 (Y)}{Y}{White}{RedViolet}{upper}{up} + \funcgroup{256.0 (R); 266.2 (W)}{RW}{White}{Black}{upper}{up} + \fi + \fi + \else + \xdef\second@{accessible area} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{\ 13,9 (C); Zug\"angliche Seitenkettenfl\"ache % + (\AA$^2$)}% + {CIV}{Black}{BrickRed}{upper}{up} + \funcgroup{\ 23,0 (I); 23,5 (V); 25,2 (G)}% + {IVG}{Black}{Orange}{upper}{up} + \funcgroup{\ 28,7 (F); 29,0 (L); 30,5 (M); 31,5 (A)}% + {FLMA}{Black}{Yellow}{upper}{up} + \funcgroup{\ 41,7 (W); 44,2 (S); 46,0 (T); 46,7 (H)}% + {WSTH}{Black}{YellowGreen}{upper}{up} + \funcgroup{\ 53,7 (P)}{P}{White}{PineGreen}{upper}{up} + \funcgroup{\ 59,1 (Y); 60,9 (D); 62,2 (N)}% + {YDN}{Black}{SkyBlue}{upper}{up} + \funcgroup{\ 72,3 (E); 74,0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up} + \funcgroup{\ 93,8 (R)}{R}{White}{RedViolet}{upper}{up} + \funcgroup{110,3 (K)}{K}{White}{Black}{upper}{up} + \else + \ifsp@nish + \funcgroup{\ 13.9 (C); Superficie accesible de la cadena lateral (\AA$^2$)}% + {CIV}{Black}{BrickRed}{upper}{up} + \funcgroup{\ 23.0 (I); 23.5 (V); 25.2 (G)}% + {IVG}{Black}{Orange}{upper}{up} + \funcgroup{\ 28.7 (F); 29.0 (L); 30.5 (M); 31.5 (A)}% + {FLMA}{Black}{Yellow}{upper}{up} + \funcgroup{\ 41.7 (W); 44.2 (S); 46.0 (T); 46.7 (H)}% + {WSTH}{Black}{YellowGreen}{upper}{up} + \funcgroup{\ 53.7 (P)}{P}{White}{PineGreen}{upper}{up} + \funcgroup{\ 59.1 (Y); 60.9 (D); 62.2 (N)}% + {YDN}{Black}{SkyBlue}{upper}{up} + \funcgroup{\ 72.3 (E); 74.0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up} + \funcgroup{\ 93.8 (R)}{R}{White}{RedViolet}{upper}{up} + \funcgroup{110.3 (K)}{K}{White}{Black}{upper}{up} + \else + \funcgroup{\ 13.9 (C); Accessible sidechain area (\AA$^2$)}% + {CIV}{Black}{BrickRed}{upper}{up} + \funcgroup{\ 23.0 (I); 23.5 (V); 25.2 (G)}% + {IVG}{Black}{Orange}{upper}{up} + \funcgroup{\ 28.7 (F); 29.0 (L); 30.5 (M); 31.5 (A)}% + {FLMA}{Black}{Yellow}{upper}{up} + \funcgroup{\ 41.7 (W); 44.2 (S); 46.0 (T); 46.7 (H)}% + {WSTH}{Black}{YellowGreen}{upper}{up} + \funcgroup{\ 53.7 (P)}{P}{White}{PineGreen}{upper}{up} + \funcgroup{\ 59.1 (Y); 60.9 (D); 62.2 (N)}% + {YDN}{Black}{SkyBlue}{upper}{up} + \funcgroup{\ 72.3 (E); 74.0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up} + \funcgroup{\ 93.8 (R)}{R}{White}{RedViolet}{upper}{up} + \funcgroup{110.3 (K)}{K}{White}{Black}{upper}{up} + \fi + \fi + \else + \xdef\second@{rasmol} + \ifx\temp@\second@ + \funcgroup{Asp, Glu}{DE}{Red}{White}{upper}{up} + \funcgroup{Arg, Lys, His}{KRH}{Blue}{White}{upper}{up} + \funcgroup{Phe, Tyr, Trp}{FYW}{MidnightBlue}{White}{upper}{up} + \funcgroup{Ala, Gly}{AG}{Gray}{White}{upper}{up} + \funcgroup{Cys, Met}{CM}{Yellow}{White}{upper}{up} + \funcgroup{Ser, Thr}{ST}{Orange}{White}{upper}{up} + \funcgroup{Asn, Gln}{NQ}{Cyan}{White}{upper}{up} + \funcgroup{Leu, Val, Ile}{LVI}{Green}{White}{upper}{up} + \funcgroup{Pro}{P}{Apricot}{White}{upper}{up} + \else + \message{<Unknown shading mode - clearing `funcgroups'>} + \fi\fi\fi\fi\fi\fi\fi +} +\def\shadeallresidues{\all@fshadetrue} +\def\get@fromstack#1;#2;#3;#4;#5@{% + \xdef\first@{#1} \xdef\second@{#2} + \xdef\third@{#3} \xdef\fourth@{#4} \xdef\last@{#5@} +} +\def\getregion@fromstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@reg\temp@\endcsname} + \expandafter\get@fromstack\first@ + \expandafter\xdef\csname style\temp@\endcsname{\first@} + \expandafter\xdef\csname start\temp@\endcsname{\second@} + \expandafter\xdef\csname stop\temp@\endcsname{\third@} + \expandafter\xdef\csname all\temp@\endcsname{\fourth@} + \expandafter\xdef\csname stack@reg\temp@\endcsname{\last@} +} +\def\sort@stack{% + \expandafter\get@fromstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;&;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;% + \first@;\second@;\third@;\fourth@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} + \sort@stack + \fi\fi +} +\def\get@regions#1..#2,#3@{% + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@reg\seq@\endcsname} + \xdef\tmpstack{} + \sort@stack + \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack} +} +\def\get@fromemphstack#1;#2;#3;#4@{% + \xdef\first@{#1} \xdef\second@{#2} + \xdef\third@{#3} \xdef\last@{#4@} +} +\def\getregion@fromemphstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@emphreg\temp@\endcsname} + \expandafter\get@fromemphstack\first@ + \expandafter\xdef\csname emphstart\temp@\endcsname{\first@} + \expandafter\xdef\csname emphstop\temp@\endcsname{\second@} + \expandafter\xdef\csname emphall\temp@\endcsname{\third@} + \expandafter\xdef\csname stack@emphreg\temp@\endcsname{\last@} +} +\def\sort@emphstack{% + \expandafter\get@fromemphstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@emphstack + \fi\fi +} +\def\get@emphregions#1..#2,#3@{% + \regionalemphtrue + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@emphreg\seq@\endcsname} + \xdef\tmpstack{} + \sort@emphstack + \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack} +} +\def\getregion@fromlowerstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@lowerreg\temp@\endcsname} + \expandafter\get@fromemphstack\first@ + \expandafter\xdef\csname lowerstart\temp@\endcsname{\first@} + \expandafter\xdef\csname lowerstop\temp@\endcsname{\second@} + \expandafter\xdef\csname lowerall\temp@\endcsname{\third@} + \expandafter\xdef\csname stack@lowerreg\temp@\endcsname{\last@} +} +\def\sort@lowerstack{% + \expandafter\get@fromemphstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@lowerstack + \fi\fi +} +\def\get@lowerregions#1..#2,#3@{% + \regionallowertrue + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@lowerreg\seq@\endcsname} + \xdef\tmpstack{} + \sort@lowerstack + \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack} +} +\def\get@fromdomstack#1;#2;#3@{% + \xdef\first@{#1} \xdef\second@{#2} + \xdef\last@{#3@} +} +\def\sort@domstack{% + \expandafter\get@fromdomstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\st@rt;\st@p;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\first@;\second@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;} \sort@domstack + \fi\fi +} +\def\get@domainregions#1..#2,#3@{% + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\stack@dom} + \xdef\tmpstack{} + \sort@domstack + \xdef\stack@dom{\tmpstack} +} +\def\get@domain{% + \expandafter\get@fromdomstack\last@ + \ifx\first@\ampers@nd + \else + \loopcount=\first@ + \loop + \xdef\domain@num@list{\domain@num@list \the\loopcount,} + \advance\loopcount by 1 + \ifnum\loopcount>\second@\else\repeat + \get@domain + \fi +} +\def\getregion@fromtintstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@tintreg\temp@\endcsname} + \expandafter\get@fromemphstack\first@ + \expandafter\xdef\csname tintstart\temp@\endcsname{\first@} + \expandafter\xdef\csname tintstop\temp@\endcsname{\second@} + \expandafter\xdef\csname tintall\temp@\endcsname{\third@} + \expandafter\xdef\csname stack@tintreg\temp@\endcsname{\last@} +} +\def\get@tintregions#1..#2,#3@{% + \regionaltinttrue + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@tintreg\seq@\endcsname} + \xdef\tmpstack{} + \sort@emphstack + \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} +} +\def\getregion@fromframestack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@framereg\temp@\endcsname} + \expandafter\get@fromemphstack\first@ + \expandafter\xdef\csname framestart\temp@\endcsname{\first@} + \expandafter\xdef\csname framestop\temp@\endcsname{\second@} + \expandafter\xdef\csname framestyle\temp@\endcsname{\third@} + \expandafter\xdef\csname stack@framereg\temp@\endcsname{\last@} +} +\def\get@frameregions#1..#2,#3@{% + \frame@true + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@framereg\seq@\endcsname} + \xdef\tmpstack{} + \sort@emphstack + \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack} +} +\def\getregion@fromshadingstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@shadingreg\temp@\endcsname} + \expandafter\get@fromemphstack\first@ + \expandafter\xdef\csname shadingstart\temp@\endcsname{\first@} + \expandafter\xdef\csname shadingstop\temp@\endcsname{\second@} + \expandafter\xdef\csname shadingstyle\temp@\endcsname{\third@} + \expandafter\xdef\csname stack@shadingreg\temp@\endcsname{\last@} +} +\def\get@shadingregions#1..#2,#3@{% + \shading@true + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@shadingreg\seq@\endcsname} + \xdef\tmpstack{} + \sort@emphstack + \expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack} +} +\def\getregion@fromfstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@\bottop@\temp@\endcsname} + \expandafter\get@fromstack\first@ + \expandafter\xdef\csname text\bottop@\temp@\endcsname{\first@} + \expandafter\xdef\csname start\bottop@\temp@\endcsname{\second@} + \expandafter\xdef\csname stop\bottop@\temp@\endcsname{\third@} + \ifx\fourth@\ampers@nd \xdef\fourth@{///} \fi + \expandafter\xdef\csname style\bottop@\temp@\endcsname{\fourth@} + \expandafter\xdef\csname stack@\bottop@\temp@\endcsname{\last@} +} +\def\sort@fstack{% + \expandafter\get@fromstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\f@text@;\st@rt;\st@p;\style@;&;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\f@text@;\st@rt;\st@p;\style@;% + \first@;\second@;\third@;\fourth@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} + \sort@fstack + \fi\fi +} +\def\get@fregions#1..#2,#3@{% + \xdef\st@rt{#1} + \ifx\temp@\y@ + \xdef\st@p{#1} + \else + \xdef\st@p{#2} + \fi + \xdef\list@{#3} + \xdef\last@{\csname stack@\bottop@\seq@\endcsname} + \xdef\tmpstack{} + \sort@fstack + \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack} +} +\def\getarrow@shape#1#2#3#4&{% + \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}\xdef\fourth@@{#4} + \ifx\temp@@\y@ + \if\first@@ ` \xdef\first@@{a} \else + \if\first@@ ' \xdef\first@@{a} \else + \if\first@@ , \xdef\first@@{b} \else + \if\first@@ S \xdef\first@@{c} \xdef\second@@{-} + \fi\fi\fi\fi + \if\third@@ ` \xdef\third@@{a} \else + \if\third@@ ' \xdef\third@@{a} \else + \if\third@@ , \xdef\third@@{b} \else + \if\third@@ S \xdef\third@@{c} \xdef\second@@{-} + \fi\fi\fi\fi + \xdef\style@{\first@@ -\third@@\fourth@@} + \fi + \if\first@@ S + \xdef\style@{\first@@ -\third@@\fourth@@} + \else + \if\first@@ v + \if\second@@ = + \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi + \else + \if\third@@ S + \xdef\style@{\first@@ -\third@@\fourth@@} + \else + \if\third@@ v + \if\second@@ = + \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi + \fi\fi\fi\fi +} +\def\get@shape#1#2#3{% + \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}% + \if\second@@ v \xdef\second@@{arrow}% + \fi% + \if\second@@ = \xdef\second@@{doublearrow}% + \fi% +} +\def\getstyle@left#1#2#3#4@{% + \ifstop@ + \xdef\style@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \else + \xdef\style@@{#2} + \xdef\temp@{-} + \ifx\style@@\temp@ \xdef\style@@{#1#2-#4} + \else + \xdef\temp@{v} + \ifx\style@@\temp@ \xdef\style@@{#1#2-#4} + \else + \xdef\temp@{=} + \ifx\style@@\temp@ \xdef\style@@{#1#2=#4} + \else + \xdef\style@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \fi\fi\fi\fi +} +\def\getstyle@right#1#2#3#4@{% + \xdef\style@@{#2} + \xdef\temp@{-} + \ifx\style@@\temp@ + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{-#2#3#4} + \fi + \xdef\temp@{v} + \ifx\style@@\temp@ + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{-#2#3#4} + \fi + \xdef\temp@{=} + \ifx\style@@\temp@ + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{=#2#3#4} + \fi +} +\def\opt@color#1[#2]#3&{\xdef\fourth@{#1}\xdef\f@color{#2}} +\def\graph@opt@color#1[#2]:#3[#4][#5]#6&{% + \xdef\fourth@{#1} + \xdef\f@color{#2} + \xdef\ffourth@{#3} + \xdef\ff@color{#4} + \xdef\fffourth@{#5}} +\def\arrow@col@width#1[#2][#3]#4&{\xdef\fourth@{#1}\xdef\f@color{#2}\xdef\rule@@thick{#3}} +\def\second@color#1,&{\xdef\back@color{#1}} +\def\two@opt@color#1,#2@{% + \xdef\sixth@{#1}% + \xdef\seventh@{#2}% + \ifx\first@\ampers@nd% + \else% + \xdef\frame@color{#1}% + \ifx\seventh@\ampers@nd% + \xdef\back@color{#1}% + \xdef\backtext@color{White}% + \else% + \expandafter\second@color\seventh@% + \fi% + \fi% +} +\def\test@get#1#2@{% + \xdef\temp@{#1} \xdef\third@@{#2@} + \ifx\temp@\ampers@nd + \else + \if \temp@ X + \xdef\temp@{\second@@} + \fi + \ifx\temp@\second@@ + \xdef\third@@{\second@@} + \else + \expandafter\test@get\third@@ + \fi + \fi +} +\def\get@@second@#1#2@{\xdef\second@@{#1}\xdef\first@@{#2@}} +\def\get@@third@#1]#2@{\xdef\third@@{#1&@}\xdef\fifth@@{#2@}} +\def\get@third@#1#2@{\xdef\third@@{#1}\xdef\fifth@@{#2@}} +\def\find@motif{% + \expandafter\get@@second@\first@@ + \ifx\second@@\ampers@nd + \else + \ifx\second@@\d@t + \else + \advance\temp@count by 1 + \if \third@@ X + \xdef\third@@{\second@@} + \fi + \ifx\third@@\br@cket + \expandafter\get@@third@\fifth@@ + \expandafter\test@get\third@@ + \fi + \ifx\second@@\third@@ + \ifx\nineth@@\n@ + \xdef\st@rt{\the\temp@count} + \xdef\st@p{n} + \fi + \xdef\nineth@@{y} + \expandafter\get@third@\fifth@@ + \ifx\third@@\ampers@nd + \xdef\st@p{\the\temp@count} + \xdef\list@{} + \xdef\tmpstack{} + \xdef\temp@{shade} + \ifx\temp@\temp@@ + \xdef\last@{\csname stack@reg\seq@\endcsname} + \loopcount=\style@ + \sort@stack + \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{emph} + \ifx\temp@\temp@@ + \regionalemphtrue + \xdef\last@{\csname stack@emphreg\seq@\endcsname} + \sort@emphstack + \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{lower} + \ifx\temp@\temp@@ + \regionallowertrue + \xdef\last@{\csname stack@lowerreg\seq@\endcsname} + \sort@lowerstack + \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{tint} + \ifx\temp@\temp@@ + \regionaltinttrue + \xdef\last@{\csname stack@tintreg\seq@\endcsname} + \sort@emphstack + \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{frame} + \ifx\temp@\temp@@ + \frame@true + \xdef\last@{\csname stack@framereg\seq@\endcsname} + \sort@emphstack + \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{shading} + \ifx\temp@\temp@@ + \shading@true + \xdef\last@{\csname stack@shadingreg\seq@\endcsname} + \sort@emphstack + \expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{ttttop} + \ifx\temp@\temp@@ + \xdef\last@{\csname stack@ttttop\seq@\endcsname} + \sort@fstack + \expandafter\xdef\csname stack@ttttop\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{tttop} + \ifx\temp@\temp@@ + \xdef\last@{\csname stack@tttop\seq@\endcsname} + \sort@fstack + \expandafter\xdef\csname stack@tttop\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{ttop} + \ifx\temp@\temp@@ + \xdef\last@{\csname stack@ttop\seq@\endcsname} + \sort@fstack + \expandafter\xdef\csname stack@ttop\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{top} + \ifx\temp@\temp@@ + \xdef\last@{\csname stack@top\seq@\endcsname} + \sort@fstack + \expandafter\xdef\csname stack@top\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{bottom} + \ifx\temp@\temp@@ + \xdef\last@{\csname stack@bottom\seq@\endcsname} + \sort@fstack + \expandafter\xdef\csname stack@bottom\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{bbottom} + \ifx\temp@\temp@@ + \xdef\last@{\csname stack@bbottom\seq@\endcsname} + \sort@fstack + \expandafter\xdef\csname stack@bbottom\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{bbbottom} + \ifx\temp@\temp@@ + \xdef\last@{\csname stack@bbbottom\seq@\endcsname} + \sort@fstack + \expandafter\xdef\csname stack@bbbottom\seq@\endcsname{\tmpstack} + \else + \xdef\temp@{bbbbottom} + \ifx\temp@\temp@@ + \xdef\last@{\csname stack@bbbbottom\seq@\endcsname} + \sort@fstack + \expandafter\xdef\csname stack@bbbbottom\seq@\endcsname{\tmpstack} + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@ + \xdef\nineth@@{n} + \fi + \else + \ifx\nineth@@\y@ + \xdef\first@@{\second@@\first@@} + \advance\temp@count by -1 + \fi + \xdef\nineth@@{n} \xdef\st@p{n} + \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@ + \fi + \fi + \find@motif + \fi +} +\def\prep@motif{% + + \def\get@motif@specs##1,##2,##3,##4,##5,&{% + \xdef\seq@{##1} \xdef\temp@@{##2} \xdef\@ll{##3} \def\fourth@@{##4} \xdef\fifth@@{##5&@} + } + + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{\csname style\the\loopcount\endcsname;% + \csname start\the\loopcount\endcsname;% + \csname stop\the\loopcount\endcsname;% + \csname all\the\loopcount\endcsname;% + \csname stack@reg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{\csname emphstart\the\loopcount\endcsname;% + \csname emphstop\the\loopcount\endcsname;% + \csname emphall\the\loopcount\endcsname;% + \csname stack@emphreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{\csname lowerstart\the\loopcount\endcsname;% + \csname lowerstop\the\loopcount\endcsname;% + \csname lowerall\the\loopcount\endcsname;% + \csname stack@lowerreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{\csname tintstart\the\loopcount\endcsname;% + \csname tintstop\the\loopcount\endcsname;% + \csname tintall\the\loopcount\endcsname;% + \csname stack@tintreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{\csname framestart\the\loopcount\endcsname;% + \csname framestop\the\loopcount\endcsname;% + \csname framestyle\the\loopcount\endcsname;% + \csname stack@framereg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{\csname shadingstart\the\loopcount\endcsname;% + \csname shadingstop\the\loopcount\endcsname;% + \csname shadingstyle\the\loopcount\endcsname;% + \csname stack@shadingreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{\csname textttttop\the\loopcount\endcsname;% + \csname startttttop\the\loopcount\endcsname;% + \csname stopttttop\the\loopcount\endcsname;% + \csname stylettttop\the\loopcount\endcsname;% + \csname stack@ttttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{\csname texttttop\the\loopcount\endcsname;% + \csname starttttop\the\loopcount\endcsname;% + \csname stoptttop\the\loopcount\endcsname;% + \csname styletttop\the\loopcount\endcsname;% + \csname stack@tttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{\csname textttop\the\loopcount\endcsname;% + \csname startttop\the\loopcount\endcsname;% + \csname stopttop\the\loopcount\endcsname;% + \csname stylettop\the\loopcount\endcsname;% + \csname stack@ttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@top\the\loopcount\endcsname{\csname texttop\the\loopcount\endcsname;% + \csname starttop\the\loopcount\endcsname;% + \csname stoptop\the\loopcount\endcsname;% + \csname styletop\the\loopcount\endcsname;% + \csname stack@top\the\loopcount\endcsname} + \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{\csname textbottom\the\loopcount\endcsname;% + \csname startbottom\the\loopcount\endcsname;% + \csname stopbottom\the\loopcount\endcsname;% + \csname stylebottom\the\loopcount\endcsname;% + \csname stack@bottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{\csname textbbottom\the\loopcount\endcsname;% + \csname startbbottom\the\loopcount\endcsname;% + \csname stopbbottom\the\loopcount\endcsname;% + \csname stylebbottom\the\loopcount\endcsname;% + \csname stack@bbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{\csname textbbbottom\the\loopcount\endcsname;% + \csname startbbbottom\the\loopcount\endcsname;% + \csname stopbbbottom\the\loopcount\endcsname;% + \csname stylebbbottom\the\loopcount\endcsname;% + \csname stack@bbbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{\csname textbbbbottom\the\loopcount\endcsname;% + \csname startbbbbottom\the\loopcount\endcsname;% + \csname stopbbbbottom\the\loopcount\endcsname;% + \csname stylebbbbottom\the\loopcount\endcsname;% + \csname stack@bbbbottom\the\loopcount\endcsname} + \ifnum\loopcount<\seq@num\repeat + \temp@@count=0 + \loop + \advance\temp@@count by 1 + \xdef\first@@{\csname motif\the\temp@@count\endcsname} + \expandafter\get@motif@specs\first@@ + \xdef\first@@{\csname sequence\seq@\endcsname &@} + \temp@count=\csname res@count\seq@\endcsname + \xdef\f@text@{\@ll} + \xdef\style@{\fourth@@} + \xdef\m@tif{\fifth@@} \expandafter\get@third@\fifth@@ + \xdef\nineth@@{n} \xdef\st@p{n} + \find@motif + \ifnum\temp@@count<\motif@num\repeat + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\getregion@fromtintstack{\the\loopcount} + \expandafter\getregion@fromemphstack{\the\loopcount} + \expandafter\getregion@fromlowerstack{\the\loopcount} + \expandafter\getregion@fromframestack{\the\loopcount} + \expandafter\getregion@fromshadingstack{\the\loopcount} + \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \ifnum\loopcount<\seq@num\repeat +} + +\def\test@motif#1#2@{% + \xdef\temp@{shade} + \ifx\temp@\temp@@ \xdef\style@{\the\loopcount} \fi + \xdef\temp@{emph} + \ifx\temp@\temp@@ \xdef\style@{0} \fi + \xdef\temp@{lower} + \ifx\temp@\temp@@ \xdef\style@{0} \fi + \xdef\temp@{tint} + \ifx\temp@\temp@@ \xdef\style@{0} \fi + \xdef\temp@{frame} + \ifx\temp@\temp@@ \xdef\style@{0} \fi + \xdef\temp@{shading} + \ifx\temp@\temp@@ \xdef\style@{0} \fi + \xdef\temp@{#1#2} + \xdef\first@{#1} + \ifx\first@\br@cket + \xdef\label@motif{y} + \temp@count=\motif@num + \advance\temp@count by 1 + \xdef\motif@num{\the\temp@count} + \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@} + \xdef\list@{&} + \else + \expandafter\check@char\first@ + \ifletter + \xdef\label@motif{y} + \temp@count=\motif@num + \advance\temp@count by 1 + \xdef\motif@num{\the\temp@count} + \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@} + \xdef\list@{&} + \fi + \fi +} + +\def\test@PDB#1:#2,#3,#4,#5,#6@{% + \xdef\last@{#1[,]&}\expandafter\opt@color\last@ + \xdef\PDB@distance{no} + \ifx\f@color\comm@ + \else + \xdef\f@color{\f@color .&&@} + \expandafter\coord@get\f@color + \xdef\temp@{\c@@rd @} + \expandafter\check@letter\temp@ + \ifletter + \else + \temp@count=\c@@rd + \multiply\temp@count by \temp@count + \xdef\PDB@distance{\the\temp@count} + \fi + \fi + \xdef\PDB@hitpos{0} + \xdef\PDB@stack{} + \xdef\PDB@name{#2} + \xdef\PDB@type{point} + \ifx\fourth@\PDB@type + \xdef\PDB@{y} + \xdef\last@{#3[,]&}\expandafter\opt@color\last@ + \xdef\PDB@refnum@a{\fourth@} + \ifx\f@color\C@lpha + \xdef\PDB@back@side@a{CA} + \else + \xdef\PDB@back@side@a{side} + \fi + \xdef\PDB@refnum@b{0} \xdef\PDB@back@side@b{x} + \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x} + \ifx\PDB@distance\n@ \xdef\PDB@distance{3600}\fi + \load@PDB + \expandafter\get@item\PDB@stack \xdef\list@{\first@@} + \else + \xdef\PDB@type{line} + \ifx\fourth@\PDB@type + \xdef\PDB@{y} + \xdef\last@{#3[,]&}\expandafter\opt@color\last@ + \xdef\PDB@refnum{\fourth@} + \ifx\f@color\C@lpha + \xdef\PDB@back@side{CA} + \else + \xdef\PDB@back@side{side} + \fi + \xdef\last@{#4[,]&}\expandafter\opt@color\last@ + \ifnum\PDB@refnum<\fourth@ + \xdef\PDB@refnum@a{\PDB@refnum} + \xdef\PDB@refnum@b{\fourth@} + \xdef\PDB@back@side@a{\PDB@back@side} + \ifx\f@color\C@lpha + \xdef\PDB@back@side@b{CA} + \else + \xdef\PDB@back@side@b{side} + \fi + \else + \xdef\PDB@refnum@b{\PDB@refnum} + \xdef\PDB@refnum@a{\fourth@} + \xdef\PDB@back@side@b{\PDB@back@side} + \ifx\f@color\C@lpha + \xdef\PDB@back@side@a{CA} + \else + \xdef\PDB@back@side@a{side} + \fi + \fi + \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x} + \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi + \load@PDB + \expandafter\get@item\PDB@stack \xdef\list@{\first@@} + \else + \xdef\PDB@type{plane} + \ifx\fourth@\PDB@type + \xdef\PDB@{y} + \xdef\last@{#3[,]&}\expandafter\opt@color\last@ + \xdef\PDB@refnum{\fourth@} + \ifx\f@color\C@lpha + \xdef\PDB@back@side{CA} + \else + \xdef\PDB@back@side{side} + \fi + \xdef\last@{#4[,]&}\expandafter\opt@color\last@ + \ifnum\PDB@refnum<\fourth@ + \xdef\PDB@refnum@a{\PDB@refnum} + \xdef\PDB@refnum@b{\fourth@} + \xdef\PDB@back@side@a{\PDB@back@side} + \ifx\f@color\C@lpha + \xdef\PDB@back@side@b{CA} + \else + \xdef\PDB@back@side@b{side} + \fi + \else + \xdef\PDB@refnum@b{\PDB@refnum} + \xdef\PDB@refnum@a{\fourth@} + \xdef\PDB@back@side@b{\PDB@back@side} + \ifx\f@color\C@lpha + \xdef\PDB@back@side@a{CA} + \else + \xdef\PDB@back@side@a{side} + \fi + \fi + \xdef\last@{#5[,]&}\expandafter\opt@color\last@ + \xdef\PDB@refnum{\fourth@} + \ifx\f@color\C@lpha + \xdef\PDB@back@side{CA} + \else + \xdef\PDB@back@side{side} + \fi + \ifnum\PDB@refnum>\PDB@refnum@b + \xdef\PDB@refnum@c{\PDB@refnum} + \xdef\PDB@back@side@c{\PDB@back@side} + \else + \ifnum\PDB@refnum>\PDB@refnum@a + \xdef\PDB@refnum@c{\PDB@refnum@b} + \xdef\PDB@back@side@c{\PDB@back@side@b} + \xdef\PDB@refnum@b{\PDB@refnum} + \xdef\PDB@back@side@b{\PDB@back@side} + \else + \xdef\PDB@refnum@c{\PDB@refnum@b} + \xdef\PDB@back@side@c{\PDB@back@side@b} + \xdef\PDB@refnum@b{\PDB@refnum@a} + \xdef\PDB@back@side@b{\PDB@back@side@a} + \xdef\PDB@refnum@a{\PDB@refnum} + \xdef\PDB@back@side@a{\PDB@back@side} + \fi + \fi + \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi + \load@PDB + \expandafter\get@item\PDB@stack \xdef\list@{\first@@} + \else + \xdef\temp@{\list@ @} + \expandafter\test@motif\temp@ + \fi + \fi + \fi +} + +\def\test@fill#1:#2:#3&{% + \xdef\last@{#1[,][,]&}\expandafter\arrow@col@width\last@% + \xdef\second@@{\fourth@}% + \xdef\last@{///}% + \ifx\fourth@\last@% + \xdef\second@@{empty}% + \else + \xdef\last@{translate}% + \ifx\fourth@\last@% + \xdef\second@@{translate}% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{fill}% + \ifx\fourth@\last@ + \xdef\second@@{fill}% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{bar}% + \ifx\fourth@\last@ + \xdef\second@@{bar}% + \xdef\b@r{bar}% + \ifx\f@color\comm@ + \xdef\g@min{,}\xdef\g@max{,}% + \else + \xdef\f@color{\f@color @}% + \expandafter\get@item\f@color% + \xdef\g@min{\fourth@} \xdef\g@max{\first@@}% + \xdef\pm@shift{\fourth@}% + \fi% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi% + \xdef\fill@char{\fourth@}% + \xdef\box@color{\f@color,&@}% + \expandafter\two@opt@color\box@color% + \else + \xdef\last@{color}% + \ifx\fourth@\last@ + \xdef\second@@{color}% + \ifx\f@color\comm@ + \xdef\g@min{,}\xdef\g@max{,}% + \else + \xdef\f@color{\f@color @}% + \expandafter\get@item\f@color% + \xdef\g@min{\fourth@} \xdef\g@max{\first@@}% + \fi% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{box}% + \ifx\fourth@\last@% + \xdef\second@@{box}% + \ifx\f@color\comm@\xdef\f@color{White}\fi% + \xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@% + \ifnumber% + \ifx\rule@@thick\comm@% + \xdef\rule@@thick{\f@color}% + \xdef\box@color{White,&@}% + \else% + \xdef\seventh@{\rule@@thick}% + \xdef\rule@@thick{\f@color}% + \xdef\box@color{\seventh@,&@}% + \fi% + \else% + \xdef\box@color{\f@color,&@}% + \fi% + \expandafter\two@opt@color\box@color% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{plotcolor}% + \ifx\fourth@\last@% + \xdef\second@@{plotcolor}% + \ifx\f@color\comm@% + \xdef\pm@shift{0}% + \else% + \xdef\pm@shift{\f@color}% + \fi% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{plotbar}% + \ifx\fourth@\last@% + \xdef\second@@{plotbar}% + \xdef\b@r{bar}% + \ifx\f@color\comm@ + \xdef\pm@shift{0}% + \else + \xdef\pm@shift{\f@color}% + \fi% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi% + \xdef\fill@char{\fourth@}% + \xdef\box@color{\f@color,&@}% + \expandafter\two@opt@color\box@color% + \else + \xdef\arrow@color{\f@color}% + \ifx\arrow@color\comm@\xdef\arrow@color{Black}\fi% + \xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@% + \ifnumber% + \ifx\rule@@thick\comm@% + \xdef\rule@@thick{\f@color}% + \xdef\arrow@color{Black}% + \else% + \xdef\seventh@{\rule@@thick}% + \xdef\rule@@thick{\f@color}% + \xdef\arrow@color{\seventh@}% + \fi% + \fi% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \xdef\fill@char{\fourth@}% + \ifx\f@color\comm@\xdef\f@color{Black,White}\fi% + \xdef\backtext@color{White}% + \xdef\f@color{\f@color,&@}% + \expandafter\two@opt@color\f@color% + \xdef\f@color{\arrow@color}% + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@% + \ifnumber% + \ifx\rule@@thick\comm@% + \xdef\rule@@thick{\f@color}% + \xdef\f@color{Black}% + \else% + \xdef\seventh@{\rule@@thick}% + \xdef\rule@@thick{\f@color}% + \xdef\f@color{\seventh@}% + \fi% + \fi% + \ifx\rule@@thick\comm@\xdef\rule@@thick{\the\rule@thick}\fi% + \ifx\f@color\comm@\xdef\f@color{Black}\fi} +\def\clear@groups{% + \expandafter\xdef\csname \prfx grpA\endcsname{ -1} + \expandafter\xdef\csname \prfx grpB\endcsname{ -2} + \expandafter\xdef\csname \prfx grpC\endcsname{ -3} + \expandafter\xdef\csname \prfx grpD\endcsname{ -4} + \expandafter\xdef\csname \prfx grpE\endcsname{ -5} + \expandafter\xdef\csname \prfx grpF\endcsname{ -6} + \expandafter\xdef\csname \prfx grpG\endcsname{ -7} + \expandafter\xdef\csname \prfx grpH\endcsname{ -8} + \expandafter\xdef\csname \prfx grpI\endcsname{ -9} + \expandafter\xdef\csname \prfx grpJ\endcsname{-10} + \expandafter\xdef\csname \prfx grpK\endcsname{-11} + \expandafter\xdef\csname \prfx grpL\endcsname{-12} + \expandafter\xdef\csname \prfx grpM\endcsname{-13} + \expandafter\xdef\csname \prfx grpN\endcsname{-14} + \expandafter\xdef\csname \prfx grpO\endcsname{-15} + \expandafter\xdef\csname \prfx grpP\endcsname{-16} + \expandafter\xdef\csname \prfx grpQ\endcsname{-17} + \expandafter\xdef\csname \prfx grpR\endcsname{-18} + \expandafter\xdef\csname \prfx grpS\endcsname{-19} + \expandafter\xdef\csname \prfx grpT\endcsname{-20} + \expandafter\xdef\csname \prfx grpU\endcsname{-21} + \expandafter\xdef\csname \prfx grpV\endcsname{-22} + \expandafter\xdef\csname \prfx grpW\endcsname{-23} + \expandafter\xdef\csname \prfx grpX\endcsname{-24} + \expandafter\xdef\csname \prfx grpY\endcsname{-25} + \expandafter\xdef\csname \prfx grpZ\endcsname{-26} + \expandafter\xdef\csname \prfx grp-\endcsname{-999} + \expandafter\xdef\csname \prfx grp.\endcsname{-999} + \expandafter\xdef\csname \prfx grp=\endcsname{-999} +} +\def\inactivate@chars{% + \catcode`\#=12 + \catcode`\"=12 + \catcode`\~=12 + \catcode`\^=12 + \catcode`\_=12 + } +\def\numcount{\the\loopcount} +\def\Alphacount{\@Alph\loopcount} +\def\alphacount{\@alph\loopcount} +\def\romancount{\@roman\loopcount} +\def\Romancount{\@Roman\loopcount} +\def\cut@name#1.#2@{\global\xdef\file@n@me{#1}} +\def\coord@get#1.#2#3@{% + \xdef\temp@{#2} + \ifx\temp@\ampers@nd \xdef\temp@{0} \fi + \xdef\c@@rd{#1\temp@} +} +\def\struc@get#1 #2 #3 #4 #5 #6 #7 #8 #9@{% + \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\fourth@{#4} + \xdef\fifth@{#5} \xdef\sixth@{#6} \xdef\seventh@{#7}\xdef\eighth@{#8} + \xdef\nineth@{#9}} +\def\get@PHD#1|#2|#3@{\xdef\PHD@line{\PHD@line #2}} +\def\write@PHDsec{% + \expandafter\get@sim\last@ + \ifx\sim@char\c@mp + \def\end@{\the\innerloopcount} + \advance\innerloopcount by 1 + \else + \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi + \if\c@mp . + \else + \if\c@mp L + \else + \if\c@mp H + \ifx\show@Hsec\yes + \loopcount=\first@ + \advance\loopcount by 1 + \xdef\first@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Hsec}{\begin@..\end@}% + {\label@Hsec}{\text@Hsec}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Hsec}{\st@rt}{\begin@..\end@}% + {\label@Hsec}{\text@Hsec}}\fi + \fi + \else + \if\c@mp E + \ifx\show@Esec\yes + \loopcount=\second@ + \advance\loopcount by 1 + \xdef\second@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Esec}{\begin@..\end@}% + {\label@Esec}{\text@Esec}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Esec}{\st@rt}{\begin@..\end@}% + {\label@Esec}{\text@Esec}}\fi + \fi + \fi\fi\fi\fi + \xdef\c@mp{\sim@char} + \advance\innerloopcount by 1 + \xdef\begin@{\the\innerloopcount} + \fi + \ifx\sim@char\ampers@nd\else\write@PHDsec\fi +} +\def\write@PHDtopo{% + \expandafter\get@sim\last@ + \ifx\sim@char\c@mp + \def\end@{\the\innerloopcount} + \advance\innerloopcount by 1 + \else + \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi + \if\c@mp . + \else + \if\c@mp L + \else + \if\c@mp T + \ifx\show@TMtop\yes + \loopcount=\first@ + \advance\loopcount by 1 + \xdef\first@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@TMtop}{\begin@..\end@}% + {\label@TMtop}{\text@TMtop}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@TMtop}{\st@rt}{\begin@..\end@}% + {\label@TMtop}{\text@TMtop}}\fi + \fi + \else + \if\c@mp i + \ifx\show@itop\yes + \loopcount=\second@ + \advance\loopcount by 1 + \xdef\second@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@itop}{\begin@..\end@}% + {\label@itop}{\text@itop}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@itop}{\st@rt}{\begin@..\end@}% + {\label@itop}{\text@itop}}\fi + \fi + \else + \if\c@mp o + \ifx\show@etop\yes + \loopcount=\second@ + \advance\loopcount by 1 + \xdef\second@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@etop}{\begin@..\end@}% + {\label@etop}{\text@etop}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@etop}{\st@rt}{\begin@..\end@}% + {\label@etop}{\text@etop}}\fi + \fi + \fi\fi\fi\fi\fi + \xdef\c@mp{\sim@char} + \advance\innerloopcount by 1 + \xdef\begin@{\the\innerloopcount} + \fi + \ifx\sim@char\ampers@nd\else\write@PHDtopo\fi +} +\def\include@T@coffee{% + \bgroup + \immediate\openin\structurefile = \TC@first@\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\TC@first@' not found} + {\MessageBreak + The file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No T-Coffee shading will be displayed (using "similar"). \MessageBreak + Type <return> to proceed. \MessageBreak + Type X <return> to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \simmodetrue \funcmodefalse \T@coffeefalse + \else + \message{<T-Coffee shading>} + \xdef\first@{} \xdef\temp@{*} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\temp@ \xdef\temp@{y} + \read\structurefile to \readline + \read\structurefile to \readline + \fi + \fi + \ifx\temp@\y@ \else\repeat + \loopcount=0 + \xdef\temp@{cons} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \if\second@ : + \advance\loopcount by 1\relax + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} + \fi + \fi + \ifx\first@\temp@\expandafter\xdef\csname T@coffee0\endcsname{} \else\repeat + \xdef\temp@{\the\loopcount} + \loopcount=0 + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \advance\loopcount by 1 + \ifnum\loopcount=\temp@ \loopcount=0 \fi + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname \third@} + \fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \loopcount=0 + \loop + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} + \advance\loopcount by 1 + \ifnum\loopcount=\temp@ \else\repeat + \egroup + \def\n@m@tch{{$\bullet$}} + \expandafter\def\csname fg@color0\endcsname{TC0} + \expandafter\def\csname fg@color1\endcsname{TC1} + \expandafter\def\csname fg@color2\endcsname{TC2} + \expandafter\def\csname fg@color3\endcsname{TC3} + \expandafter\def\csname fg@color4\endcsname{TC4} + \expandafter\def\csname fg@color5\endcsname{TC5} + \expandafter\def\csname fg@color6\endcsname{TC6} + \expandafter\def\csname fg@color7\endcsname{TC7} + \expandafter\def\csname fg@color8\endcsname{TC8} + \expandafter\def\csname fg@color9\endcsname{TC9} + \expandafter\def\csname fg@textcolor0\endcsname{Black} + \expandafter\def\csname fg@textcolor1\endcsname{Black} + \expandafter\def\csname fg@textcolor2\endcsname{Black} + \expandafter\def\csname fg@textcolor3\endcsname{Black} + \expandafter\def\csname fg@textcolor4\endcsname{Black} + \expandafter\def\csname fg@textcolor5\endcsname{Black} + \expandafter\def\csname fg@textcolor6\endcsname{Black} + \expandafter\def\csname fg@textcolor7\endcsname{Black} + \expandafter\def\csname fg@textcolor8\endcsname{Black} + \expandafter\def\csname fg@textcolor9\endcsname{Black} + \fi + } + +\def\include@DSSP{% + \xdef\first@{\csname optiondssp\the\loopcount\endcsname} + \xdef\bottop@{\csname bottopdssp\the\loopcount\endcsname} + \xdef\st@rt{\csname doseqdssp\the\loopcount\endcsname} + \xdef\structurefilename{\csname filenamedssp\the\loopcount\endcsname} + \bgroup + \xdef\file@n@me{\structurefilename .@} + \expandafter\cut@name\file@n@me + \xdef\file@n@me{\file@n@me.sec} + \ifx\first@\file@n@me + \else + \immediate\openin\alignfile = \file@n@me\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \fi + \xdef\temp@{make new} + \ifx\first@\temp@ + \def\par{} + \inactivate@chars + \immediate\openin\structurefile = \structurefilename\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\structurefilename' not found} + {\MessageBreak + The `DSSP' file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No labels for secondary structures will be displayed. \MessageBreak + Type <return> to proceed. \MessageBreak + Type X <return> to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \message{[\structurefilename] ->} + \xdef\second@{} \xdef\temp@{RESIDUE} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\second@\temp@ \xdef\temp@{AA}\fi + \ifx\third@\temp@ \else\repeat + \immediate\openout\featurefile = \file@n@me + \xdef\c@mp{+} + \xdef\begin@{\csname seq@start\st@rt\endcsname} + \xdef\end@{\csname seq@start\st@rt\endcsname} + \xdef\st@rt@{\begin@} + \expandafter\innerloopcount=\csname seq@start\st@rt\endcsname + \advance\innerloopcount by -1 + \xdef\first@@{0} \xdef\second@@{0} \xdef\third@@{0} + \xdef\fourth@@{0} \xdef\fifth@@{0} \xdef\sixth@@{0} + \xdef\seventh@@{0} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \if\c@mp + \xdef\c@mp{\fifth@}\fi + \ifx\fifth@\c@mp + \ifx\fc@DSSP\y@ + \temp@count=\first@ + \else + \temp@count=\second@ + \fi + \advance\temp@count by \st@rt@ + \advance\temp@count by -1 + \xdef\end@{\the\temp@count} + \else + \ifnum\begin@>0 + \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi + \if\c@mp C + \else + \if\c@mp H + \ifx\show@Hdssp\yes + \loopcount=\first@@ + \advance\loopcount by 1 + \xdef\first@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Hdssp}{\begin@..\end@}% + {\label@Hdssp}{\text@Hdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Hdssp}{\st@rt}{\begin@..\end@}% + {\label@Hdssp}{\text@Hdssp}}\fi + \fi + \else + \if\c@mp G + \ifx\show@Gdssp\yes + \loopcount=\second@@ + \advance\loopcount by 1 + \xdef\second@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Gdssp}{\begin@..\end@}% + {\label@Gdssp}{\text@Gdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Gdssp}{\st@rt}{\begin@..\end@}% + {\label@Gdssp}{\text@Gdssp}}\fi + \fi + \else + \if\c@mp I + \ifx\show@Idssp\yes + \loopcount=\third@@ + \advance\loopcount by 1 + \xdef\third@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Idssp}{\begin@..\end@}% + {\label@Idssp}{\text@Idssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Idssp}{\st@rt}{\begin@..\end@}% + {\label@Idssp}{\text@Idssp}}\fi + \fi + \else + \if\c@mp E + \ifx\show@Edssp\yes + \loopcount=\fourth@@ + \advance\loopcount by 1 + \xdef\fourth@@{\the\loopcount} + \advance\innerloopcount by 1 + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Edssp}{\begin@..\end@}% + {\label@Edssp}{\text@Edssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Edssp}{\st@rt}{\begin@..\end@}% + {\label@Edssp}{\text@Edssp}}\fi + \fi + \else + \if\c@mp B + \ifx\show@Bdssp\yes + \loopcount=\fifth@@ + \advance\loopcount by 1 + \xdef\fifth@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Bdssp}{\begin@..\end@}% + {\label@Bdssp}{\text@Bdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Bdssp}{\st@rt}{\begin@..\end@}% + {\label@Bdssp}{\text@Bdssp}}\fi + \fi + \else + \if\c@mp T + \ifx\show@Tdssp\yes + \loopcount=\sixth@@ + \advance\loopcount by 1 + \xdef\sixth@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Tdssp}{\begin@..\end@}% + {\label@Tdssp}{\text@Tdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Tdssp}{\st@rt}{\begin@..\end@}% + {\label@Tdssp}{\text@Tdssp}}\fi + \fi + \else + \if\c@mp S + \ifx\show@Sdssp\yes + \loopcount=\seventh@@ + \advance\loopcount by 1 + \xdef\seventh@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Sdssp}{\begin@..\end@}% + {\label@Sdssp}{\text@Sdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Sdssp}{\st@rt}{\begin@..\end@}% + {\label@Sdssp}{\text@Sdssp}}\fi + \fi + \fi\fi\fi\fi\fi\fi\fi\fi + \fi + \xdef\c@mp{\fifth@} + \ifx\fc@DSSP\y@ + \temp@count=\first@ + \else + \temp@count=\second@ + \fi + \advance\temp@count by \st@rt@ + \advance\temp@count by -1 + \xdef\begin@{\the\temp@count} + \fi + \fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \immediate\closeout\featurefile + \egroup + \input{\file@n@me} + \fi + \else + \egroup + \message{using existing file:} + \input{\file@n@me} + \fi + } + +\def\include@HMMTOP{% + \def\get@HMMTOP@TMs##1-##2 ##3@{% + \xdef\temp@@{\temp@@\fourth@@##1\fourth@@##2} + \xdef\structureline{##3 @} + } + \def\get@HMMTOP{% + \ifnum\temp@count<\fifth@ + \advance\temp@count by 1 + \expandafter\get@HMMTOP@TMs\structureline + \get@HMMTOP + \fi + } + \def\rem@ve@TM@info Transmembrane helices: ##1@{% + \xdef\structureline{##1 @} + \temp@count=0 + \get@HMMTOP + } + \xdef\bottop@{\csname bottopHMMTOP\the\loopcount\endcsname} + \xdef\st@rt{\csname doseqHMMTOP\the\loopcount\endcsname} + \xdef\first@{\csname optionHMMTOP\the\loopcount\endcsname} + \xdef\structurefilename{\csname filenameHMMTOP\the\loopcount\endcsname} + \bgroup + \xdef\file@n@me{\structurefilename .@} + \expandafter\cut@name\file@n@me + \xdef\file@n@me{\file@n@me.top} + \ifx\first@\file@n@me + \else + \immediate\openin\alignfile = \file@n@me\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \fi + \xdef\temp@{make new} + \ifx\first@\temp@ + \def\par{} + \inactivate@chars + \immediate\openin\structurefile = \structurefilename\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\structurefilename' not found} + {\MessageBreak + The `HMMTOP' file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No labels for secondary structures will be displayed. \MessageBreak + Type <return> to proceed. \MessageBreak + Type X <return> to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \message{[\structurefilename] ->} + \immediate\openout\featurefile = \file@n@me + + \xdef\first@{\csname fileseqHMMTOP\the\loopcount\endcsname @} + \expandafter\check@letter\first@ + \ifletter + \xdef\st@p{\csname fileseqHMMTOP\the\loopcount\endcsname} + \else + \xdef\first@{\csname fileseqHMMTOP\the\loopcount\endcsname} + \ifnum\first@=0 + \xdef\st@p{0} + \else + \xdef\st@p{\csname fileseqHMMTOP\the\loopcount\endcsname} + \fi + \fi + \xdef\temp@{yes} \innerloopcount=0 + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\@HP + \ifx\temp@\yes \xdef\temp@{\readline} \fi + \ifletter + \ifx\st@p\third@ \xdef\temp@{\readline} \fi + \else + \ifnum\st@p=0 + \expandafter\ifx\csname seqname\st@rt\endcsname\third@ + \xdef\temp@{\readline} \xdef\st@p{-1} + \else + \expandafter\ifx\csname newseqname\st@rt\endcsname\third@ + \xdef\temp@{\readline} \xdef\st@p{-1} + \fi + \fi + \else + \advance\innerloopcount by 1 + \ifnum\st@p=\innerloopcount \xdef\temp@{\readline} \fi + \fi + \fi + \else + \xdef\first@@{Protein:} + \ifx\first@\first@@ + \xdef\second@@{\second@} + \xdef\temp@@{>HP:} \xdef\fourth@@{ } + \read\structurefile to \readline + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \xdef\temp@@{\temp@@\fourth@@\second@\fourth@@\second@@} + \read\structurefile to \readline + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \xdef\temp@@{\temp@@\fourth@@\second@} + \read\structurefile to \readline + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \xdef\temp@@{\temp@@\fourth@@\fifth@} + \read\structurefile to \readline + \xdef\structureline{\readline @} + \expandafter\rem@ve@TM@info\structureline + \xdef\temp@@{\temp@@\fourth@@} + \ifx\temp@\yes \xdef\temp@{\temp@@} \fi + \ifletter + \ifx\st@p\third@ \xdef\temp@{\temp@@} \fi + \else + \ifnum\st@p=0 + \expandafter\ifx\csname seqname\st@rt\endcsname\second@@ + \xdef\temp@{\temp@@} + \else + \expandafter\ifx\csname newseqname\st@rt\endcsname\second@@ + \xdef\temp@{\temp@@} + \fi + \fi + \else + \advance\innerloopcount by 1 + \ifnum\st@p=\innerloopcount \xdef\temp@{\temp@@} \fi + \fi + \fi + \fi + \fi + \fi + \ifeof\structurefile \else\repeat + \xdef\seq@line{\temp@ @} + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \expandafter\seq@get\seq@line + \xdef\seq@line{\seq@line @} + \ifnum\innerloopcount=4 \xdef\c@mp{\first@} \fi + \ifnum\innerloopcount=5 \xdef\st@p{\first@} \else \repeat + \xdef\first@{IN} + \ifx\c@mp\first@ \xdef\c@mp{i} \else \xdef\c@mp{e} \fi + \xdef\begin@{1} \xdef\first@@{0} \xdef\second@@{0} + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \expandafter\seq@get\seq@line + \xdef\seq@line{\seq@line @} + \temp@count=\first@ + \advance\temp@count by -1 + \xdef\end@{\the\temp@count} + \loopcount=\second@@ + \advance\loopcount by 1 + \xdef\second@@{\the\loopcount} + \if\c@mp i + \ifx\show@i@HMMTOP\yes + \immediate\write\featurefile{% + \string\feature{\bottop@i@HMMTOP}{\st@rt}{\begin@..\end@}% + {\label@i@HMMTOP}{\text@i@HMMTOP}}\fi + \xdef\c@mp{e} + \else + \ifx\show@e@HMMTOP\yes + \immediate\write\featurefile{% + \string\feature{\bottop@e@HMMTOP}{\st@rt}{\begin@..\end@}% + {\label@e@HMMTOP}{\text@e@HMMTOP}}\fi + \xdef\c@mp{i} + \fi + \advance\temp@count by 1 + \xdef\begin@{\the\temp@count} + \expandafter\seq@get\seq@line + \xdef\seq@line{\seq@line @} + \xdef\end@{\first@} + \loopcount=\first@@ + \advance\loopcount by 1 + \xdef\first@@{\the\loopcount} + \ifx\show@TM@HMMTOP\yes + \immediate\write\featurefile{% + \string\feature{\bottop@TM@HMMTOP}{\st@rt}{\begin@..\end@}% + {\label@TM@HMMTOP}{\text@TM@HMMTOP}}\fi + \temp@count=\end@ \advance\temp@count by 1 \xdef\begin@{\the\temp@count} + \ifnum\innerloopcount=\st@p\else\repeat + \closein\structurefile + \immediate\closeout\featurefile + \egroup + + \input{\file@n@me} + \fi + \else + \egroup + \message{using existing file:} + \input{\file@n@me} + \fi + } + +\def\include@stride{% + \xdef\first@{\csname optionstride\the\loopcount\endcsname} + \xdef\bottop@{\csname bottopstride\the\loopcount\endcsname} + \xdef\st@rt{\csname doseqstride\the\loopcount\endcsname} + \xdef\structurefilename{\csname filenamestride\the\loopcount\endcsname} + \bgroup + \xdef\file@n@me{\structurefilename .@} + \expandafter\cut@name\file@n@me + \xdef\file@n@me{\file@n@me.sec} + \ifx\first@\file@n@me + \else + \immediate\openin\alignfile = \file@n@me\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \fi + \xdef\temp@{make new} + \ifx\first@\temp@ + \def\par{} + \inactivate@chars + \immediate\openin\structurefile = \structurefilename\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\structurefilename' not found} + {\MessageBreak + The `STRIDE' file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No labels for secondary structures will be displayed. \MessageBreak + Type <return> to proceed. \MessageBreak + Type X <return> to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \message{[\structurefilename] ->} + \immediate\openout\featurefile = \file@n@me + \xdef\c@mp{+} + \xdef\begin@{\csname seq@start\st@rt\endcsname} + \xdef\end@{\csname seq@start\st@rt\endcsname} + \xdef\st@rt@{\begin@} + \expandafter\innerloopcount=\csname seq@start\st@rt\endcsname + \advance\innerloopcount by -1 + \xdef\first@@{0} \xdef\second@@{0} \xdef\third@@{0} + \xdef\fourth@@{0} \xdef\fifth@@{0} \xdef\sixth@@{0} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\@asg + \if\c@mp + \xdef\c@mp{\sixth@}\fi + \ifx\sixth@\c@mp + \temp@count=\fifth@ + \advance\temp@count by \st@rt@ + \advance\temp@count by -1 + \xdef\end@{\the\temp@count} + \else + \ifnum\begin@>0 + \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi + \if\c@mp C + \else + \if\c@mp H + \ifx\show@Hstride\yes + \loopcount=\first@@ + \advance\loopcount by 1 + \xdef\first@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Hstride}{\begin@..\end@}% + {\label@Hstride}{\text@Hstride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Hstride}{\st@rt}{\begin@..\end@}% + {\label@Hstride}{\text@Hstride}}\fi + \fi + \else + \if\c@mp G + \ifx\show@Gstride\yes + \loopcount=\second@@ + \advance\loopcount by 1 + \xdef\second@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Gstride}{\begin@..\end@}% + {\label@Gstride}{\text@Gstride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Gstride}{\st@rt}{\begin@..\end@}% + {\label@Gstride}{\text@Gstride}}\fi + \fi + \else + \if\c@mp I + \ifx\show@Istride\yes + \loopcount=\third@@ + \advance\loopcount by 1 + \xdef\third@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Istride}{\begin@..\end@}% + {\label@Istride}{\text@Istride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Istride}{\st@rt}{\begin@..\end@}% + {\label@Istride}{\text@Istride}}\fi + \fi + \else + \if\c@mp E + \ifx\show@Estride\yes + \loopcount=\fourth@@ + \advance\loopcount by 1 + \xdef\fourth@@{\the\loopcount} + \advance\innerloopcount by 1 + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Estride}{\begin@..\end@}% + {\label@Estride}{\text@Estride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Estride}{\st@rt}{\begin@..\end@}% + {\label@Estride}{\text@Estride}}\fi + \fi + \else + \if\c@mp B + \ifx\show@Bstride\yes + \loopcount=\fifth@@ + \advance\loopcount by 1 + \xdef\fifth@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Bstride}{\begin@..\end@}% + {\label@Bstride}{\text@Bstride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Bstride}{\st@rt}{\begin@..\end@}% + {\label@Bstride}{\text@Bstride}}\fi + \fi + \else + \if\c@mp T + \ifx\show@Tstride\yes + \loopcount=\sixth@@ + \advance\loopcount by 1 + \xdef\sixth@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Tstride}{\begin@..\end@}% + {\label@Tstride}{\text@Tstride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Tstride}{\st@rt}{\begin@..\end@}% + {\label@Tstride}{\text@Tstride}}\fi + \fi + \fi\fi\fi\fi\fi\fi\fi + \fi + \xdef\c@mp{\sixth@} + \temp@count=\fifth@ + \advance\temp@count by \st@rt@ + \advance\temp@count by -1 + \xdef\begin@{\the\temp@count} + \fi + \fi + \fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \immediate\closeout\featurefile + \egroup + \input{\file@n@me} + \fi + \else + \egroup + \message{using existing file:} + \input{\file@n@me} + \fi + } +\def\include@PHD{% + \xdef\first@{\csname optionphd\the\loopcount\endcsname} + \xdef\bottop@{\csname bottopphd\the\loopcount\endcsname} + \xdef\st@rt{\csname doseqphd\the\loopcount\endcsname} + \xdef\m@de{\csname modephd\the\loopcount\endcsname} + \xdef\structurefilename{\csname filenamephd\the\loopcount\endcsname} + \bgroup + \xdef\file@n@me{\structurefilename .@} + \expandafter\cut@name\file@n@me + \xdef\temp@{structure} + \ifx\m@de\temp@ + \xdef\temp@{\file@n@me .sec} + \immediate\openin\alignfile = \temp@\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \else + \xdef\temp@{topology} + \ifx\m@de\temp@ + \xdef\temp@{\file@n@me .top} + \immediate\openin\alignfile = \temp@\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \else + \message{<Unknown type - ignoring \noexpand\includePHD>} + \xdef\first@{ignore} + \fi\fi + \xdef\temp@{make new} + \ifx\first@\temp@ + \def\par{} + \xdef\PHD@line{} + \inactivate@chars + \immediate\openin\structurefile=\structurefilename\relax + \ifeof\structurefile + \PackageError{TeXshade}% + {File `\structurefilename' not found}% + {\MessageBreak + The `PHD' file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No labels for secondary structures will be displayed. \MessageBreak + Type <return> to proceed. \MessageBreak + Type X <return> to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \message{[\structurefilename] ->} + \loop + \read\structurefile to \readline + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \xdef\temp@{structure} + \ifx\m@de\temp@ + \xdef\temp@{SUB} + \ifx\temp@\first@ + \xdef\temp@{sec} + \ifx\temp@\second@ + \xdef\third@{\third@ @} + \expandafter\get@PHD\third@ + \fi + \else + \ifx\temp@\second@ + \xdef\temp@{sec} + \ifx\temp@\third@ + \xdef\fourth@{\fourth@ @} + \expandafter\get@PHD\fourth@ + \fi + \fi + \fi + \else + \xdef\temp@{topology} + \ifx\m@de\temp@ + \xdef\temp@{PHDThtm} + \ifx\temp@\first@ + \xdef\second@{\second@ @} + \expandafter\get@PHD\second@ + \fi + \fi\fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \xdef\c@mp{+} + \xdef\begin@{\csname seq@start\st@rt\endcsname} + \xdef\end@{\csname seq@start\st@rt\endcsname} + \expandafter\innerloopcount=\csname seq@start\st@rt\endcsname + \advance\innerloopcount by -1 + \xdef\first@{0} \xdef\second@{0} \xdef\third@{0} + \xdef\fourth@{0} \xdef\fifth@{0} \xdef\sixth@{0} + \xdef\last@{\PHD@line &@} + \xdef\temp@{structure} + \ifx\temp@\m@de + \xdef\file@n@me{\file@n@me .sec} + \immediate\openout\featurefile = \file@n@me\relax + \write@PHDsec + \fi + \xdef\temp@{topology} + \ifx\temp@\m@de + \xdef\file@n@me{\file@n@me .top} + \immediate\openout\featurefile = \file@n@me\relax + \write@PHDtopo + \fi + \immediate\closeout\featurefile + \egroup + \input{\file@n@me} + \fi + \else + \egroup + \xdef\temp@{ignore} + \ifx\temp@\first@ + \else + \message{using existing file:} + \xdef\temp@{structure} + \ifx\temp@\m@de \xdef\file@n@me{\file@n@me .sec} \fi + \xdef\temp@{topology} + \ifx\temp@\m@de \xdef\file@n@me{\file@n@me .top} \fi + \input{\file@n@me} + \fi + \fi} +\def\show@DSSP{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{alpha} + \ifx\fourth@\temp@ \xdef\show@Hdssp{\second@}\fi + \xdef\temp@{3-10} + \ifx\fourth@\temp@ \xdef\show@Gdssp{\second@}\fi + \xdef\temp@{pi} + \ifx\fourth@\temp@ \xdef\show@Idssp{\second@}\fi + \xdef\temp@{beta} + \ifx\fourth@\temp@ \xdef\show@Edssp{\second@}\fi + \xdef\temp@{bridge} + \ifx\fourth@\temp@ \xdef\show@Bdssp{\second@}\fi + \xdef\temp@{turn} + \ifx\fourth@\temp@ \xdef\show@Tdssp{\second@}\fi + \xdef\temp@{bend} + \ifx\fourth@\temp@ \xdef\show@Sdssp{\second@}\fi + \show@DSSP + \fi} +\def\show@HMMTOP{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{internal} + \ifx\fourth@\temp@ \xdef\show@i@HMMTOP{\second@}\fi + \xdef\temp@{external} + \ifx\fourth@\temp@ \xdef\show@e@HMMTOP{\second@}\fi + \xdef\temp@{TM} + \ifx\fourth@\temp@ \xdef\show@TM@HMMTOP{\second@}\fi + \show@HMMTOP + \fi} +\def\show@STRIDE{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{alpha} + \ifx\fourth@\temp@ \xdef\show@Hstride{\second@}\fi + \xdef\temp@{3-10} + \ifx\fourth@\temp@ \xdef\show@Gstride{\second@}\fi + \xdef\temp@{pi} + \ifx\fourth@\temp@ \xdef\show@Istride{\second@}\fi + \xdef\temp@{beta} + \ifx\fourth@\temp@ \xdef\show@Estride{\second@}\fi + \xdef\temp@{bridge} + \ifx\fourth@\temp@ \xdef\show@Bstride{\second@}\fi + \xdef\temp@{turn} + \ifx\fourth@\temp@ \xdef\show@Tstride{\second@}\fi + \show@STRIDE + \fi} +\def\show@PHDtopo{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{internal} + \ifx\fourth@\temp@ \xdef\show@itop{\second@}\fi + \xdef\temp@{external} + \ifx\fourth@\temp@ \xdef\show@etop{\second@}\fi + \xdef\temp@{TM} + \ifx\fourth@\temp@ \xdef\show@TMtop{\second@}\fi + \show@PHDtopo + \fi} +\def\show@PHDsec{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{alpha} + \ifx\fourth@\temp@ \xdef\show@Hsec{\second@}\fi + \xdef\temp@{beta} + \ifx\fourth@\temp@ \xdef\show@Esec{\second@}\fi + \show@PHDsec + \fi} +\def\get@triplet#1,#2@{% + \xdef\third@{#1} + \ifx\third@\ampers@nd + \else + \expandafter\xdef\csname @\third@\endcsname{\first@} + \expandafter\xdef\csname rev@\first@\endcsname{\third@} + \xdef\fourth@{#2,&,@} + \expandafter\get@triplet\fourth@ + \fi} +\def\get@dom@count#1,#2@{\res@count=#1 \xdef\temp@{#2 @}} +\def\get@name@number{% + \xdef\second@{n} + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\ifx\csname newseqname\the\loopcount\endcsname\first@ + \xdef\first@{\the\loopcount} \loopcount=\seq@count + \xdef\second@{y} + \fi + \ifnum\loopcount=\seq@count \else \repeat + \ifx\second@\n@ + \message{<Sequence name `\first@' was not found - using first sequence.>} + \xdef\first@{1} + \fi +} +\def\get@name@number@table{% + \xdef\second@{n}% + \loopcount=0% + \loop% + \advance\loopcount by 1% + \expandafter\ifx\csname newseqname\the\loopcount\endcsname\first@% + \xdef\first@{\the\loopcount}\loopcount=\seq@num% + \xdef\second@{y}% + \fi% + \ifnum\loopcount=\seq@num\else\repeat% + \ifx\second@\n@% + \message{<Sequence name `\first@' was not found - using first sequence.>}% + \xdef\first@{1}% + \fi% +} + +\def\calc@distance@point{% + \loopcount=\xref@coord@a \advance\loopcount by -\x@coord\relax + \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount} + \loopcount=\yref@coord@a \advance\loopcount by -\y@coord\relax + \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount} + \loopcount=\zref@coord@a \advance\loopcount by -\z@coord\relax + \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount} + \advance\loopcount by \y@distance\relax + \advance\loopcount by \x@distance\relax + \ifnum\loopcount > \PDB@distance \else + \loopcount=\PDB@hitpos \advance\loopcount by 1 + \ifnum\loopcount=\PDB@pos + \else + \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..} + \fi + \xdef\PDB@hitpos{\PDB@pos} + \fi +} + +\def\calc@distance@line{% + \loopcount=\x@coord\relax \multiply\loopcount by \x@orient + \temp@count=\y@coord \relax \multiply\temp@count by \y@orient + \advance\loopcount by \temp@count + \temp@count=\z@coord \relax \multiply\temp@count by \z@orient + \advance\loopcount by \temp@count + \advance\loopcount by -\c@nst@ + \xdef\z@hler{\the\loopcount} + \multiply\loopcount by \x@orient \divide\loopcount by \f@ct@r \advance\loopcount by \xref@coord@a + \advance\loopcount by -\x@coord + \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount} + \loopcount=\z@hler + \multiply\loopcount by \y@orient \divide\loopcount by \f@ct@r \advance\loopcount by \yref@coord@a + \advance\loopcount by -\y@coord + \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount} + \loopcount=\z@hler + \multiply\loopcount by \z@orient \divide\loopcount by \f@ct@r \advance\loopcount by \zref@coord@a + \advance\loopcount by -\z@coord + \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount} + \advance\loopcount by \y@distance\relax + \advance\loopcount by \x@distance\relax + \ifnum\loopcount > \PDB@distance \else + \loopcount=\PDB@hitpos \advance\loopcount by 1 + \ifnum\loopcount=\PDB@pos + \else + \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..} + \fi + \xdef\PDB@hitpos{\PDB@pos} + \fi +} + + +\def\intr@@t{% + \loopcount=\r@@t + \temp@count=1 + \loop + \advance\loopcount by \temp@count + \divide\loopcount by 2 + \temp@count=\r@@t + \divide\temp@count by \loopcount + \ifnum\loopcount>\temp@count\repeat +} + + +\def\calc@distance@plane{% + \loopcount=\x@coord\relax + \multiply\loopcount by \x@orient + \temp@count=\y@coord \relax + \multiply\temp@count by \y@orient + \advance\loopcount by \temp@count + \temp@count=\z@coord \relax + \multiply\temp@count by \z@orient + \advance\loopcount by \temp@count + \advance\loopcount by \c@nst@ + \divide\loopcount by \f@ct@r + \multiply\loopcount by \loopcount + \ifnum\loopcount > \PDB@distance \else + \loopcount=\PDB@hitpos \advance\loopcount by 1 + \ifnum\loopcount=\PDB@pos + \else + \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..} + \fi + \xdef\PDB@hitpos{\PDB@pos} + \fi +} + + +\def\load@PDB{% + \bgroup + \immediate\openin\structurefile = \PDB@name\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\PDB@name' not found} + {\MessageBreak + The file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No PDB domain labeling will be displayed. \MessageBreak + Type <return> to proceed. \MessageBreak + Type X <return> to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \message{<reading PDB: \PDB@name>} + \xdef\first@{} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\@TOM + \ifx\PDB@back@side@a\C@lpha + \ifx\third@\C@lpha + \xdef\temp@@@{\fifth@ &&@} + \expandafter\check@letter\temp@@@ + \ifnumber + \ifnum\fifth@=\PDB@refnum@a + \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd} + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd} + \fi + \else + \ifnum\sixth@=\PDB@refnum@a + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd} + \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd} + \fi + \fi + \fi + \else + \xdef\temp@@@{\fifth@ &&@} + \expandafter\check@letter\temp@@@ + \ifnumber + \ifnum\fifth@=\PDB@refnum@a + \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd} + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd} + \fi + \else + \ifnum\sixth@=\PDB@refnum@a + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd} + \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd} + \fi + \fi + \fi + \ifx\PDB@back@side@b\C@lpha + \ifx\third@\C@lpha + \xdef\temp@@@{\fifth@ &&@} + \expandafter\check@letter\temp@@@ + \ifnumber + \ifnum\fifth@=\PDB@refnum@b + \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd} + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd} + \fi + \else + \ifnum\sixth@=\PDB@refnum@b + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd} + \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd} + \fi + \fi + \fi + \else + \xdef\temp@@@{\fifth@ &&@} + \expandafter\check@letter\temp@@@ + \ifnumber + \ifnum\fifth@=\PDB@refnum@b + \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd} + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd} + \fi + \else + \ifnum\sixth@=\PDB@refnum@b + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd} + \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd} + \fi + \fi + \fi + \ifx\PDB@back@side@c\C@lpha + \ifx\third@\C@lpha + \xdef\temp@@@{\fifth@ &&@} + \expandafter\check@letter\temp@@@ + \ifnumber + \ifnum\fifth@=\PDB@refnum@c + \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd} + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd} + \fi + \else + \ifnum\sixth@=\PDB@refnum@c + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd} + \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd} + \fi + \fi + \fi + \else + \xdef\temp@@@{\fifth@ &&@} + \expandafter\check@letter\temp@@@ + \ifnumber + \ifnum\fifth@=\PDB@refnum@c + \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd} + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd} + \fi + \else + \ifnum\sixth@=\PDB@refnum@c + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd} + \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd} + \fi + \fi + \fi + \fi + \fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \ifx\PDB@type\@line@ + \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient{\the\loopcount} + \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient{\the\loopcount} + \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient{\the\loopcount} + \loopcount=\xref@coord@a \multiply\loopcount by \x@orient + \temp@count=\yref@coord@a \multiply\temp@count by \y@orient + \advance\loopcount by \temp@count + \temp@count=\zref@coord@a \multiply\temp@count by \z@orient + \advance\loopcount by \temp@count + \xdef\c@nst@{\the\loopcount} + \loopcount=\x@orient \multiply\loopcount by \x@orient + \temp@count=\y@orient \multiply\temp@count by \y@orient + \advance\loopcount by \temp@count + \temp@count=\z@orient \multiply\temp@count by \z@orient + \advance\loopcount by \temp@count + \xdef\f@ct@r{\the\loopcount} + \fi + \ifx\PDB@type\@plane@ + \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient@r{\the\loopcount} + \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient@r{\the\loopcount} + \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient@r{\the\loopcount} + \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@c \xdef\x@orient@s{\the\loopcount} + \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@c \xdef\y@orient@s{\the\loopcount} + \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@c \xdef\z@orient@s{\the\loopcount} + \loopcount=\y@orient@r \multiply\loopcount by \z@orient@s + \temp@count=\z@orient@r \multiply\temp@count by \y@orient@s + \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\x@orient{\the\loopcount} + \loopcount=\z@orient@r \multiply\loopcount by \x@orient@s + \temp@count=\x@orient@r \multiply\temp@count by \z@orient@s + \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\y@orient{\the\loopcount} + \loopcount=\x@orient@r \multiply\loopcount by \y@orient@s + \temp@count=\y@orient@r \multiply\temp@count by \x@orient@s + \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\z@orient{\the\loopcount} + \loopcount=\x@orient \multiply\loopcount by \xref@coord@a + \temp@count=\y@orient \multiply\temp@count by \yref@coord@a + \advance\loopcount by \temp@count + \temp@count=\z@orient \multiply\temp@count by \zref@coord@a + \advance\loopcount by \temp@count + \multiply\loopcount by -1\relax + \xdef\c@nst@{\the\loopcount} + \loopcount=\x@orient \multiply\loopcount by \loopcount + \temp@count=\y@orient \multiply\temp@count by \temp@count + \advance\loopcount by \temp@count + \temp@count=\z@orient \multiply\temp@count by \temp@count + \advance\loopcount by \temp@count + \xdef\r@@t{\the\loopcount} \intr@@t + \xdef\f@ct@r{\the\loopcount} + \fi + \immediate\openin\structurefile = \PDB@name\relax + \xdef\first@{} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\@TOM + \xdef\temp@@@{\fifth@ &&@} + \expandafter\check@letter\temp@@@ + \ifnumber + \xdef\PDB@pos{\fifth@} + \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\x@coord{\c@@rd} + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\y@coord{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\z@coord{\c@@rd} + \else + \xdef\PDB@pos{\sixth@} + \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\x@coord{\c@@rd} + \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\y@coord{\c@@rd} + \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\z@coord{\c@@rd} + \fi + \ifnum\PDB@hitpos=\PDB@pos + \else + \ifx\PDB@type\@point@ + \calc@distance@point + \else + \ifx\PDB@type\@line@ + \calc@distance@line + \else + \ifx\PDB@type\@plane@ + \calc@distance@plane + \fi + \fi + \fi + \fi + \fi + \fi + \ifeof\structurefile \xdef\PDB@stack{\PDB@stack\PDB@hitpos,&@} + \else\repeat + \closein\structurefile + + \fi + \egroup + } + + + +%%%%% Definition of user commands + +\def\clearfuncgroups{\xdef\prfx{func} \clear@groups \xdef\fgroup@num{0}} +\clearfuncgroups +\def\germanlanguage{\germ@ntrue \sp@nishfalse \def\cons@name{Konsensus}} +\def\spanishlanguage{\germ@nfalse \sp@nishtrue \def\cons@name{consenso}} +\def\englishlanguage{\germ@nfalse \sp@nishfalse \def\cons@name{consensus}} +\def\showlegend{\legend@true} +\def\hidelegend{\legend@false} +\def\movelegend#1#2{% + \setlength\hspace@legend{#1} + \setlength\vspace@legend{#2} +} +\newcommand{\showcaption}[2][bottom]{\def\cap@pos{#1}\def\c@p{#2}} +\def\shortcaption#1{\def\c@pshort{#1}} +\def\funcgroup#1#2#3#4#5#6{% + \xdef\first@{#1} + \loopcount=0 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifx\csname fgroup@name\the\loopcount\endcsname\first@ + \innerloopcount=\loopcount \loopcount=\fgroup@num + \fi + \ifnum\loopcount<\fgroup@num \repeat + \ifnum\innerloopcount=0 + \ifnum\fgroup@num<9 + \innerloopcount=\fgroup@num + \advance\innerloopcount by 1 \xdef\fgroup@num{\the\innerloopcount} + \else \message{<Too many \noexpand\funcgroups>} + \fi + \fi + \ifnum\innerloopcount>0 + \expandafter\xdef\csname fgroup@name\the\innerloopcount\endcsname{\first@} + \expandafter\xdef\csname fg@textcolor\the\innerloopcount\endcsname{#3} + \expandafter\xdef\csname fg@color\the\innerloopcount\endcsname{#4} + \expandafter\xdef\csname funcm@tch\the\innerloopcount\endcsname{#5} + \expandafter\def\csname func@style\the\innerloopcount\endcsname{% + \csname text#6\endcsname} + \xdef\prfx{func} + \xdef\third@{#2&,@} \loopcount=\innerloopcount + \expandafter\group@get\third@ + \fi} +\def\pepgroups#1{% + \xdef\prfx{pep} + \clear@groups + \xdef\third@{#1&,@} \loopcount=0 + \loop \expandafter\group@get\third@ \advance\loopcount by 1 + \ifnum\loopcount<10 \repeat} +\def\DNAgroups#1{% + \xdef\prfx{DNA} + \clear@groups + \xdef\third@{#1&,@} \loopcount=0 + \loop \expandafter\group@get\third@ \advance\loopcount by 1 + \ifnum\loopcount<10 \repeat} +\def\pepsims#1#2{\xdef\prfx{pep} + \def\sim@set{\expandafter\residue@get\second@ + \ifx\first@\ampers@nd + \else \advance\innerloopcount by 1 + + \expandafter\xdef\csname simpair\third@\first@\endcsname{1} + \expandafter\xdef\csname simpair\first@\third@\endcsname{1} + + \xdef\second@{\csname sequence\the\loopcount\endcsname} \sim@set + \fi} + \xdef\first@{#1} \make@upper \xdef\third@{\first@} + \xdef\last@{#2} \xdef\second@{#2 &@} \innerloopcount=0 \sim@set + \expandafter\xdef\csname \prfx sim\third@\endcsname{% + (\the\innerloopcount)\last@}} +\def\DNAsims#1#2{\xdef\prfx{DNA} + \def\sim@set{\expandafter\residue@get\second@ + \ifx\first@\ampers@nd + \else \advance\innerloopcount by 1 + \xdef\second@{\csname sequence\the\loopcount\endcsname} \sim@set + \fi} + \xdef\first@{#1} \make@upper \xdef\third@{\first@} + \xdef\last@{#2} \xdef\second@{#2 &@} \innerloopcount=0 \sim@set + \expandafter\xdef\csname \prfx sim\third@\endcsname{% + (\the\innerloopcount)\last@}} +\def\fingerprint#1{% + \ifnum #1 >0 + \residuesperline*{#1} + \def\finger@linenum{#1} + \shownames{left} + \hidenumbering + \rulersteps{100} + \nomatchresidues{}{Gray10}{}{} + \loopcount=0 + \loop + \advance\loopcount by 1 + \separationline{\the\loopcount} + \ifnum\loopcount<\seq@count\repeat + \fi} +\def\printPDBlist#1{% + \xdef\list@{} + \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@ + \xdef\first@{\list@ &} + \ifx\first@\ampers@nd + \else + \xdef\first@{\list@ @} + \loop + \expandafter\get@item\first@ + \fourth@ + \ifx\first@@\ampers@nd\else{,\ }\repeat + \fi +} +\def\messagePDBlist#1{% + \xdef\list@{} + \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@ + \xdef\first@{\list@ &} + \ifx\first@\ampers@nd + \else + \message{(#1:} + \xdef\first@{\list@ @}% + \loop% + \expandafter\get@item\first@% + \message{\fourth@}% + \ifx\first@@\ampers@nd\else\repeat% + \message{)} + \fi +} +\def\shaderegion#1#2#3#4{% + \regionalshadetrue + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{<Ignored `\seq@' in \noexpand\shaderegion or \noexpand\shadeblock>} + \else + \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi + \loopcount=\seq@regions + \advance\loopcount by 1 + \xdef\seq@regions{\the\loopcount} + \expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3} + \expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4} + \xdef\list@{#2,&} + \xdef\temp@@{shade} + \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ + \ifx\list@\ampers@nd + \else + \loop + \xdef\list@{\list@ @} + \expandafter\get@regions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi + \fi +} +\def\shadeblock#1#2#3#4{% + \xdef\seq@{#1} + \xdef\@ll{yes} + \shaderegion{#1}{#2}{#3}{#4} + \xdef\@ll{} +} +\def\tintregion#1#2{% + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{<Ignored seq `\seq@' in \noexpand\tintregion or \noexpand\tintblock>} + \else + \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi + \xdef\list@{#2,&} + \xdef\temp@@{tint} \loopcount=0 + \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ + \ifx\list@\ampers@nd + \else + \loop + \xdef\list@{\list@ @} + \expandafter\get@tintregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi + \fi +} +\def\tintblock#1#2{% + \xdef\seq@{#1} + \xdef\@ll{yes} + \tintregion{#1}{#2} + \xdef\@ll{} +} +\def\tintdefault#1{% + \xdef\first@{#1} + \xdef\second@{strong} + \ifx\first@\second@ + \xdef\light@{LightLightLight} + \else + \xdef\second@{medium} + \ifx\first@\second@ + \xdef\light@{LightLight} + \else + \xdef\second@{weak} + \ifx\first@\second@ + \xdef\light@{Light} + \else + \xdef\light@{LightLight} + \fi\fi\fi +} +\def\lowerregion#1#2{% + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{<Ignored seq `\seq@' in \noexpand\lowerregion or \noexpand\lowerblock>} + \else + \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi + \xdef\list@{#2,&} + \xdef\temp@@{lower} \loopcount=0 + \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ + \ifx\list@\ampers@nd + \else + \loop + \xdef\list@{\list@ @} + \expandafter\get@lowerregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi + \fi +} +\def\lowerblock#1#2{% + \xdef\seq@{#1} + \xdef\@ll{yes} + \lowerregion{#1}{#2} + \xdef\@ll{} +} +\def\emphregion#1#2{% + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{<Ignored seq `\seq@' in \noexpand\emphregion or \noexpand\emphblock>} + \else + \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi + \xdef\list@{#2,&} + \xdef\temp@@{emph} \loopcount=0 + \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ + \ifx\list@\ampers@nd + \else + \loop + \xdef\list@{\list@ @} + \expandafter\get@emphregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi + \fi +} +\def\emphblock#1#2{% + \xdef\seq@{#1} + \xdef\@ll{yes} + \emphregion{#1}{#2} + \xdef\@ll{} +} +\def\emphdefault#1{\def\res@style{\csname text#1\endcsname}} +\def\frameblock#1#2#3{% + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{<Ignored seq `\seq@' in \noexpand\frameblock>} + \else + \xdef\@ll{#3} + \xdef\list@{#2,&} + \xdef\temp@@{frame} \loopcount=0 + \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ + \ifx\list@\ampers@nd + \else + \loop + \xdef\list@{\list@ @} + \expandafter\get@frameregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi + \fi +} +\def\changeshadingcolors#1#2#3{% + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{<Ignored seq `\seq@' in \noexpand\changeshadingcolors>} + \else + \xdef\@ll{#3} + \xdef\list@{#2,&} + \xdef\temp@@{shading} \loopcount=0 + \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ + \ifx\list@\ampers@nd + \else + \loop + \xdef\list@{\list@ @} + \expandafter\get@shadingregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi + \fi +} +\def\bargraphstretch#1{\def\b@r@stretch{#1}} +\def\colorscalestretch#1{\def\sc@le@stretch{#1}} +\def\rm@@measure#1#2@{% + \xdef\test@{#1} + \ifx\test@\ampers@nd + \else + \expandafter\check@char\test@ + \ifnumber\xdef\first@{\first@ #1} + \xdef\second@{#2 &@} + \expandafter\rm@@measure\second@ + \fi + \fi +} +\def\rm@measure#1.#2@{\xdef\first@{#1.}\xdef\second@{#2 @}\xdef\third@{#1}\expandafter\rm@@measure\second@} +\def\pm@calc{% + \temp@@length=100000sp + \temp@@length=\g@min\temp@@length + \innerloopcount=\temp@@length + \xdef\min@{\the\innerloopcount} + \arrow@height=\temp@@length + \temp@@length=100000sp + \temp@@length=\g@max\temp@@length + \advance\temp@@length by -\arrow@height + \innerloopcount=\temp@@length + \divide\innerloopcount by 100 + \ifnum\innerloopcount=0 \innerloopcount=1 \fi + \xdef\m@x{\the\innerloopcount} + \xdef\test@{\g@min pt} + \setlength\arrow@width{\test@} + \xdef\test@{\g@max pt} + \setlength\arrow@height{\test@} + \advance\arrow@height by -\arrow@width + \ifdim\arrow@width<0pt\temp@@length=-\arrow@width\xdef\test@{y}\else\temp@@length=\arrow@width\xdef\test@{n}\fi + \ifdim\arrow@height>0pt + \ifx\test@\n@ \xdef\test@{y} \else \xdef\test@{n} \fi + \ifdim\temp@@length<\arrow@height\temp@@length=\arrow@height\fi + \else + \ifdim\temp@@length>-\arrow@height\temp@@length=\arrow@height\fi + \fi + \ifdim\temp@@length<100pt\arrow@width=100\arrow@width\arrow@height=100\arrow@height\else + \ifdim\temp@@length<10pt\arrow@width=1000\arrow@width\arrow@height=1000\arrow@height\else + \ifdim\temp@@length<1pt\arrow@width=10000\arrow@width\arrow@height=10000\arrow@height\else + \ifdim\temp@@length<0.1pt\arrow@width=100000\arrow@width\arrow@height=100000\arrow@height\else + \ifdim\temp@@length<0.01pt\arrow@width=1000000\arrow@width \arrow@height=1000000\arrow@height\else + \ifdim\temp@@length<0.001pt\arrow@width=10000000\arrow@width \arrow@height=10000000\arrow@height\else + \ifdim\temp@@length<0.0001pt\arrow@width=100000000\arrow@width \arrow@height=100000000\arrow@height\else + \ifdim\temp@@length<0.00001pt\arrow@width=1000000000\arrow@width \arrow@height=1000000000\arrow@height + \fi\fi\fi\fi\fi\fi\fi\fi + \ifx\test@\y@ + \xdef\pm@{0} + \else + \xdef\test@{-\the\arrow@height @} + \expandafter\rm@measure\test@ + \divide\arrow@width by \third@ + \xdef\pm@{\the\arrow@width @} + \expandafter\rm@measure\pm@ + \xdef\pm@{\first@} + \fi +} +\def\read@graph{% + \bgroup + \immediate\openin\structurefile = \fill@char\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\fill@char' not found} + {\MessageBreak + The file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No feature graph will be displayed. \MessageBreak + Type <return> to proceed. \MessageBreak + Type X <return> to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \ifx\g@min\comm@ + \def\par@{} + \xdef\g@min{,} \xdef\g@max{,} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\second@{\test@ @} + \expandafter\check@letter\second@ + \ifletter + \xdef\second@{\expandafter\string\readline} + \xdef\second@{\second@ @} + \expandafter\firstchar@get\second@ + \if\first@ - \numbertrue\fi + \fi + \ifnumber + \temp@@length=1pt + \temp@@length=\test@\temp@@length + \innerloopcount=\temp@@length + \ifx\g@min\comm@ \xdef\min@{\test@ pt} \xdef\g@min{\test@} + \else + \ifdim\temp@@length<\min@\relax \xdef\min@{\the\temp@@length} \xdef\g@min{\test@} \fi\fi% + \ifx\g@max\comm@ \xdef\m@x{\test@ pt} \xdef\g@max{\test@} + \else + \ifdim\temp@@length>\m@x\relax \xdef\m@x{\the\temp@@length} \xdef\g@max{\test@} \fi\fi% + \fi + \fi + \ifeof\structurefile\else\repeat + \fi + \immediate\closein\structurefile + \pm@calc + \expandafter\temp@count=\csname seq@start\seq@\endcsname + \advance\temp@count by -1 + \xdef\temp@@@{n} + \immediate\openin\structurefile = \fill@char\relax + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\second@{\test@ @} + \expandafter\check@letter\second@ + \ifletter + \xdef\second@{\expandafter\string\readline} + \xdef\second@{\second@ @} + \expandafter\firstchar@get\second@ + \if\first@ - \numbertrue + \else + \if\first@ N + \expandafter\firstchar@get\third@ + \if\first@ a + \expandafter\firstchar@get\third@ + \if\first@ N + \advance\temp@count by 1 + \ifnum\temp@count=0 \temp@count=1 \fi + \ifnum\temp@count<\st@rt + \else + \ifnum\temp@count>\st@p + \else + \ifx\temp@@@\n@ + \xdef\temp@@@{N} + \else + \xdef\temp@@@{\temp@@@,N} + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \ifnumber + \advance\temp@count by 1 + \ifnum\temp@count=0 \temp@count=1 \fi + \ifnum\temp@count<\st@rt + \else + \ifnum\temp@count>\st@p + \else + \temp@@length=100000sp + \temp@@length=\test@\temp@@length + \innerloopcount=\temp@@length + \advance\innerloopcount by 1 + \xdef\test@{\pm@ pt} + \ifdim\test@=0pt + \advance\innerloopcount by -\min@ + \else + \ifx\b@r\n@ + \advance\innerloopcount by -\min@ + \fi + \fi + \divide\innerloopcount by \m@x + \ifx\temp@@@\n@ + \xdef\temp@@@{\the\innerloopcount} + \else + \xdef\temp@@@{\temp@@@,\the\innerloopcount} + \fi + \fi + \fi + \fi + \fi + \ifeof\structurefile\else\repeat + \immediate\closein\structurefile + \xdef\temp@@@{\temp@@@,@} \xdef\temp@@{y} + \fi + \egroup +} +\def\sort@gstack{% + \expandafter\get@fromstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\f@text@&;&;&;&;@} + \else + \ifnum\loopcount<\second@ + \xdef\tmpstack{\tmpstack\f@text@\first@;\second@;\third@;\fourth@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} + \sort@gstack + \fi\fi +} +\def\get@gregion#1..#2,#3&{% + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} +} +\def\do@bargraph{% + \expandafter\get@gregion\list@ + \expandafter\ifnum\csname seq@start\seq@\endcsname>\st@rt + \else + \xdef\temp@@{n} + \xdef\b@r{y} + \xdef\pm@{0} + \xdef\temp@@@{\fill@char,@} + \expandafter\check@letter\temp@@@ + \ifletter + \read@graph + \else + \ifx\g@min\comm@ \xdef\g@min{0} \fi + \ifx\g@max\comm@ \xdef\g@max{100} \fi + \pm@calc + \xdef\temp@@@{\fill@char,@} + \xdef\temp@@{y} + \fi + \ifx\temp@@\y@ + \loopcount=\st@rt + \xdef\tmpstack{} + \loop + \expandafter\get@item\temp@@@ + \xdef\temp@@@{\first@} + \xdef\style@{bar[\pm@,0]:\fourth@[\f@color]} + \xdef\tmpstack{\tmpstack\f@text@;\the\loopcount;\the\loopcount;\style@;} + \advance\loopcount by 1 + \ifnum\loopcount=0 \loopcount=1 \fi + \ifnum\loopcount>\st@p + \else\repeat + \xdef\f@text@{\tmpstack} \xdef\tmpstack{} + \xdef\last@{\csname stack@\bottop@\seq@\endcsname} + \sort@gstack + \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack} + \fi + \fi + \xdef\list@{\list@ &} + \ifx\list@\ampers@nd\else\do@bargraph\fi +} +\def\do@colorgraph{% + \expandafter\get@gregion\list@ + \expandafter\ifnum\csname seq@start\seq@\endcsname>\st@rt + \else + \xdef\temp@@{n} + \xdef\b@r{n} + \xdef\pm@{0} + \xdef\temp@@@{\fill@char,@} + \expandafter\check@letter\temp@@@ + \ifletter + \read@graph + \else + \ifx\g@min\comm@ \xdef\g@min{0} \fi + \ifx\g@max\comm@ \xdef\g@max{100} \fi + \pm@calc + \xdef\temp@@@{\fill@char,@} + \xdef\temp@@{y} + \fi + \ifx\temp@@\y@ + \loopcount=\st@rt + \xdef\tmpstack{} + \loop + \xdef\last@{\csname stack@\bottop@\seq@\endcsname} + \expandafter\get@item\temp@@@ + \xdef\temp@@@{\first@} + \ifx\fourth@\N@ + \xdef\style@{color:50[White]} + \else + \ifnum\fourth@<1 \xdef\fourth@{1} \fi + \innerloopcount=\fourth@ + \advance\innerloopcount by 4 + \divide\innerloopcount by 5 + \multiply\innerloopcount by 5 + \ifnum\innerloopcount>100 \innerloopcount=100 \fi + \xdef\style@{color:50[\f@color\the\innerloopcount]} + \fi + \xdef\tmpstack{\tmpstack\f@text@;\the\loopcount;\the\loopcount;\style@;} + \advance\loopcount by 1 + \ifnum\loopcount=0 \loopcount=1 \fi + \ifnum\loopcount>\st@p + \else\repeat + \xdef\f@text@{\tmpstack} \xdef\tmpstack{} + \xdef\last@{\csname stack@\bottop@\seq@\endcsname} + \sort@gstack + \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack} + \fi + \fi + \xdef\list@{\list@ &} + \ifx\list@\ampers@nd\else\do@colorgraph\fi +} +\def\feature#1#2#3#4#5{% + \xdef\bottop@{#1} + \xdef\temp@{top} + \ifx\bottop@\temp@ \topfeaturetrue\fi + \xdef\temp@{ttop} + \ifx\bottop@\temp@ \ttopfeaturetrue\fi + \xdef\temp@{tttop} + \ifx\bottop@\temp@ \tttopfeaturetrue\fi + \xdef\temp@{ttttop} + \ifx\bottop@\temp@ \ttttopfeaturetrue\fi + \xdef\temp@{bottom} + \ifx\bottop@\temp@ \bottomfeaturetrue\fi + \xdef\temp@{bbottom} + \ifx\bottop@\temp@ \bbottomfeaturetrue\fi + \xdef\temp@{bbbottom} + \ifx\bottop@\temp@ \bbbottomfeaturetrue\fi + \xdef\temp@{bbbbottom} + \ifx\bottop@\temp@ \bbbbottomfeaturetrue\fi + \xdef\seq@{#2} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{<Ignored seq `\seq@' in \noexpand\feature>} + \else + \ifnum\seq@>-1 + \xdef\temp@{#4::&}\expandafter\test@fill\temp@ + \xdef\last@{bar} + \ifx\second@@\last@ + \xdef\last@{hydrophobicity} + \ifx\last@\fourth@ + \xdef\second@@{bh} + \else + \xdef\last@{molweight} + \ifx\last@\fourth@ + \xdef\second@@{bm} + \else + \xdef\last@{charge} + \ifx\last@\fourth@ + \xdef\second@@{bc} + \else + \xdef\last@{conservation} + \ifx\last@\fourth@ + \xdef\second@@{bcons} + \fi + \fi + \fi + \fi + \fi + \xdef\last@{color} + \ifx\second@@\last@ + \xdef\last@{hydrophobicity} + \ifx\last@\fourth@ + \xdef\second@@{ch} + \else + \xdef\last@{molweight} + \ifx\last@\fourth@ + \xdef\second@@{cm} + \else + \xdef\last@{charge} + \ifx\last@\fourth@ + \xdef\second@@{cc} + \else + \xdef\last@{conservation} + \ifx\last@\fourth@ + \xdef\second@@{ccons} + \fi + \fi + \fi + \fi + \fi + \xdef\last@{bar} + \ifx\second@@\last@ + \xdef\list@{#3,&} + \xdef\style@{#4} + \def\f@text@{#5} + \do@bargraph + \xdef\temp@{bottom} + \ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi + \xdef\temp@{bbottom} + \ifx\bottop@\temp@ \xdef\bbottom@stretch{y}\fi + \xdef\temp@{bbbottom} + \ifx\bottop@\temp@ \xdef\bbbottom@stretch{y}\fi + \xdef\temp@{bbbbottom} + \ifx\bottop@\temp@ \xdef\bbbbottom@stretch{y}\fi + \else + \xdef\last@{color} + \ifx\second@@\last@ + \xdef\list@{#3,&} + \xdef\style@{#4} + \def\f@text@{#5} + \do@colorgraph + \else + \xdef\f@@color{\f@color} + \def\f@text@{#5} + \xdef\f@color{\f@@color} + \xdef\temp@{#4&} + \ifx\temp@\ampers@nd + \xdef\list@{#3,&} + \xdef\style@{&} + \def\f@text@{#5} + \else + \xdef\last@{restriction} + \ifx\second@@\last@ + \xdef\temp@{\bottop@ @} + \expandafter\firstchar@get\temp@ + \xdef\temp@{y} + \if\first@ t + \xdef\style@{fill:\kern0.9\box@width$\blacktriangledown$[\f@color]} + \else + \xdef\style@{fill:\kern0.9\box@width$\blacktriangle$[\f@color]} + \fi + \xdef\f@text@{\kern0.9\box@width#5} + \else + \xdef\last@{bh} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\style@{plot[bar]:Hydro[\f@color][-53]} + \else + \xdef\last@{bm} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\style@{plot[bar]:molw[\f@color][0]} + \else + \xdef\last@{bc} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\style@{plot[bar]:charge[\f@color][-50]} + \else + \xdef\last@{bcons} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\last@{T-Coffee} + \ifx\f@color\last@ + \xdef\T@coffee@bcons{y} + \xdef\f@color{Gray50} + \fi + \xdef\style@{cons[bar]:cons[\f@color][0]} + \else + \xdef\last@{ch} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{RedGreen}\fi + \xdef\style@{plot[color]:Hydro[\f@color][-53]} + \else + \xdef\last@{cm} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray}\fi + \xdef\style@{plot[color]:molw[\f@color][0]} + \else + \xdef\last@{cc} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{RedBlue}\fi + \xdef\style@{plot[color]:charge[\f@color][-50]} + \else + \xdef\last@{ccons} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{ColdHot}\fi + \xdef\last@{T-Coffee} + \ifx\f@color\last@ + \xdef\T@coffee@ccons{y} + \xdef\f@color{TC} + \fi + \xdef\style@{cons[color]:cons[\f@color][0]} + \else + \xdef\style@{#4} \xdef\temp@@{n} + \expandafter\get@firstfill\temp@ + \if\second@@ ^ \xdef\second@@{_} \fi + \if\second@@ _ \xdef\temp@{\fill@char} \xdef\temp@@{y}\fi + \expandafter\getarrow@shape\temp@ + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \xdef\list@{#3,&} + \xdef\@ll{\f@text@} + \xdef\temp@@{\bottop@} + \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@ + \fi + \loopcount=0 + \ifx\list@\ampers@nd + \else + \loop + \advance\loopcount by 1\relax + \xdef\list@{\list@ @} + \expandafter\get@fregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi + \fi\fi\fi + \fi +} +\def\showfeaturename#1#2{\expandafter\xdef\csname featuretextn@me#1\endcsname{#2}} +\def\showfeaturestylename#1#2{\expandafter\xdef\csname featurestylesn@me#1\endcsname{#2}} +\def\hidefeaturename#1{\expandafter\xdef\csname featuretextn@me#1\endcsname{}} +\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{} + \xdef\featuretextn@metttop{}\xdef\featuretextn@mettttop{}\xdef\featuretextn@mebbbbottom{}\xdef\featuretextn@mebbbottom{}} +\def\hidefeaturestylename#1{\expandafter\xdef\csname featurestylesn@me#1\endcsname{}} +\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{} + \xdef\featurestylesn@metttop{}\xdef\featurestylesn@mettttop{}\xdef\featurestylesn@mebbbbottom{}\xdef\featurestylesn@mebbbottom{}} +\def\seqtype#1{\xdef\seq@type{#1} + \if\seq@type P \xdef\prefix@{pep} + \else \if\seq@type p \xdef\seq@type{P} \xdef\prefix@{pep} + \else \xdef\seq@type{N} \xdef\prefix@{DNA} \fi\fi} +\def\nameseq#1#2{% + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \expandafter\xdef\csname newseqname\first@\endcsname{#2} +} +\newcommand\threshold[2][n]{% + \xdef\first@{#1} + \ifx\first@\n@ + \xdef\thresh@ld{#2} + \else + \all@shadetrue + \ifnum\first@>#2 + \xdef\thresh@ld{#2} + \xdef\all@thresh@ld{#1} + \else + \xdef\thresh@ld{#1} + \xdef\all@thresh@ld{#2} + \fi + \fi +} +\def\constosingleseq#1{% + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count + \message{<Ignored seq `#1' in \noexpand\constosingleseq>} + \else + \ifnum\first@>0 \xdef\cons@num{\first@} \hideconsensus\fi\fi +} +\def\constoallseqs{\xdef\cons@num{0}} +\def\residuesperline{% + \def\@rplfix*##1{% + \res@perline=##1 + \ifnum\res@perline<1 \res@perline=1\fi \rpl@fixtrue} + \def\@rplvar ##1{% + \res@perline=##1 + \ifnum\res@perline<5 \res@perline=5\fi \rpl@fixfalse} + \def\decide@{\ifx\l@@k * \let\next\@rplfix \else \let\next\@rplvar \fi \next} + \futurelet\l@@k\decide@} +\def\numberingwidth#1{\def\num@width{#1}} +\def\charstretch#1{% + \def\char@stretch{#1} + \xdef\temp@{\char@stretch .00@} \expandafter\coord@get\temp@ \loopcount=\c@@rd + \multiply \loopcount by 7 + \divide \loopcount by 10 + \ifnum\loopcount<10 + \xdef\temp@{0\the\loopcount @} + \else + \xdef\temp@{\the\loopcount @} + \fi + \expandafter\decimal@B\temp@ + \ifnum\loopcount>99 + \xdef\char@stretch@W{#1} + \else + \xdef\char@stretch@W{\temp@} + \fi +} +\def\linestretch#1{\def\line@stretch{#1}} +\def\logostretch#1{% + \def\logo@stretch{#1} + \setlength\temp@@length{1000sp} + \setlength\temp@@length{\logo@stretch\temp@@length} + \loopcount=\temp@@length + \xdef\logo@stretch@IOOO{\the\loopcount} +} +\def\noblockskip{\def\block@skip{\vspace{0pt}}} +\def\smallblockskip{\def\block@skip{\vspace{\baselineskip}}} +\def\medblockskip{\def\block@skip{\vspace{1.5\baselineskip}}} +\def\bigblockskip{\def\block@skip{\vspace{2\baselineskip}}} +\def\vblockspace#1{\def\block@skip{\vspace{#1}}} +\def\topspace#1{\def\t@sp@ce{#1}} +\def\ttopspace#1{\def\tt@sp@ce{#1}} +\def\tttopspace#1{\def\ttt@sp@ce{#1}} +\def\ttttopspace#1{\def\tttt@sp@ce{#1}} +\def\bottomspace#1{\def\b@sp@ce{#1}} +\def\bbottomspace#1{\def\bb@sp@ce{#1}} +\def\bbbottomspace#1{\def\bbb@sp@ce{#1}} +\def\bbbbottomspace#1{\def\bbbb@sp@ce{#1}} +\def\rulerspace#1{\def\ruler@sp@ce{#1}} +\def\fixblockspace{\fix@true} +\def\flexblockspace{\fix@false} +\def\nosepline{\def\seq@skip{\relax}} +\def\smallsepline{\def\seq@skip{\vspace{3pt}}\def\sep@space{3pt}} +\def\medsepline{\def\seq@skip{\vspace{6pt}}\def\sep@space{6pt}} +\def\bigsepline{\def\seq@skip{\vspace{12pt}}\def\sep@space{12pt}} +\def\vsepspace#1{\def\seq@skip{\vspace{#1}}\xdef\sep@space{#1}} +\def\separationline#1{% + \xdef\first@@{#1} + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} + \ifletter \get@name@number \xdef\first@@{\first@} \fi + \ifnum\first@@>\seq@count \xdef\first@@{1} + \else + \ifnum\first@@<0 \xdef\first@@{1} + \else + \expandafter\def\csname seq@gap\first@@\endcsname{yes} + \loopcount=\seq@gap@num + \advance\loopcount by 1 + \xdef\seq@gap@num{\the\loopcount} + \fi + \fi} +\newcommand{\shadingmode}[2][-1]{% + \T@coffeefalse + \xdef\last@{#2} + \xdef\first@{identical} + \ifx\first@\last@ + \simmodefalse \funcmodefalse + \xdef\second@{#1 @} \expandafter\check@letter\second@ + \ifnumber \all@shadetrue + \ifnum#1<0 \all@shadefalse + \else + \ifnum#1>100 \xdef\all@thresh@ld{100} + \else + \xdef\all@thresh@ld{#1} + \fi\fi + \else + \xdef\last@{#1} + \xdef\first@{allmatchspecial} + \ifx\last@\first@ + \xdef\all@thresh@ld{100} \all@shadetrue + \fi + \fi + \else + \xdef\first@{similar} + \ifx\first@\last@ + \simmodetrue \funcmodefalse + \xdef\second@{#1 @} \expandafter\check@letter\second@ + \ifnumber \all@shadetrue + \ifnum#1<0 \all@shadefalse + \else + \ifnum#1>100 \xdef\all@thresh@ld{100} + \else + \xdef\all@thresh@ld{#1} + \fi\fi + \else + \xdef\last@{#1} + \xdef\first@{allmatchspecial} + \ifx\last@\first@ + \xdef\all@thresh@ld{100} \all@shadetrue + \fi + \fi + \else + \xdef\first@{functional} + \ifx\first@\last@ + \if\seq@type N \message{<No functional shading on DNA sequences>} + \else \simmodefalse \funcmodetrue \func@shading{#1} + \xdef\seq@type{P} \xdef\prefix@{pep} \fi + \else + \xdef\first@{T-Coffee} + \ifx\first@\last@ + \simmodefalse \funcmodefalse \T@coffeetrue + \xdef\second@{#1 @} \expandafter\check@letter\second@ + \ifletter \xdef\TC@first@{#1}\include@T@coffee\fi + \else + \xdef\first@{diverse} + \ifx\first@\last@ + \xdef\last@{#1} + \ifnum\last@>\seq@count \xdef\last@{1}\fi + \ifnum\last@<1 \xdef\last@{1}\fi + \simmodetrue \funcmodefalse + \threshold{0} + \xdef\divref@{\last@} + \constosingleseq{\last@} + \nomatchresidues{Black}{White}{lower}{up} + \similarresidues{Black}{White}{lower}{up} + \conservedresidues{Black}{White}{{.}}{up} + \allmatchresidues{Black}{White}{{.}}{up} + \gapchar{-} + \hideconsensus + \else + \message{<Unknown shading mode - using `similar'>} + \simmodetrue \funcmodefalse + \fi\fi\fi\fi\fi} +\def\hideallmatchpositions{\xdef\all@out{y}} +\def\showallmatchpositions{\xdef\all@out{n}} +\newcommand\allmatchspecial[1][100]{% + \ifnum#1<0 + \xdef\all@thresh@ld{0} + \else + \ifnum#1>100 + \xdef\all@thresh@ld{100} + \else + \xdef\all@thresh@ld{#1} + \fi\fi + \all@shadetrue} +\def\allmatchspecialoff{\all@shadefalse} +\def\stopchar#1{\def\st@p@char{#1}} +\def\gapchar#1{% + \xdef\first@{rule}\xdef\second@{#1} + \ifx\first@\second@\def\gap@char{o} + \else\def\gap@char{#1}\fi} +\def\gaprule#1{\def\gap@rulethick{#1}} +\def\domaingaprule#1{\def\domgap@rulethick{#1}} +\newcommand{\setends}[3][&]{% + \xdef\start@seq{#2} + \xdef\temp@{consensus} + \ifx\start@seq\temp@ +%%% \message{<\noexpand\setends does not accept `consensus'>} + \xdef\start@seq{0} +%%%%%%%%%% + \xdef\second@{#3@} \expandafter\get@nums\second@ + \xdef\start@num{\first@} \xdef\end@num{\second@} + \ifnum\start@num<1 \xdef\start@num{1}\fi + \ifnum\end@num<\start@num \xdef\end@num{\start@num}\fi + \loopcount=\end@num + \advance\loopcount by 1 + \advance\loopcount by -\start@num + \xdef\end@num{\the\loopcount} + \start@false +%%%%%%%%%% + \else + \xdef\first@{\start@seq @} \expandafter\check@letter\first@ + \xdef\first@{\start@seq} + \ifletter \get@name@number \xdef\start@seq{\first@} \fi + \ifnum\start@seq>\seq@count + \message{<\noexpand\setends{} error: sequence `#2' not defined>} + \xdef\start@seq{0} + \else + \ifnum\start@seq<1 + \message{<\noexpand\setends{} error: sequence `#2' not defined>} + \xdef\start@seq{0} + \else + \xdef\second@{#3@} \expandafter\get@nums\second@ + \xdef\start@num{\first@} \xdef\end@num{\second@} + \ifnum\start@num=0 \xdef\allow@zero{y}\fi + \ifnum\end@num=0 \xdef\allow@zero{y}\fi + \start@false + \fi + \fi + \fi + \xdef\first@{#1}\ifx\first@\ampers@nd\else\startnumber{#2}{#1}\fi +} +\newcommand{\startnumber}[3][&]{% + \xdef\first@{#2} \xdef\second@{consensus} + \ifx\first@\second@ + \ifnum#3=0 \xdef\allow@zero{y} \fi + \expandafter\xdef\csname seq@start0\endcsname{#2} + \cons@count=#3 \advance\cons@count by -1\relax + \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} + \else + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count \message{<Ignored seq `#2' in \noexpand\startnumber>} + \else + \xdef\second@{#3} + \ifnum\second@=0 \xdef\allow@zero{y} \fi + \expandafter\xdef\csname seq@start\first@\endcsname{\second@} + \res@count=\second@ + \advance\res@count by -1 + \expandafter\xdef\csname res@count\first@\endcsname{\the\res@count} + \fi + \fi + \xdef\first@{#1}\ifx\first@\ampers@nd\else\setends{#2}{#1}\fi + } +\def\seqlength#1#2{% + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count \message{<Ignored seq `#1' in \noexpand\seqlength>} + \else + \xdef\second@{#2} \ifnum\second@<0 \xdef\second@{1} \fi + \expandafter\xdef\csname seq@len\first@\endcsname{\second@} + \fi} +\newcommand\shownumbering[2][n]{% + \xdef\first@{#1}\ifx\first@\n@\else\xdef\numbering@fg{#1}\fi + \xdef\first@{#2} + \xdef\second@{left} + \ifx\first@\second@ \numbers@lefttrue \numbers@rightfalse \numbers@true \fi + \xdef\second@{right} + \ifx\first@\second@ \numbers@leftfalse \numbers@righttrue \numbers@true \fi + \xdef\second@{leftright} + \ifx\first@\second@ \numbers@lefttrue \numbers@righttrue \numbers@true \fi + } +\def\hidenumbering{\numbers@false} +\def\hidenumber#1{\xdef\first@{#1,&,@} \hidenumber@} +\newcommand\shownames[2][n]{% + \xdef\first@{#1}\ifx\first@\n@\else\xdef\names@fg{#1}\fi + \xdef\first@{#2} \xdef\second@{left} + \ifx\first@\second@ \names@rightfalse \else \names@righttrue \fi + \names@true} +\def\hidenames{\names@false} +\def\hidename#1{\xdef\first@{#1,&,@} \hidename@} +\def\hideresidues{\hidechartrue} +\def\showresidues{\hidecharfalse} +\def\alignment#1{% + \xdef\first@{#1} + \xdef\temp@{left} + \ifx\first@\temp@ \xdef\c@factor{0} + \else + \xdef\temp@{center} + \ifx\first@\temp@ \xdef\c@factor{0.5} + \else + \xdef\temp@{right} + \ifx\first@\temp@ \xdef\c@factor{1} + \fi\fi\fi} +\def\donotshade#1{% + \xdef\temp@{consensus} + \xdef\first@{#1} + \ifx\first@\temp@ + \consensuscolors{Black}{White}{Black}{White}{Black}{White} + \else + \xdef\first@{#1,&,@} \donot@shade + \fi} +\def\hideseqs{\xdef\hide@seqs{y}} +\def\showseqs{\xdef\hide@seqs{n}} +\def\hideseq#1{\xdef\first@{#1,&,@} \hideseq@} +\def\killseq#1{\xdef\first@{#1,&,@} \killseq@} +\def\hidesequencelogo{\show@logofalse} +\def\hidesubfamilylogo{\show@sublogofalse} +\def\logo@group@get#1#2@{% + \xdef\first@{#1}\xdef\third@{#2@} + \ifx\first@\ampers@nd + \else + \ifnum`#1>96 \make@upper\fi + \expandafter\xdef\csname logo@col\first@\endcsname{\second@} + \expandafter\logo@group@get\third@ + \fi +} +\def\logocolor#1#2{% + \xdef\logo@colors@set{yes} + \xdef\second@{#2} + \xdef\third@{#1&@} + \expandafter\logo@group@get\third@ +} +\newcommand\clearlogocolors[1][Black]{% + \logocolor{ABCDEFGHIJKLMNOPQRSTUVWXYZ}{#1} +} +\def\dofrequencycorrection{\xdef\do@freq@correction{y}} +\def\undofrequencycorrection{\xdef\do@freq@correction{n}} +\newcommand\showlogoscale[2][Black]{\xdef\logo@scalecol{#1}\xdef\show@logoscale{#2}} +\def\hidelogoscale{\xdef\show@logoscale{n}} +\def\hidenegatives{\xdef\hide@negatives{y}\xdef\sublogo@tint{}} +\newcommand\shownegatives[1][medium]{% + \xdef\hide@negatives{n} + \xdef\first@{#1} + \xdef\second@{full} + \ifx\first@\second@ + \xdef\sublogo@tint{} + \else + \xdef\second@{strong} + \ifx\first@\second@ + \xdef\sublogo@tint{Light} + \else + \xdef\second@{medium} + \ifx\first@\second@ + \xdef\sublogo@tint{LightLight} + \else + \xdef\second@{weak} + \ifx\first@\second@ + \xdef\sublogo@tint{LightLightLight} + \else + \xdef\sublogo@tint{LightLight} + \fi\fi\fi\fi +} +\def\set@logocolors{% + \xdef\second@{undefined} + \ifx\first@\second@ + \if\logo@colors@set\n@ + \xdef\first@{standard} + \fi + \fi + \xdef\second@{standard} + \ifx\first@\second@ + \if\seq@type A + \xdef\logo@colors@set{n} + \else + \if\seq@type P + \xdef\first@{rasmol} + \else + \xdef\first@{nucleotide} + \fi + \fi + \fi + \xdef\second@{nucleotide} + \ifx\first@\second@ + \clearlogocolors + \logocolor{G}{Black} + \logocolor{A}{Green} + \logocolor{TU}{Red} + \logocolor{C}{Blue} + \else + \xdef\second@{rasmol} + \ifx\first@\second@ + \clearlogocolors + \logocolor{DE}{Red} + \logocolor{CM}{Yellow} + \logocolor{KR}{Blue} + \logocolor{ST}{Orange} + \logocolor{FY}{MidnightBlue} + \logocolor{NQ}{Cyan} + \logocolor{G}{LightGray} + \logocolor{LVI}{Green} + \logocolor{A}{DarkGray} + \logocolor{W}{CarnationPink} + \logocolor{H}{CornflowerBlue} + \logocolor{P}{Apricot} + \logocolor{BZ}{LightMagenta} + \else + \xdef\second@{chemical} + \ifx\first@\second@ + \clearlogocolors + \logocolor{DE}{Red} + \logocolor{VIL}{Black} + \logocolor{AG}{Gray} + \logocolor{NQ}{Green} + \logocolor{FYW}{Brown} + \logocolor{KRH}{Blue} + \logocolor{ST}{Magenta} + \logocolor{P}{Orange} + \logocolor{CM}{Yellow} + \else + \xdef\second@{hydropathy} + \ifx\first@\second@ + \clearlogocolors + \logocolor{DE}{Red} + \logocolor{KRH}{Blue} + \logocolor{YSTGNQC}{Yellow} + \logocolor{AFPMWVIL}{Green} + \else + \xdef\second@{structure} + \ifx\first@\second@ + \clearlogocolors + \logocolor{DEHKNQR}{Orange} + \logocolor{ACGPSTWY}{Yellow} + \logocolor{FILMV}{Green} + \else + \xdef\second@{standard area} + \ifx\first@\second@ + \clearlogocolors + \logocolor{G}{BrickRed} + \logocolor{AS}{Orange} + \logocolor{CP}{Yellow} + \logocolor{TDVN}{YellowGreen} + \logocolor{IE}{PineGreen} + \logocolor{LQHM}{SkyBlue} + \logocolor{FK}{RoyalPurple} + \logocolor{Y}{RedViolet} + \logocolor{RW}{Black} + \else + \xdef\second@{accessible area} + \ifx\first@\second@ + \clearlogocolors + \logocolor{C}{BrickRed} + \logocolor{IVG}{Orange} + \logocolor{FLMA}{Yellow} + \logocolor{WSTH}{YellowGreen} + \logocolor{P}{PineGreen} + \logocolor{YDN}{SkyBlue} + \logocolor{EQ}{RoyalPurple} + \logocolor{R}{RedViolet} + \logocolor{K}{Black} + \fi\fi\fi\fi\fi\fi\fi +} +\newcommand\findsubfamily[2][n]{% + \xdef\first@{#1} + \ifx\first@\n@ + \else + \xdef\subfamily@threshold{#1} + \fi + \xdef\subfamily@seq{#2} +} +\def\setsubfamily#1{% + \xdef\sub@family@setting{#1} + \loopcount=1 + \loop + \expandafter\xdef\csname subfamily@num\the\loopcount\endcsname{1} + \advance\loopcount by 1 + \ifnum\loopcount>\seq@count\else\repeat + \xdef\subfamily@count{2} + \res@count=0 + \xdef\first@{#1,&,@} + \setsubfamily@ + \clear@res@nums{1} + \clear@res@nums{2} + \expandafter\xdef\csname group@num2\endcsname{\the\res@count} + \loopcount=\seq@count + \advance\loopcount by -\res@count + \expandafter\xdef\csname group@num1\endcsname{\the\loopcount} +} +\def\subfamilythreshold#1{\xdef\subfamily@threshold{#1}} +\newcommand\showsubfamilylogo[2][undefined]{% + \xdef\first@{#1} \set@logocolors + \xdef\first@{#2} \xdef\last@{top} + \ifx\first@\last@\xdef\sublogo@top{0}\else\xdef\sublogo@top{1}\fi + \show@sublogotrue +} +\def\relevance#1{% + \def\sig@max{#1} + \setlength\temp@@length{1000sp} + \setlength\temp@@length{\sig@max\temp@@length} + \loopcount=\temp@@length + \xdef\sig@max{\the\loopcount} +} +\newcommand\showrelevance[2][Black]{\def\sig@color{#1}\def\sig@char{#2}\xdef\hide@sig{n}} +\def\hiderelevance{\xdef\hide@sig{y}} +\newcommand\showsequencelogo[2][undefined]{% + \xdef\first@{#1} \set@logocolors + \xdef\first@{#2} \xdef\last@{top} + \ifx\first@\last@\xdef\logo@top{0}\else\xdef\logo@top{1}\fi + \show@logotrue +} +\newcommand\showconsensus[2][n]{% + \xdef\text@scale{n} + \xdef\box@scale{n} + \xdef\first@{#1} + \ifx\first@\n@ + \xdef\collect@cons@colors{no} + \else + \xdef\first@{#1,&,@} + \expandafter\get@item\first@ + \xdef\c@nsc@l{\fourth@} + \xdef\first@@{Gray} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{RedBlue} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{BlueRed} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{RedGreen} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{GreenRed} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{ColdHot} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{HotCold} + \ifx\c@nsc@l\first@@\xdef\text@scale{y} + \fi\fi\fi\fi\fi\fi\fi + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \xdef\c@nssc@le{White} + \else + \xdef\c@nssc@le{\fourth@} + \xdef\first@{Gray} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{RedBlue} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{BlueRed} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{RedGreen} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{GreenRed} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{ColdHot} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{HotCold} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \fi\fi\fi\fi\fi\fi\fi + \fi + \xdef\collect@cons@colors{y} + \fi + \xdef\first@{#2} \xdef\last@{top} + \ifx\first@\last@\xdef\cons@top{0}\else\xdef\cons@top{1}\fi + \show@construe} +\def\consensuscolors#1#2#3#4#5#6{% + \xdef\last@{\ampers@nd} + \xdef\first@{#1&}\xdef\second@{#2&} + \ifx\first@\last@\else\def\ConsTextNomatch{#1}\fi + \ifx\second@\last@\else\def\ConsNomatch{#2}\fi + \xdef\first@{#3&}\xdef\second@{#4&} + \ifx\first@\last@\else\def\ConsTextMatch{#3}\fi + \ifx\second@\last@\else\def\ConsMatch{#4}\fi + \xdef\first@{#5&}\xdef\second@{#6&} + \ifx\first@\last@\else\def\ConsTextAllmatch{#5}\fi + \ifx\second@\last@\else\def\ConsAllmatch{#6}\fi +} +\def\defconsensus#1#2#3{% + \xdef\second@{#1&} + \ifx\second@\ampers@nd \else \def\n@m@tch{#1}\fi + \xdef\second@{#2&} + \ifx\second@\ampers@nd \else \def\m@tch{#2}\fi + \xdef\second@{#3&} + \ifx\second@\ampers@nd \else \def\@llm@tch{#3}\fi} +\def\hideconsensus{\show@consfalse} +\def\nameconsensus#1{\def\cons@name{#1}} +\def\namesequencelogo#1{\def\logo@name@user{#1}} +\newcommand\namesubfamilylogo[2][]{\def\sublogo@name@neg{#1}\def\sublogo@name@user{#2}} +\def\hideleadinggaps{\sh@wg@psfalse} +\def\showleadinggaps{\sh@wg@pstrue} +\newcommand\showruler[3][n]{% + \xdef\first@{#1} + \ifx\first@\n@\else\xdef\ruler@fg{#1}\fi + \xdef\first@{consensus} \xdef\second@{#3} + \xdef\third@{bottom} \xdef\fourth@{#2} + \ifx\third@\fourth@ \xdef\rule@top{1}\else\xdef\rule@top{0}\fi + \ifx\first@\second@ \xdef\rule@num{0} + \else + \xdef\first@{#3 @} \expandafter\check@letter\first@ + \xdef\first@{#3} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count + \else + \ifnum\first@>0 + \xdef\rule@num{\first@} + \fi + \fi + \fi + \xdef\ruler@{}} +\def\hideruler{\xdef\rule@num{-1}} +\def\allowzero{\xdef\allow@zero{y}} +\def\disallowzero{\xdef\allow@zero{n}} +\def\rulersteps#1{% + \xdef\ruler@step{#1} + \ifnum#1<4 \xdef\ruler@rot{90}\fi +} +\def\rotateruler{\xdef\ruler@rot{90}} +\def\unrotateruler{\xdef\ruler@rot{0}} +\def\namerulerpos#1#2{% + \expandafter\xdef\csname alt@ruler#1\endcsname{#2} +} +\def\featurerule#1{\setlength\rule@thick{#1}} +\def\orderseqs#1{% + \def\order@loop{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \xdef\seq@order{\seq@order,\first@} + \xdef\first@{\first@@ @} + \order@loop + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\seq@order{\seq@order,\fourth@} + \order@loop + \fi + \fi} + \xdef\first@{#1,&,@} + \xdef\seq@order{} + \order@loop + \xdef\seq@order{\seq@order @} + \expandafter\get@item\seq@order + \xdef\seq@order{\first@@,@} +} +\def\setfamily#1#2{% + \xdef\second@{#2&} + \ifx\second@\ampers@nd + \else + \xdef\first@{#1} + \xdef\second@{#2} + \xdef\temp@{rm} + \ifx\second@\temp@ + \xdef\third@{\rmdefault} + \else + \xdef\temp@{sf} + \ifx\second@\temp@ + \xdef\third@{\sfdefault} + \else + \xdef\temp@{tt} + \ifx\second@\temp@ + \xdef\third@{\ttdefault} + \else + \xdef\third@{\second@} + \fi\fi\fi + \xdef\temp@{featurenames} + \ifx\first@\temp@ \xdef\ftext@family{\third@} + \else + \xdef\temp@{featurestylenames} + \ifx\first@\temp@ \xdef\fstyles@family{\third@} + \else + \xdef\temp@{features} + \ifx\first@\temp@ \xdef\featuretext@family{\third@} + \else + \xdef\temp@{featurestyles} + \ifx\first@\temp@ \xdef\featurestyles@family{\third@} + \else + \xdef\temp@{numbering} + \ifx\first@\temp@ \xdef\numbertext@family{\third@} + \else + \xdef\temp@{names} + \ifx\first@\temp@ \xdef\namestext@family{\third@} + \else + \xdef\temp@{residues} + \ifx\first@\temp@ \xdef\residues@family{\third@} + \else + \xdef\temp@{legend} + \ifx\first@\temp@ \xdef\legend@family{\third@} + \else + \xdef\temp@{labels} + \ifx\first@\temp@ \xdef\label@family{\third@} + \else + \xdef\temp@{ruler} + \ifx\first@\temp@ \xdef\ruler@family{\second@} + \else + \xdef\temp@{all} + \ifx\first@\temp@ + \xdef\ftext@family{\third@} + \xdef\fstyles@family{\third@} + \xdef\featuretext@family{\third@} + \xdef\featurestyles@family{\third@} + \xdef\numbertext@family{\third@} + \xdef\namestext@family{\third@} + \xdef\residues@family{\third@} + \xdef\legend@family{\third@} + \xdef\label@family{\third@} + \xdef\ruler@family{\second@} + \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi + \fi +} +\def\setseries#1#2{% + \xdef\second@{#2&} + \ifx\second@\ampers@nd + \else + \xdef\first@{#1} + \xdef\second@{#2} + \xdef\temp@{bf} + \ifx\second@\temp@ + \xdef\third@{\bfdefault} + \else + \xdef\temp@{md} + \ifx\second@\temp@ + \xdef\third@{\mddefault} + \else + \xdef\third@{\second@} + \fi\fi + \xdef\temp@{featurenames} + \ifx\first@\temp@ \xdef\ftext@series{\third@} + \else + \xdef\temp@{featurestylenames} + \ifx\first@\temp@ \xdef\fstyles@series{\third@} + \else + \xdef\temp@{features} + \ifx\first@\temp@ \xdef\featuretext@series{\third@} + \else + \xdef\temp@{featurestyles} + \ifx\first@\temp@ \xdef\featurestyles@series{\third@} + \else + \xdef\temp@{numbering} + \ifx\first@\temp@ \xdef\numbertext@series{\third@} + \else + \xdef\temp@{names} + \ifx\first@\temp@ \xdef\namestext@series{\third@} + \else + \xdef\temp@{residues} + \ifx\first@\temp@ \xdef\residues@series{\third@} + \else + \xdef\temp@{legend} + \ifx\first@\temp@ \xdef\legend@series{\third@} + \else + \xdef\temp@{labels} + \ifx\first@\temp@ \xdef\label@series{\third@} + \else + \xdef\temp@{all} + \ifx\first@\temp@ + \xdef\ftext@series{\third@} + \xdef\fstyles@series{\third@} + \xdef\featuretext@series{\third@} + \xdef\featurestyles@series{\third@} + \xdef\numbertext@series{\third@} + \xdef\namestext@series{\third@} + \xdef\residues@series{\third@} + \xdef\legend@series{\third@} + \xdef\label@series{\third@} + \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi + \fi +} +\def\setshape#1#2{% + \xdef\second@{#2&} + \ifx\second@\ampers@nd + \else + \xdef\first@{#1} + \xdef\second@{#2} + \xdef\temp@{it} + \ifx\second@\temp@ + \xdef\third@{\itdefault} + \else + \xdef\temp@{sl} + \ifx\second@\temp@ + \xdef\third@{\sldefault} + \else + \xdef\temp@{sc} + \ifx\second@\temp@ + \xdef\third@{\scdefault} + \else + \xdef\temp@{up} + \ifx\second@\temp@ + \xdef\third@{\updefault} + \else + \xdef\third@{\second@} + \fi\fi\fi\fi + \xdef\temp@{featurenames} + \ifx\first@\temp@ \xdef\ftext@shape{\third@} + \else + \xdef\temp@{featurestylenames} + \ifx\first@\temp@ \xdef\fstyles@shape{\third@} + \else + \xdef\temp@{features} + \ifx\first@\temp@ \xdef\featuretext@shape{\third@} + \else + \xdef\temp@{featurestyles} + \ifx\first@\temp@ \xdef\featurestyles@shape{\third@} + \else + \xdef\temp@{numbering} + \ifx\first@\temp@ \xdef\numbertext@shape{\third@} + \else + \xdef\temp@{names} + \ifx\first@\temp@ \xdef\namestext@shape{\third@} + \else + \xdef\temp@{residues} + \ifx\first@\temp@ \xdef\residues@shape{\third@} + \else + \xdef\temp@{legend} + \ifx\first@\temp@ \xdef\legend@shape{\third@} + \else + \xdef\temp@{labels} + \ifx\first@\temp@ \xdef\label@shape{\third@} + \else + \xdef\temp@{all} + \ifx\first@\temp@ + \xdef\ftext@shape{\third@} + \xdef\fstyles@shape{\third@} + \xdef\featuretext@shape{\third@} + \xdef\featurestyles@shape{\third@} + \xdef\numbertext@shape{\third@} + \xdef\namestext@shape{\third@} + \xdef\residues@shape{\third@} + \xdef\legend@shape{\third@} + \xdef\label@shape{\third@} + \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi + \fi +} +\def\setsize#1#2{% + \xdef\second@{#2&} + \ifx\second@\ampers@nd + \else + \xdef\first@{#1} + \xdef\temp@{features} + \ifx\first@\temp@ + \def\featuretext@size{\csname #2\endcsname} + \else + \xdef\temp@{featurestyles} + \ifx\first@\temp@ + \def\featurestyles@size{\csname #2\endcsname} + \else + \xdef\temp@{featurenames} + \ifx\first@\temp@ + \def\ftext@size{\csname #2\endcsname} + \else + \xdef\temp@{featurestylenames} + \ifx\first@\temp@ + \def\fstyles@size{\csname #2\endcsname} + \else + \xdef\temp@{numbering} + \ifx\first@\temp@ + \def\numbertext@size{\csname #2\endcsname} + \else + \xdef\temp@{names} + \ifx\first@\temp@ + \def\namestext@size{\csname #2\endcsname} + \else + \xdef\temp@{legend} + \ifx\first@\temp@ + \def\legend@size{\csname #2\endcsname} + \else + \xdef\temp@{labels} + \ifx\first@\temp@ + \def\label@size{\csname #2\endcsname} + \else + \xdef\temp@{residues} + \ifx\first@\temp@ + \def\residues@size{\csname #2\endcsname} + \xdef\res@size{#2} + \else + \xdef\temp@{all} + \ifx\first@\temp@ + \def\featuretext@size{\csname #2\endcsname} + \def\featurestyles@size{\csname #2\endcsname} + \def\ftext@size{\csname #2\endcsname} + \def\fstyles@size{\csname #2\endcsname} + \def\numbertext@size{\csname #2\endcsname} + \def\namestext@size{\csname #2\endcsname} + \def\legend@size{\csname #2\endcsname} + \def\label@size{\csname #2\endcsname} + \def\residues@size{\csname #2\endcsname} + \xdef\res@size{#2} + \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi + \xdef\temp@{Huge} + \ifx\temp@\res@size + \def\bottomruler@size{\csname Large\endcsname} + \else + \xdef\temp@{huge} + \ifx\temp@\res@size + \def\bottomruler@size{\csname large\endcsname} + \else + \xdef\temp@{LARGE} + \ifx\temp@\res@size + \def\bottomruler@size{\csname normalsize\endcsname} + \else + \xdef\temp@{Large} + \ifx\temp@\res@size + \def\bottomruler@size{\csname small\endcsname} + \else + \xdef\temp@{large} + \ifx\temp@\res@size + \def\bottomruler@size{\csname footnotesize\endcsname} + \else + \xdef\temp@{normalsize} + \ifx\temp@\res@size + \def\bottomruler@size{\csname scriptsize\endcsname} + \else + \def\bottomruler@size{\csname tiny\endcsname} + \fi\fi\fi\fi\fi\fi + \fi + \xdef\temp@{ruler} + \ifx\first@\temp@ + \def\bottomruler@size{\csname #2\endcsname} + \fi +} +\def\setfont#1#2#3#4#5{% + \setfamily{#1}{#2}\setseries{#1}{#3} + \setshape{#1}{#4}\setsize{#1}{#5}} +\def\featurenamesrm{\setfamily{featurenames}{rm}} +\def\featurenamessf{\setfamily{featurenames}{sf}} +\def\featurenamestt{\setfamily{featurenames}{tt}} +\def\featurenamesmd{\setseries{featurenames}{md}} +\def\featurenamesbf{\setseries{featurenames}{bf}} +\def\featurenamesup{\setshape {featurenames}{up}} +\def\featurenamesit{\setshape {featurenames}{it}} +\def\featurenamessl{\setshape {featurenames}{sl}} +\def\featurenamessc{\setshape {featurenames}{sc}} +\def\featurenamestiny {\setsize{featurenames}{tiny}} +\def\featurenamesscriptsize {\setsize{featurenames}{scriptsize}} +\def\featurenamesfootnotesize{\setsize{featurenames}{footnotesize}} +\def\featurenamessmall {\setsize{featurenames}{small}} +\def\featurenamesnormalsize {\setsize{featurenames}{normalsize}} +\def\featurenameslarge {\setsize{featurenames}{large}} +\def\featurenamesLarge {\setsize{featurenames}{Large}} +\def\featurenamesLARGE {\setsize{featurenames}{LARGE}} +\def\featurenameshuge {\setsize{featurenames}{huge}} +\def\featurenamesHuge {\setsize{featurenames}{Huge}} +\def\featurestylenamesrm{\setfamily{featurestylenames}{rm}} +\def\featurestylenamessf{\setfamily{featurestylenames}{sf}} +\def\featurestylenamestt{\setfamily{featurestylenames}{tt}} +\def\featurestylenamesmd{\setseries{featurestylenames}{md}} +\def\featurestylenamesbf{\setseries{featurestylenames}{bf}} +\def\featurestylenamesup{\setshape {featurestylenames}{up}} +\def\featurestylenamesit{\setshape {featurestylenames}{it}} +\def\featurestylenamessl{\setshape {featurestylenames}{sl}} +\def\featurestylenamessc{\setshape {featurestylenames}{sc}} +\def\featurestylenamestiny {\setsize{featurestylenames}{tiny}} +\def\featurestylenamesscriptsize {\setsize{featurestylenames}{scriptsize}} +\def\featurestylenamesfootnotesize{\setsize{featurestylenames}{footnotesize}} +\def\featurestylenamessmall {\setsize{featurestylenames}{small}} +\def\featurestylenamesnormalsize {\setsize{featurestylenames}{normalsize}} +\def\featurestylenameslarge {\setsize{featurestylenames}{large}} +\def\featurestylenamesLarge {\setsize{featurestylenames}{Large}} +\def\featurestylenamesLARGE {\setsize{featurestylenames}{LARGE}} +\def\featurestylenameshuge {\setsize{featurestylenames}{huge}} +\def\featurestylenamesHuge {\setsize{featurestylenames}{Huge}} +\def\featuresrm{\setfamily{features}{rm}} +\def\featuressf{\setfamily{features}{sf}} +\def\featurestt{\setfamily{features}{tt}} +\def\featuresmd{\setseries{features}{md}} +\def\featuresbf{\setseries{features}{bf}} +\def\featuresup{\setshape {features}{up}} +\def\featuresit{\setshape {features}{it}} +\def\featuressl{\setshape {features}{sl}} +\def\featuressc{\setshape {features}{sc}} +\def\featurestiny {\setsize{features}{tiny}} +\def\featuresscriptsize {\setsize{features}{scriptsize}} +\def\featuresfootnotesize{\setsize{features}{footnotesize}} +\def\featuressmall {\setsize{features}{small}} +\def\featuresnormalsize {\setsize{features}{normalsize}} +\def\featureslarge {\setsize{features}{large}} +\def\featuresLarge {\setsize{features}{Large}} +\def\featuresLARGE {\setsize{features}{LARGE}} +\def\featureshuge {\setsize{features}{huge}} +\def\featuresHuge {\setsize{features}{Huge}} +\def\featurestylesrm{\setfamily{featurestyles}{rm}} +\def\featurestylessf{\setfamily{featurestyles}{sf}} +\def\featurestylestt{\setfamily{featurestyles}{tt}} +\def\featurestylesmd{\setseries{featurestyles}{md}} +\def\featurestylesbf{\setseries{featurestyles}{bf}} +\def\featurestylesup{\setshape {featurestyles}{up}} +\def\featurestylesit{\setshape {featurestyles}{it}} +\def\featurestylessl{\setshape {featurestyles}{sl}} +\def\featurestylessc{\setshape {featurestyles}{sc}} +\def\featurestylestiny {\setsize{featurestyles}{tiny}} +\def\featurestylesscriptsize {\setsize{featurestyles}{scriptsize}} +\def\featurestylesfootnotesize{\setsize{featurestyles}{footnotesize}} +\def\featurestylessmall {\setsize{featurestyles}{small}} +\def\featurestylesnormalsize {\setsize{featurestyles}{normalsize}} +\def\featurestyleslarge {\setsize{featurestyles}{large}} +\def\featurestylesLarge {\setsize{featurestyles}{Large}} +\def\featurestylesLARGE {\setsize{featurestyles}{LARGE}} +\def\featurestyleshuge {\setsize{featurestyles}{huge}} +\def\featurestylesHuge {\setsize{featurestyles}{Huge}} +\def\numberingrm{\setfamily{numbering}{rm}} +\def\numberingsf{\setfamily{numbering}{sf}} +\def\numberingtt{\setfamily{numbering}{tt}} +\def\numberingmd{\setseries{numbering}{md}} +\def\numberingbf{\setseries{numbering}{bf}} +\def\numberingup{\setshape {numbering}{up}} +\def\numberingit{\setshape {numbering}{it}} +\def\numberingsl{\setshape {numbering}{sl}} +\def\numberingsc{\setshape {numbering}{sc}} +\def\numberingtiny {\setsize{numbering}{tiny}} +\def\numberingscriptsize {\setsize{numbering}{scriptsize}} +\def\numberingfootnotesize{\setsize{numbering}{footnotesize}} +\def\numberingsmall {\setsize{numbering}{small}} +\def\numberingnormalsize {\setsize{numbering}{normalsize}} +\def\numberinglarge {\setsize{numbering}{large}} +\def\numberingLarge {\setsize{numbering}{Large}} +\def\numberingLARGE {\setsize{numbering}{LARGE}} +\def\numberinghuge {\setsize{numbering}{huge}} +\def\numberingHuge {\setsize{numbering}{Huge}} +\def\namesrm{\setfamily{names}{rm}} +\def\namessf{\setfamily{names}{sf}} +\def\namestt{\setfamily{names}{tt}} +\def\namesmd{\setseries{names}{md}} +\def\namesbf{\setseries{names}{bf}} +\def\namesup{\setshape {names}{up}} +\def\namesit{\setshape {names}{it}} +\def\namessl{\setshape {names}{sl}} +\def\namessc{\setshape {names}{sc}} +\def\namestiny {\setsize{names}{tiny}} +\def\namesscriptsize {\setsize{names}{scriptsize}} +\def\namesfootnotesize{\setsize{names}{footnotesize}} +\def\namessmall {\setsize{names}{small}} +\def\namesnormalsize {\setsize{names}{normalsize}} +\def\nameslarge {\setsize{names}{large}} +\def\namesLarge {\setsize{names}{Large}} +\def\namesLARGE {\setsize{names}{LARGE}} +\def\nameshuge {\setsize{names}{huge}} +\def\namesHuge {\setsize{names}{Huge}} +\def\residuesrm{\setfamily{residues}{rm}} +\def\residuessf{\setfamily{residues}{sf}} +\def\residuestt{\setfamily{residues}{tt}} +\def\residuesmd{\setseries{residues}{md}} +\def\residuesbf{\setseries{residues}{bf}} +\def\residuesup{\setshape {residues}{up}} +\def\residuesit{\setshape {residues}{it}} +\def\residuessl{\setshape {residues}{sl}} +\def\residuessc{\setshape {residues}{sc}} +\def\residuestiny {\setsize{residues}{tiny}} +\def\residuesscriptsize {\setsize{residues}{scriptsize}} +\def\residuesfootnotesize{\setsize{residues}{footnotesize}} +\def\residuessmall {\setsize{residues}{small}} +\def\residuesnormalsize {\setsize{residues}{normalsize}} +\def\residueslarge {\setsize{residues}{large}} +\def\residuesLarge {\setsize{residues}{Large}} +\def\residuesLARGE {\setsize{residues}{LARGE}} +\def\residueshuge {\setsize{residues}{huge}} +\def\residuesHuge {\setsize{residues}{Huge}} +\def\legendrm{\setfamily{legend}{rm}} +\def\legendsf{\setfamily{legend}{sf}} +\def\legendtt{\setfamily{legend}{tt}} +\def\legendmd{\setseries{legend}{md}} +\def\legendbf{\setseries{legend}{bf}} +\def\legendup{\setshape {legend}{up}} +\def\legendit{\setshape {legend}{it}} +\def\legendsl{\setshape {legend}{sl}} +\def\legendsc{\setshape {legend}{sc}} +\def\legendtiny {\setsize{legend}{tiny}} +\def\legendscriptsize {\setsize{legend}{scriptsize}} +\def\legendfootnotesize{\setsize{legend}{footnotesize}} +\def\legendsmall {\setsize{legend}{small}} +\def\legendnormalsize {\setsize{legend}{normalsize}} +\def\legendlarge {\setsize{legend}{large}} +\def\legendLarge {\setsize{legend}{Large}} +\def\legendLARGE {\setsize{legend}{LARGE}} +\def\legendhuge {\setsize{legend}{huge}} +\def\legendHuge {\setsize{legend}{Huge}} +\def\rulerrm{\setfamily{ruler}{rm}} +\def\rulersf{\setfamily{ruler}{sf}} +\def\rulertt{\setfamily{ruler}{tt}} +\def\rulertiny {\setsize{ruler}{tiny}} +\def\rulerscriptsize {\setsize{ruler}{scriptsize}} +\def\rulerfootnotesize{\setsize{ruler}{footnotesize}} +\def\rulersmall {\setsize{ruler}{small}} +\def\rulernormalsize {\setsize{ruler}{normalsize}} +\def\rulerlarge {\setsize{ruler}{large}} +\def\rulerLarge {\setsize{ruler}{Large}} +\def\rulerLARGE {\setsize{ruler}{LARGE}} +\def\rulerhuge {\setsize{ruler}{huge}} +\def\rulerHuge {\setsize{ruler}{Huge}} +\def\funcshadingstyle#1#2#3#4#5{% + \xdef\temp@{nomatch} \xdef\first@{#1} + \ifx\temp@\first@ + \xdef\first@{0} + \else + \xdef\first@{\csname funcgrp#1\endcsname} + \fi + \ifnum\first@>-1 + \expandafter\xdef\csname fg@textcolor\first@\endcsname{#2} + \expandafter\xdef\csname fg@color\first@\endcsname{#3} + \expandafter\xdef\csname funcm@tch\first@\endcsname{#4} + \expandafter\def\csname func@style\first@\endcsname{\csname text#5\endcsname} + \fi} +\def\defshadingcolors#1{% + \expandafter\xdef\csname TextNomatch@#1\endcsname{\TextNomatch} + \expandafter\xdef\csname Nomatch@#1\endcsname{\Nomatch} + \expandafter\xdef\csname resn@m@tch@#1\endcsname{\resn@m@tch} + + \expandafter\xdef\csname TextSimilar@#1\endcsname{\TextSimilar} + \expandafter\xdef\csname Similar@#1\endcsname{\Similar} + \expandafter\xdef\csname ressimm@tch@#1\endcsname{\ressimm@tch} + + \expandafter\xdef\csname TextIdentical@#1\endcsname{\TextIdentical} + \expandafter\xdef\csname Identical@#1\endcsname{\Identical} + \expandafter\xdef\csname resm@tch@#1\endcsname{\resm@tch} + + \expandafter\xdef\csname TextAllmatch@#1\endcsname{\TextAllmatch} + \expandafter\xdef\csname Allmatch@#1\endcsname{\Allmatch} + \expandafter\xdef\csname res@llm@tch@#1\endcsname{\res@llm@tch} + + \expandafter\xdef\csname gap@fg@#1\endcsname{\gap@fg} + \expandafter\xdef\csname gap@bg@#1\endcsname{\gap@bg} + +} +\def\shadingcolors#1{% + \gapcolors{Black}{White} + \nomatchresidues{Black}{White}{upper}{up} + \xdef\first@{#1} \xdef\second@{blues} + \ifx\first@\second@ + \similarresidues{Black}{Magenta}{upper}{up} + \conservedresidues{White}{RoyalBlue}{upper}{up} + \allmatchresidues{Goldenrod}{RoyalPurple}{upper}{up} + \else \xdef\second@{greens} + \ifx\first@\second@ + \similarresidues{Black}{GreenYellow}{upper}{up} + \conservedresidues{White}{PineGreen}{upper}{up} + \allmatchresidues{YellowOrange}{OliveGreen}{upper}{up} + \else \xdef\second@{reds} + \ifx\first@\second@ + \similarresidues{Black}{YellowOrange}{upper}{up} + \conservedresidues{White}{BrickRed}{upper}{up} + \allmatchresidues{YellowGreen}{Mahagony}{upper}{up} + \else \xdef\second@{black} + \ifx\first@\second@ + \similarresidues{Black}{White}{upper}{sl} + \conservedresidues{White}{Black}{upper}{up} + \allmatchresidues{White}{Black}{upper}{sl} + \else \xdef\second@{grays} + \ifx\first@\second@ + \similarresidues{Black}{LightGray}{upper}{up} + \conservedresidues{White}{DarkGray}{upper}{up} + \allmatchresidues{White}{Black}{upper}{up} + \else + \xdef\TextNomatch{\csname TextNomatch@#1\endcsname} + \xdef\Nomatch {\csname Nomatch@#1\endcsname} + \xdef\resn@m@tch {\csname resn@m@tch@#1\endcsname} + \xdef\TextSimilar{\csname TextSimilar@#1\endcsname} + \xdef\Similar {\csname Similar@#1\endcsname} + \xdef\ressimm@tch{\csname ressimm@tch@#1\endcsname} + \xdef\TextIdentical{\csname TextIdentical@#1\endcsname} + \xdef\Identical {\csname Identical@#1\endcsname} + \xdef\resm@tch {\csname resm@tch@#1\endcsname} + \xdef\TextAllmatch{\csname TextAllmatch@#1\endcsname} + \xdef\Allmatch {\csname Allmatch@#1\endcsname} + \xdef\res@llm@tch {\csname res@llm@tch@#1\endcsname} + \xdef\gap@fg {\csname gap@fg@#1\endcsname} + \xdef\gap@bg {\csname gap@bg@#1\endcsname} + \xdef\domgap@fg {\csname domgap@fg@#1\endcsname} + \xdef\domgap@bg {\csname domgap@bg@#1\endcsname} + \fi\fi\fi\fi\fi + \xdef\first@{#1} + \expandafter\defshadingcolors{\first@} +} +\def\nomatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\TextNomatch{#1} + \expandafter\def\csname fg@textcolor0\endcsname{#1} + \fi + \ifx\second@\last@\else\gdef\Nomatch{#2} + \expandafter\def\csname fg@color0\endcsname{#2} + \fi + \ifx\third@\last@\else\def\resn@m@tch{#3} + \fi + \xdef\first@{#4&} + \ifx\first@\last@\else + \def\no@style{\csname text#4\endcsname} + \expandafter\def\csname func@style0\endcsname% + {\csname text#4\endcsname}\fi} +\def\similarresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\TextSimilar{#1}\fi + \ifx\second@\last@\else\gdef\Similar{#2}\fi + \ifx\third@\last@\else\def\ressimm@tch{#3}\fi + \xdef\first@{#4&} + \ifx\first@\last@\else + \def\sim@style{\csname text#4\endcsname}\fi} +\def\conservedresidues#1#2#3#4{\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\TextIdentical{#1}\fi + \ifx\second@\last@\else\gdef\Identical{#2}\fi + \ifx\third@\last@\else\def\resm@tch{#3}\fi + \xdef\first@{#4&} + \ifx\first@\last@\else + \def\id@style{\csname text#4\endcsname}\fi} +\def\allmatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\TextAllmatch{#1}\fi + \ifx\second@\last@\else\gdef\Allmatch{#2}\fi + \ifx\third@\last@\else\def\res@llm@tch{#3}\fi + \xdef\first@{#4&} + \ifx\first@\last@\else + \def\all@style{\csname text#4\endcsname}\fi} +\def\gapcolors#1#2 {\xdef\first@{#1&}\xdef\second@{#2&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\gap@fg{#1} + \expandafter\def\csname fg@textcolor*\endcsname{#1}\fi + \ifx\second@\last@\else\def\gap@bg{#2} + \expandafter\def\csname fg@color*\endcsname{#2}\fi} +\def\domaingapcolors#1#2 {\xdef\first@{#1&}\xdef\second@{#2&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\domgap@fg{#1} + \expandafter\def\csname fg@textcolor!\endcsname{#1}\fi + \ifx\second@\last@\else\def\domgap@bg{#2} + \expandafter\def\csname fg@color!\endcsname{#2}\fi} +\def\shadebox#1{% + \xdef\first@{White}% + \xdef\third@{#1}% + \xdef\second@{nomatch}% + \ifx\second@\third@ + \ifx\Nomatch\first@\white@box\else\textcolor{\Nomatch}{\box@rule}\fi% + \else + \xdef\second@{similar}% + \ifx\second@\third@ + \ifx\Similar\first@\white@box\else\textcolor{\Similar}{\box@rule}\fi% + \else + \xdef\second@{conserved}% + \ifx\second@\third@ + \ifx\Identical\first@\white@box\else\textcolor{\Identical}{\box@rule}\fi% + \else + \xdef\second@{allmatch}% + \ifx\second@\third@ + \ifx\Allmatch\first@\white@box\else\textcolor{\Allmatch}{\box@rule}\fi% + \else + \ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi + \fi\fi\fi\fi} +\def\featurenamescolor#1{% + \expandafter\xdef\csname ftext@fg@ttttop\endcsname{#1} + \expandafter\xdef\csname ftext@fg@tttop\endcsname{#1} + \expandafter\xdef\csname ftext@fg@ttop\endcsname{#1} + \expandafter\xdef\csname ftext@fg@top\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bottom\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bbottom\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bbbottom\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bbbbottom\endcsname{#1} +} +\def\featurestylenamescolor#1{% + \expandafter\xdef\csname fstyles@fg@ttttop\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@tttop\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@ttop\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@top\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bottom\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bbottom\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bbbottom\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bbbbottom\endcsname{#1} +} +\def\featurenamecolor#1#2{\expandafter\xdef\csname ftext@fg@#1\endcsname{#2}} +\def\featurestylenamecolor#1#2{\expandafter\xdef\csname fstyles@fg@#1\endcsname{#2}} +\def\namescolor#1{\xdef\names@fg{#1}} +\def\namecolor#1#2{% + \xdef\first@{consensus} \xdef\second@{#1} + \ifx\first@\second@ + \expandafter\xdef\csname name@col0\endcsname{#2} + \else + \xdef\first@{featurenames} \xdef\second@{#1} + \ifx\first@\second@ + \xdef\ftext@fg{#2} + \else + \xdef\first@{featurestylenames} \xdef\second@{#1} + \ifx\first@\second@ + \xdef\fstyles@fg{#2} + \else + \xdef\first@{#1,&,@} \xdef\third@{#2} \namecolor@ + \fi\fi\fi +} +\def\numberingcolor#1{\xdef\numbering@fg{#1}} +\def\numbercolor#1#2{% + \xdef\first@{consensus} \xdef\second@{#1} + \ifx\first@\second@ + \expandafter\xdef\csname number@col0\endcsname{#2} + \else + \xdef\first@{#1,&,@} \xdef\third@{#2} \numbercolor@ + \fi +} +\def\legendcolor#1{\xdef\legend@fg{#1}} +\def\rulercolor#1{\xdef\ruler@fg{#1}} +\def\molweight#1#2{% + \xdef\temp@{Da}% + \xdef\second@{#2}% + \ifx\second@\temp@\xdef\third@{Da}\else\xdef\third@{kDa}\fi% + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \xdef\first@{\csname @rd\first@\endcsname}% + \loopcount=\csname mol@weight\first@\endcsname% + \divide\loopcount by 10\relax% + \innerloopcount=\loopcount% + \hbox{% + \ifnum\loopcount>1000% + \divide\loopcount by 1000\relax% + \pos@count=\loopcount% + \multiply\loopcount by 1000\relax% + \advance\innerloopcount by -\loopcount% + \loopcount=\innerloopcount% + \ifnum\loopcount>949\advance\pos@count by 1\relax\fi% + \the\pos@count% + \ifx\temp@\second@\ifgerm@n .\else {,}\fi\fi% + \else% + \ifx\second@\temp@ \else 0\fi% + \fi% + \ifx\second@\temp@% + \the\loopcount% + \loopcount=\csname mol@weight\first@\endcsname% + \innerloopcount=\loopcount% + \divide\loopcount by 10\relax% + \multiply\loopcount by 10\relax% + \advance\innerloopcount by -\loopcount\relax% + \else% + \divide\innerloopcount by 10\relax% + \advance\innerloopcount by 5\relax% + \divide\innerloopcount by 10\relax% + \fi% + \ifnum\innerloopcount>9\relax\innerloopcount=0\relax\fi% + \ifgerm@n {,}\else .\fi% + \the\innerloopcount~\third@}} +\newcommand\charge[2][o]{% + \xdef\temp@{pep}% + \ifx\prefix@\temp@% + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \xdef\second@{\csname @rd\first@\endcsname}% + \loopcount=\csname ch@rge\second@\endcsname% + \xdef\first@{#1}\make@lower% + \if\first@ i\fi% + \if\first@ o\advance\loopcount by \chargeNterm% + \advance\loopcount by \chargeCterm\fi% + \if\first@ n\advance\loopcount by \chargeNterm\fi% + \if\first@ c\advance\loopcount by \chargeCterm\fi% + \hbox{\ensuremath{% + \ifnum\loopcount>0 +% + \else\ifnum\loopcount=0 \pm% + \else -\multiply\loopcount by -1\relax% + \fi\fi% + \innerloopcount=\loopcount% + \divide\loopcount by 1000\relax% + \the\loopcount% + \multiply\loopcount by 1000\relax% + \advance\innerloopcount by -\loopcount\relax% + \divide\innerloopcount by 10\relax% + \ifnum\innerloopcount=0% + \else% + \ifgerm@n {,}\else .\fi% + \ifnum\innerloopcount<10 0\fi% + \the\innerloopcount% + \fi}}% + \fi} +\def\TeXshade{% + \setbox1=\hbox{\texttt{H}}% + \def\logo@rule{\vrule depth0.25\ht1 height1.25\ht1 width\wd1}% + \TeX% + \logo@rule\kern-\wd1\textcolor{White}{\texttt{s}}% + \logo@rule\kern-\wd1\textcolor{White}{\texttt{h}}% + \texttt{a}% + \logo@rule\kern-\wd1\textcolor{White}{\texttt{d}}% + \texttt{e}} + +\def\includeTCoffee#1{% + \xdef\TC@first@{#1}\include@T@coffee} + +\def\firstcolumnDSSP{\xdef\fc@DSSP{y}} +\def\secondcolumnDSSP{\xdef\fc@DSSP{n}} + +\newcommand{\includeDSSP}[3][existing]{% + \temp@count=\dssp@num + \advance\temp@count by 1 + \xdef\dssp@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optiondssp\the\temp@count\endcsname{\first@} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqdssp\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname filenamedssp\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqdssp\the\temp@count\endcsname>\seq@count + \message{<Ignoring `#2' in \noexpand\includeDSSP>} + \advance\temp@count by -1 + \xdef\dssp@num{\the\temp@count} + \fi +} + +\newcommand{\includeHMMTOP}[3][existing]{% + \temp@count=\HMMTOP@num + \advance\temp@count by 1 + \xdef\HMMTOP@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optionHMMTOP\the\temp@count\endcsname{\first@} + \xdef\first@{#2[,]&}\expandafter\opt@color\first@ + \ifx\f@color\comm@ + \expandafter\xdef\csname fileseqHMMTOP\the\temp@count\endcsname{0} + \else + \expandafter\xdef\csname fileseqHMMTOP\the\temp@count\endcsname{\f@color} + \fi + \xdef\first@{\fourth@ @} \expandafter\check@letter\first@ + \xdef\first@{\fourth@} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqHMMTOP\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname filenameHMMTOP\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqHMMTOP\the\temp@count\endcsname>\seq@count + \message{<Ignoring `#2' in \noexpand\includeHMMTOP>} + \advance\temp@count by -1 + \xdef\HMMTOP@num{\the\temp@count} + \fi +} + +\newcommand{\includeSTRIDE}[3][existing]{% + \temp@count=\stride@num + \advance\temp@count by 1 + \xdef\stride@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optionstride\the\temp@count\endcsname{\first@} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqstride\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname filenamestride\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqstride\the\temp@count\endcsname>\seq@count + \message{<Ignoring `#2' in \noexpand\includeSTRIDE>} + \advance\temp@count by -1 + \xdef\stride@num{\the\temp@count} + \fi +} +\newcommand{\includePHDsec}[3][existing]{% + \temp@count=\PHD@num + \advance\temp@count by 1 + \xdef\PHD@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optionphd\the\temp@count\endcsname{\first@} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqphd\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname modephd\the\temp@count\endcsname{structure} + \expandafter\xdef\csname filenamephd\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqphd\the\temp@count\endcsname>\seq@count + \message{<Ignoring `#2' in \noexpand\includePHDsec>} + \advance\temp@count by -1 + \xdef\PHD@num{\the\temp@count} + \fi +} +\newcommand{\includePHDtopo}[3][existing]{% + \temp@count=\PHD@num + \advance\temp@count by 1 + \xdef\PHD@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optionphd\the\temp@count\endcsname{\first@} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqphd\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname modephd\the\temp@count\endcsname{topology} + \expandafter\xdef\csname filenamephd\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqphd\the\temp@count\endcsname>\seq@count + \message{<Ignoring `#2' in \noexpand\includePHDtopo>} + \advance\temp@count by -1 + \xdef\PHD@num{\the\temp@count} + \fi +} +\def\appearance#1#2#3#4#5{% + \xdef\first@{#1} \xdef\second@{#2} + \xdef\temp@{PHDsec} + \ifx\temp@\first@ + \xdef\temp@{alpha} + \ifx\second@\temp@ + \def\bottop@Hsec{#3} + \def\label@Hsec{#4} + \def\text@Hsec{#5} + \else + \xdef\temp@{beta} + \ifx\second@\temp@ + \def\bottop@Esec{#3} + \def\label@Esec{#4} + \def\text@Esec{#5} + \fi\fi + \else + \xdef\temp@{PHDtopo} + \ifx\temp@\first@ + \xdef\temp@{internal} + \ifx\second@\temp@ + \def\bottop@itop{#3} + \def\label@itop{#4} + \def\text@itop{#5} + \else + \xdef\temp@{external} + \ifx\second@\temp@ + \def\bottop@etop{#3} + \def\label@etop{#4} + \def\text@etop{#5} + \else + \xdef\temp@{TM} + \ifx\second@\temp@ + \def\bottop@TMtop{#3} + \def\label@TMtop{#4} + \def\text@TMtop{#5} + \fi\fi\fi + \else + \xdef\temp@{STRIDE} + \ifx\temp@\first@ + \xdef\temp@{alpha} + \ifx\second@\temp@ + \def\bottop@Hstride{#3} + \def\label@Hstride{#4} + \def\text@Hstride{#5} + \else + \xdef\temp@{3-10} + \ifx\second@\temp@ + \def\bottop@Gstride{#3} + \def\label@Gstride{#4} + \def\text@Gstride{#5} + \else + \xdef\temp@{pi} + \ifx\second@\temp@ + \def\bottop@Istride{#3} + \def\label@Istride{#4} + \def\text@Istride{#5} + \else + \xdef\temp@{beta} + \ifx\second@\temp@ + \def\bottop@Estride{#3} + \def\label@Estride{#4} + \def\text@Estride{#5} + \else + \xdef\temp@{bridge} + \ifx\second@\temp@ + \def\bottop@Bstride{#3} + \def\label@Bstride{#4} + \def\text@Bstride{#5} + \else + \xdef\temp@{turn} + \ifx\second@\temp@ + \def\bottop@Tstride{#3} + \def\label@Tstride{#4} + \def\text@Tstride{#5} + \fi\fi\fi\fi\fi\fi + \else + \xdef\temp@{DSSP} + \ifx\temp@\first@ + \xdef\temp@{alpha} + \ifx\second@\temp@ + \def\bottop@Hdssp{#3} + \def\label@Hdssp{#4} + \def\text@Hdssp{#5} + \else + \xdef\temp@{3-10} + \ifx\second@\temp@ + \def\bottop@Gdssp{#3} + \def\label@Gdssp{#4} + \def\text@Gdssp{#5} + \else + \xdef\temp@{pi} + \ifx\second@\temp@ + \def\bottop@Idssp{#3} + \def\label@Idssp{#4} + \def\text@Idssp{#5} + \else + \xdef\temp@{beta} + \ifx\second@\temp@ + \def\bottop@Edssp{#3} + \def\label@Edssp{#4} + \def\text@Edssp{#5} + \else + \xdef\temp@{bridge} + \ifx\second@\temp@ + \def\bottop@Bdssp{#3} + \def\label@Bdssp{#4} + \def\text@Bdssp{#5} + \else + \xdef\temp@{turn} + \ifx\second@\temp@ + \def\bottop@Tdssp{#3} + \def\label@Tdssp{#4} + \def\text@Tdssp{#5} + \else + \xdef\temp@{bend} + \ifx\second@\temp@ + \def\bottop@Sdssp{#3} + \def\label@Sdssp{#4} + \def\text@Sdssp{#5} + \fi\fi\fi\fi\fi\fi\fi + \else + \xdef\temp@{HMMTOP} + \ifx\temp@\first@ + \xdef\temp@{internal} + \ifx\second@\temp@ + \def\bottop@i@HMMTOP{#3} + \def\label@i@HMMTOP{#4} + \def\text@i@HMMTOP{#5} + \else + \xdef\temp@{external} + \ifx\second@\temp@ + \def\bottop@e@HMMTOP{#3} + \def\label@e@HMMTOP{#4} + \def\text@e@HMMTOP{#5} + \else + \xdef\temp@{TM} + \ifx\second@\temp@ + \def\bottop@TM@HMMTOP{#3} + \def\label@TM@HMMTOP{#4} + \def\text@TM@HMMTOP{#5} + \fi\fi\fi + \fi\fi\fi\fi\fi +} + +\def\showonDSSP#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@DSSP} +\def\hideonDSSP#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@DSSP} + +\def\showonSTRIDE#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@STRIDE} +\def\hideonSTRIDE#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@STRIDE} + +\def\showonPHDtopo#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@PHDtopo} +\def\hideonPHDtopo#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@PHDtopo} + +\def\showonPHDsec#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@PHDsec} +\def\hideonPHDsec#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@PHDsec} + +\def\showonHMMTOP#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@HMMTOP} +\def\hideonHMMTOP#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@HMMTOP} + +\def\codon#1#2{% + \xdef\first@{#1} + \xdef\second@{#2,&,@} + \expandafter\get@triplet\second@} +\def\geneticcode#1{% + \xdef\first@{#1} + \xdef\temp@{standard} + \ifx\first@\temp@ + \c@d@ns + \else + \input{#1.cod} + \fi} +\newcommand{\backtranslabel}[2][tiny]{% + \def\trans@size{\csname #1\endcsname} + \xdef\first@{#2} + \xdef\temp@{horizontal} + \ifx\temp@\first@ \xdef\tr@nsstyle{0}\fi + \xdef\temp@{zigzag} + \ifx\temp@\first@ \xdef\tr@nsstyle{1}\fi + \xdef\temp@{alternating} + \ifx\temp@\first@ \xdef\tr@nsstyle{2}\fi + \xdef\temp@{oblique} + \ifx\temp@\first@ \xdef\tr@nsstyle{3}\fi + \xdef\temp@{vertical} + \ifx\temp@\first@ \xdef\tr@nsstyle{4}\fi +} +\newcommand{\backtranstext}[2][tiny]{% + \def\transtext@size{\csname #1\endcsname} + \xdef\first@{#2} + \xdef\temp@{horizontal} + \ifx\temp@\first@ \xdef\tr@nstextstyle{0}\fi + \xdef\temp@{zigzag} + \ifx\temp@\first@ \xdef\tr@nstextstyle{1}\fi + \xdef\temp@{alternating} + \ifx\temp@\first@ \xdef\tr@nstextstyle{2}\fi + \xdef\temp@{oblique} + \ifx\temp@\first@ \xdef\tr@nstextstyle{3}\fi + \xdef\temp@{vertical} + \ifx\temp@\first@ \xdef\tr@nstextstyle{4}\fi +} + +\newcommand\exportconsensus[2][export.txt]{% + \ifx\exp@rt\n@ + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \xdef\exp@rt@num{\first@} + \xdef\exp@rt{y} + \immediate\openout\exp@rtfile = #1 + \fi +} + +\def\setdomain#1#2{% + \xdef\first@{#1} + \xdef\temp@{consensus} + \ifx\first@\temp@ \xdef\domain@seq{0} + \else + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \xdef\domain@seq{\csname @rd\first@\endcsname}% + \fi + \xdef\list@{#2,&} + \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ + \loop + \xdef\list@{\list@ @} + \expandafter\get@domainregions\list@ + \ifx\list@\ampers@nd\else\repeat + \xdef\dom@in{y} +} + +\def\decimal@IOO#1#2#3{#1#2\temp@#3} +\def\decimal@IO#1#2{#1\temp@#2} +\def\decimal@I#1{0\temp@#1} + +\def\percentsimilarity#1#2{% + \xdef\first@{#2@}\expandafter\check@letter\first@% + \xdef\first@{#2}\xdef\second@@{#2}% + \ifletter\get@name@number@table\xdef\second@@{\first@}\fi% + \xdef\first@{#1@}\expandafter\check@letter\first@% + \xdef\first@{#1}\xdef\first@@{#1}% + \ifletter\get@name@number@table\xdef\first@@{\first@}\fi% + \ifnum\first@@<\second@@% + \loopcount=\csname simcount\first@@ @\second@@\endcsname% + \temp@count=\csname poscount\first@@ @\second@@\endcsname% + \else% + \ifnum\first@@=\second@@ \loopcount=1 \temp@count=1% + \else% + \loopcount=\csname simcount\second@@ @\first@@\endcsname% + \temp@count=\csname poscount\second@@ @\first@@\endcsname% + \fi% + \fi% + \multiply\loopcount by 1000% + \divide\loopcount by \temp@count% + \xdef\first@{\the\loopcount}% + \ifgerm@n\xdef\temp@{,}\else\xdef\temp@{.}\fi% + \ifnum\first@=1000 100\temp@0% + \else% + \ifnum\first@>99 \expandafter\decimal@IOO\first@% + \else% + \ifnum\first@>9 \expandafter\decimal@IO\first@% + \else% + \ifnum\first@>0 \expandafter\decimal@I\first@% + \else 0\temp@0% + \fi% + \fi% + \fi% + \fi% +} + +\def\percentidentity#1#2{% + \xdef\first@{#2@}\expandafter\check@letter\first@% + \xdef\first@{#2}\xdef\second@@{#2}% + \ifletter\get@name@number@table\xdef\second@@{\first@}\fi% + \xdef\first@{#1@}\expandafter\check@letter\first@% + \xdef\first@{#1}\xdef\first@@{#1}% + \ifletter\get@name@number@table\xdef\first@@{\first@}\fi% + \ifnum\first@@<\second@@% + \loopcount=\csname identcount\first@@ @\second@@\endcsname% + \temp@count=\csname poscount\first@@ @\second@@\endcsname% + \else% + \ifnum\first@@=\second@@ \loopcount=1 \temp@count=1% + \else% + \loopcount=\csname identcount\second@@ @\first@@\endcsname% + \temp@count=\csname poscount\second@@ @\first@@\endcsname% + \fi% + \fi% + \multiply\loopcount by 1000% + \divide\loopcount by \temp@count% + \xdef\first@{\the\loopcount}% + \ifgerm@n\xdef\temp@{,}\else\xdef\temp@{.}\fi% + \ifnum\first@=1000 100\temp@0% + \else% + \ifnum\first@>99 \expandafter\decimal@IOO\first@% + \else% + \ifnum\first@>9 \expandafter\decimal@IO\first@% + \else% + \ifnum\first@>0 \expandafter\decimal@I\first@% + \else 0\temp@0% + \fi% + \fi% + \fi% + \fi% +} + +\def\similaritytable{% + \def\name@loop{% + \advance\outerloopcount by 1 + \ifnum\outerloopcount>\seq@num\relax + \else + \immediate\write\exp@rtfile{&\string\multicolumn{1}{c}{\string\kern1ex\string\begin{rotopo}{90}\csname newseqname\the\outerloopcount\endcsname\string\end{rotopo}}} + \name@loop\fi + } + \def\inner@loop{% + \advance\innerloopcount by 1 + \ifnum\innerloopcount>\seq@num\relax + \else + \ifnum\innerloopcount=\outerloopcount\relax \immediate\write\exp@rtfile{& {---\hss}}\fi + \ifnum\innerloopcount>\outerloopcount\relax \immediate\write\exp@rtfile{& \string\percentsimilarity{\the\outerloopcount}{\the\innerloopcount}}\fi + \ifnum\innerloopcount<\outerloopcount\relax \immediate\write\exp@rtfile{& \string\percentidentity{\the\outerloopcount}{\the\innerloopcount}}\fi + \inner@loop\fi + } + \def\outer@loop{% + \advance\outerloopcount by 1 + \ifnum\outerloopcount>\seq@num\relax + \else + \immediate\write\exp@rtfile{\csname newseqname\the\outerloopcount\endcsname} + \innerloopcount=0 \inner@loop \immediate\write\exp@rtfile{&\string\\} + \outer@loop\fi + } + \xdef\temp@{l|} + \outerloopcount=0 + \loop + \advance\outerloopcount by 1 + \xdef\temp@{\temp@ r} + \ifnum\outerloopcount<\seq@num\repeat + \advance\outerloopcount by 1 \xdef\seq@num@plus{\the\outerloopcount} + \advance\outerloopcount by 1 \xdef\seq@num@plus@plus{\the\outerloopcount} + \ifnum\seq@num<3 \xdef\temp@@{$\approx$} \else + \ifnum\seq@num<5 \xdef\temp@@{simil.}\ifgerm@n\def\temp@@{\string\"{A}hnl.}\fi\ifsp@nish\xdef\temp@@{simil.}\fi\else + \xdef\temp@@{similarity} + \ifgerm@n\ifnum\seq@num=5\def\temp@@{\string\"{A}hnlichk.}\else\def\temp@@{\string\"{A}hnlichkeit}\fi\fi\ifsp@nish\xdef\temp@@{similitud}\fi\fi + \fi + \xdef\temp@@@{identity}\ifgerm@n\def\temp@@@{Identit\string\"{a}t}\fi\ifsp@nish\xdef\temp@@@{identidad}\fi + + \immediate\openout\exp@rtfile = simtable.tmp + \immediate\write\exp@rtfile{\string\begin{tabular}{\temp@ |r}} + \immediate\write\exp@rtfile{\string\multicolumn{\seq@num@plus@plus}{c}{}\string\\[\name@@width]} + \immediate\write\exp@rtfile{\string\multicolumn{1}{c}{}} + \outerloopcount=0 \name@loop \immediate\write\exp@rtfile{&\string\\ \string\cline{2-\seq@num@plus}} + \immediate\write\exp@rtfile{&\string\multicolumn{\seq@num}{|c|}{}&\string\\[-2ex]} + \outerloopcount=0 \outer@loop + \immediate\write\exp@rtfile{\string\cline{2-\seq@num@plus}} + \immediate\write\exp@rtfile{\string\multicolumn{\seq@num@plus}{c}{}&} + \immediate\write\exp@rtfile{\string\multicolumn{1}{r}{\string\kern1.5ex\string\begin{rotopo}{90}\kern1em\% \temp@@\string\end{rotopo}}\string\\[-2ex]} + \immediate\write\exp@rtfile{\string\multicolumn{1}{c}{}&\string\multicolumn{\seq@num}{l}{\% \temp@@@}&\string\\} + \immediate\write\exp@rtfile{\string\end{tabular}} + \immediate\closeout\exp@rtfile + + \input{simtable.tmp} +} + +\def\identitytable{\similaritytable} + +%%%%% Calculate consensus + +\def\check@sim{% + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\first@{\csname \prefix@ grp\first@\endcsname} + \newrestrue + \ifnum\first@<0 \newresfalse + \else + \innerloopcount=\loopcount + \ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count + \loop + \advance\innerloopcount by 1 + \xdef\second@{\csname res\the\innerloopcount\endcsname} + \expandafter\ifx\csname \prefix@ grp\second@\endcsname\first@ + \newresfalse \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count \repeat + \fi + \fi + + \ifnewres + \pos@sum=0 + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \xdef\second@{\csname res\the\innerloopcount\endcsname} + \expandafter\ifx\csname \prefix@ grp\second@\endcsname\first@ + \advance\pos@sum by 1 \fi + \ifnum\innerloopcount<\seq@count \repeat + +% \multiply\pos@sum by \seq@percent + \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum} +% \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld + \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@ + \else + \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x + \xdef\m@x{\csname pos\the\loopcount\endcsname} + \xdef\cons@seq{\the\loopcount} \xdef\match@case{\c@se} + \xdef\simgroup@{\first@} + \else + \expandafter\ifnum\csname pos\the\loopcount\endcsname=\m@x + \xdef\match@case{0} + \fi + \fi + \fi + \fi + + \ifnum\loopcount=\cons@num \loopcount=1 \fi + \advance\loopcount by -1 + \ifnum\loopcount>0 \check@sim \fi} + +\def\check@ident{% + \xdef\first@{\csname res\the\loopcount\endcsname} + \newrestrue \expandafter\check@char\first@ + \ifletter + \innerloopcount=\loopcount + \ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count + \loop + \advance\innerloopcount by 1 + \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ + \newresfalse \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count \repeat + \fi + \else + \newresfalse +% \expandafter\xdef\csname res\the\loopcount\endcsname{\d@t} %%%%% or \equ@l for domains!!! + \fi + + \ifnewres + \pos@sum=0 + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ + \advance\pos@sum by 1 \fi + \ifnum\innerloopcount<\seq@count \repeat + + \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum} + \expandafter\ifnum\csname pos\the\loopcount\endcsname=\seq@count + \xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \loopcount=1 + \else +% \multiply\pos@sum by \seq@percent + \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum} +% \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld + \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@ + \else + \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x + \xdef\m@x{\csname pos\the\loopcount\endcsname} +% \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld + \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld@ + \xdef\cons@seq{\the\loopcount} \xdef\match@case{1} + \else + \xdef\cons@seq{\the\loopcount} \xdef\match@case{2} + \fi + \else + \expandafter\ifnum\csname pos\the\loopcount\endcsname=\m@x + \xdef\match@case{0} + \fi + \fi + \fi + \fi + \fi + + \ifnum\loopcount=\cons@num \loopcount=1 \fi + \advance\loopcount by -1 + \ifnum\loopcount>0 \check@ident \fi} + +\def\get@simchar{% + \xdef\first@{\csname res\the\loopcount\endcsname} + \newrestrue \expandafter\check@char\first@ + \ifletter + \innerloopcount=\loopcount + \ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count + \loop + \advance\innerloopcount by 1 + \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ + \newresfalse \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count \repeat + \fi + \else + \newresfalse + \fi + + \ifnewres + \pos@sum=0 + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ + \xdef\second@{\csname res\the\innerloopcount\endcsname} + \expandafter\ifx\csname \prefix@ grp\second@\endcsname\simgroup@ + \advance\pos@sum by 1 \fi + \fi + \ifnum\innerloopcount<\seq@count \repeat + + \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum} + \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x + \xdef\m@x{\csname pos\the\loopcount\endcsname} + \xdef\cons@seq{\the\loopcount} + \fi + \fi + + \ifnum\loopcount=\cons@num \loopcount=1 \fi + \advance\loopcount by -1 + \ifnum\loopcount>0 \get@simchar \fi} + +\def\unc@nserved{% + \ifsimmode + \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi + \xdef\match@case{0} \xdef\m@x{1} \check@sim + \ifnum\match@case=0 + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \expandafter\ifx\csname res\the\loopcount\endcsname\d@t + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname3\gap@char} + \else + \expandafter\ifx\csname res\the\loopcount\endcsname\questi@n + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname3\st@p@char} + \else + \expandafter\ifx\csname res\the\loopcount\endcsname\equ@l + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname!\dom@char} \xdef\g@p{y} + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 3\csname res\the\loopcount\endcsname} + \fi + \fi + \fi + \else + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\equ@l + \def\first@{\dom@char} \def\third@{9} + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} \xdef\g@p{y} + \else + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\gap@char} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \ifx\first@\questi@n + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \def\first@{{}} \def\third@{8} + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\st@p@char} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi\fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname3\first@} + \fi + \fi + \fi + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else + \xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }} + \else \xdef\first@{\n@m@tch} \fi\fi + \expandafter\ifx\csname lower@seq0\endcsname\y@ + \expandafter\xdef\csname lower@seq0\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq0\endcsname\y@ + \expandafter\xdef\csname tint@seq0\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq0\endcsname\y@ + \expandafter\xdef\csname emph@seq0\endcsname{n} + \xdef\first@{,\first@}\fi + \ifx\g@p\y@ + \xdef\consensus{\consensus 8{}} + \else + \xdef\consensus{\consensus 4\first@} + \expandafter\ifx\csname res\cons@num\endcsname\d@t + \else\xdef\constopo{\constopo 0}\fi + \fi + \else + \ifnum\cons@num>0 + \xdef\tmp@{\csname res\cons@num\endcsname} + \else + \xdef\m@x{0} \loopcount=\seq@count \get@simchar + \xdef\tmp@{\csname res\cons@seq\endcsname} + \fi + \xdef\second@{\csname \prefix@ grp\tmp@\endcsname} + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\d@t\def\first@{\gap@char}\fi + \ifx\first@\questi@n\def\first@{\st@p@char}\fi + \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname3\first@} + \else + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\last@{\csname res\the\loopcount\endcsname} + \expandafter\ifnum\csname \prefix@ grp\last@\endcsname=\second@ + \xdef\third@{2} + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\ressimm@tch\low@up + \else \xdef\first@{\ressimm@tch} \fi\fi\fi + \else + \ifx\first@\equ@l + \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} + \else + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\gap@char} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \else + \ifx\first@\questi@n + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \def\first@{{}} \def\third@{8} + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\st@p@char} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \else + \xdef\third@{3} + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi\fi + \fi + \fi + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\first@{\tmp@} + \xdef\low@up{lower} \ifx\m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\m@tch\low@up + \else \xdef\first@{\m@tch} \fi\fi + \expandafter\ifx\csname lower@seq0\endcsname\y@ + \expandafter\xdef\csname lower@seq0\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq0\endcsname\y@ + \expandafter\xdef\csname tint@seq0\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq0\endcsname\y@ + \expandafter\xdef\csname emph@seq0\endcsname{n} + \xdef\first@{,\first@}\fi + \ifx\g@p\y@ + \xdef\consensus{\consensus 8{}} + \else + \xdef\consensus{\consensus5\first@} + \xdef\constopo{\constopo 1} + \fi + \fi + \else + \iffuncmode + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\equ@l + \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y} + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\gap@char}\def\third@{*} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \ifx\first@\questi@n + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \def\first@{{}} \def\third@{/} + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\st@p@char}\def\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\st@p@char}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\st@p@char}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\st@p@char}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname0\first@} + \fi + \fi + \fi + \ifnum\loopcount<\seq@count \repeat + \else + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\d@t\def\first@{\gap@char}\fi + \ifx\first@\questi@n\def\first@{\st@p@char}\fi + \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 3\first@} + \else + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\equ@l + \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\gap@char} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \ifx\first@\questi@n + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \def\first@{{}} \def\third@{8} + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\st@p@char} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi\fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname3\first@} + \fi + \fi + \fi + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else + \xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }} + \else \xdef\first@{\n@m@tch} \fi\fi + \expandafter\ifx\csname lower@seq0\endcsname\y@ + \expandafter\xdef\csname lower@seq0\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq0\endcsname\y@ + \expandafter\xdef\csname tint@seq0\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq0\endcsname\y@ + \expandafter\xdef\csname emph@seq0\endcsname{n} + \xdef\first@{,\first@}\fi + \ifx\g@p\y@ + \xdef\consensus{\consensus 8{}} + \else + \xdef\consensus{\consensus 4\first@} + \xdef\constopo{\constopo 0} + \fi + \fi\fi} + +\def\c@nserved{% + \xdef\tmp@{\csname res\cons@seq\endcsname} + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\d@t\def\first@{\gap@char}\fi + \ifx\first@\questi@n\def\first@{\st@p@char}\fi + \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 3\first@} + \else + \xdef\second@{\csname res\the\loopcount\endcsname} + \ifx\tmp@\second@ + \xdef\third@{1} + \else + \xdef\third@{3} + \ifsimmode + \xdef\last@{\csname \prefix@ sim\tmp@\endcsname &@} + \expandafter\get@count\last@ + \innerloopcount=0 \getsim@char + \fi + \fi + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifcase\third@ \or + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\resm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resm@tch\low@up + \else \xdef\first@{\resm@tch} \fi\fi\fi + \or + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\ressimm@tch\low@up + \else \xdef\first@{\ressimm@tch} \fi\fi\fi + \else + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi\fi + \fi + \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \fi + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\gap@char} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \fi + \ifx\first@\questi@n + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \def\first@{{}} \def\third@{8} + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\st@p@char} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\first@{\csname res\cons@seq\endcsname} + \xdef\second@{lower} \ifx\m@tch\second@ \make@lower \else + \xdef\second@{upper} \ifx\m@tch\second@ + \else \xdef\first@{\m@tch} \fi\fi + \expandafter\ifx\csname lower@seq0\endcsname\y@ + \expandafter\xdef\csname lower@seq0\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq0\endcsname\y@ + \expandafter\xdef\csname tint@seq0\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq0\endcsname\y@ + \expandafter\xdef\csname emph@seq0\endcsname{n} + \xdef\first@{,\first@}\fi + \ifx\g@p\y@ + \xdef\consensus{\consensus 8{}} + \else + \xdef\consensus{\consensus 5\first@} + \xdef\constopo{\constopo 2} + \fi} + +\def\allm@tch{% + \xdef\tmp@{\csname res\cons@seq\endcsname} + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\d@t\def\first@{\gap@char}\fi + \ifx\first@\questi@n\def\first@{\st@p@char}\fi + \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 3\first@} + \else + \xdef\second@{\csname res\the\loopcount\endcsname} + \ifx\tmp@\second@ + \ifall@shade \xdef\third@{0} \else \xdef\third@{1} \fi + \else + \xdef\third@{3} + \ifsimmode + \xdef\last@{\csname \prefix@ sim\tmp@\endcsname &@} + \expandafter\get@count\last@ + \innerloopcount=0 \getsim@char + \fi + \fi + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifcase\third@ + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\res@llm@tch\low@up + \else \xdef\first@{\res@llm@tch} \fi\fi\fi + \or + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\res@llm@tch\low@up + \else \xdef\first@{\res@llm@tch} \fi\fi\fi + \or + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\ressimm@tch\low@up + \else \xdef\first@{\ressimm@tch} \fi\fi\fi + \else + \ifnum\divref@=\loopcount\else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi\fi + \fi + \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \fi + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\gap@char} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \fi + \ifx\first@\questi@n + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \def\first@{{}} \def\third@{8} + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\st@p@char} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\first@{\csname res\cons@seq\endcsname} + \xdef\second@{lower} \ifx\@llm@tch\second@ \make@lower \else + \xdef\second@{upper} \ifx\@llm@tch\second@ + \else \xdef\first@{\@llm@tch} \fi\fi + \expandafter\ifx\csname lower@seq0\endcsname\y@ + \expandafter\xdef\csname lower@seq0\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq0\endcsname\y@ + \expandafter\xdef\csname tint@seq0\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq0\endcsname\y@ + \expandafter\xdef\csname emph@seq0\endcsname{n} + \xdef\first@{,\first@}\fi + \ifx\g@p\y@ + \xdef\consensus{\consensus 8{}} + \else + \xdef\consensus{\consensus 6\first@} + \xdef\constopo{\constopo 3} + \fi} + +\def\functi@nal{% + \ifnum\cons@num>0 + \xdef\first@{\csname res\cons@num\endcsname} + \else + \xdef\first@{\csname res\cons@seq\endcsname} + \fi + \xdef\second@{\csname funcgrp\first@\endcsname} + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\third@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 0\first@} + \else + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\equ@l + \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y} + \else + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\gap@char}\def\third@{*} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \fi + \fi + \else + \ifx\first@\questi@n + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \def\first@{{}} \def\third@{/} + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\st@p@char}\def\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \fi + \else + \expandafter\ifnum\csname funcgrp\first@\endcsname=\second@ + \xdef\low@up{lower} + \expandafter\ifx\csname funcm@tch\second@\endcsname\low@up + \make@lower \fi + \xdef\third@{\second@} + \else \xdef\third@{0} + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi + \fi + \fi + \fi + \fi + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat} + +\def\all@funcshade{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\second@{\csname funcgrp\first@\endcsname} + \ifnum\second@<0 \xdef\second@{0} \fi + \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!} \xdef\g@p{y} \fi + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\gap@char}\def\second@{*} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \fi + \fi + \fi + \ifx\first@\questi@n + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \def\first@{{}} \def\second@{/} + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\st@p@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \fi + \fi + \xdef\low@up{lower} + \expandafter\ifx\csname funcm@tch\second@\endcsname\low@up + \make@lower \fi + \xdef\third@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 0\first@} + \else + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + \second@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat} + +\def\T@coffee@shade{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\second@{\csname TC@num\the\loopcount\endcsname} + \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!} \xdef\g@p{y} \fi + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\gap@char}\def\second@{*} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \fi + \fi + \fi + \ifx\first@\questi@n + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \def\first@{{}} \def\second@{/} + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\st@p@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \fi + \fi + \xdef\third@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + *\first@} + \else + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + \second@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\first@{\csname res0\endcsname} + \expandafter\ifx\csname lower@seq0\endcsname\y@ + \expandafter\xdef\csname lower@seq0\endcsname{n} + \xdef\first@{;\first@}\fi + \expandafter\ifx\csname tint@seq0\endcsname\y@ + \expandafter\xdef\csname tint@seq0\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq0\endcsname\y@ + \expandafter\xdef\csname emph@seq0\endcsname{n} + \xdef\first@{,\first@}\fi + \xdef\second@{\csname TC@num0\endcsname} + \ifx\g@p\y@ + \xdef\consensus{\consensus 8{}} + \else + \xdef\consensus{\consensus\second@\n@m@tch} + \xdef\constopo{\constopo\second@} + \fi + } + +\def\getregion@fromstack@first{% + \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname stop\the\loopcount\endcsname<\first@@ + \getregion@fromstack@first + \else + \expandafter\ifx\csname all\the\loopcount\endcsname\y@ + \innerloopcount=\csname style\the\loopcount\endcsname + \fi + \expandafter\xdef\csname shade@style\the\loopcount\endcsname{% + \csname style\the\loopcount\endcsname} + \fi + \fi +} + +\def\calc@regshade{% + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname shade@style\the\loopcount\endcsname{y} + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname stop\the\loopcount\endcsname<\first@@ + \getregion@fromstack@first + \else + \expandafter\ifx\csname all\the\loopcount\endcsname\y@ + \innerloopcount=\csname style\the\loopcount\endcsname + \fi + \expandafter\xdef\csname shade@style\the\loopcount\endcsname{% + \csname style\the\loopcount\endcsname} + \expandafter\ifnum\csname stop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromstack{\the\loopcount} + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat + \loopcount=0 + \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@ + \else + \xdef\consensus{\consensus&\csname shade@style\the\loopcount\endcsname)} + \fi + \loop + \advance\loopcount by 1 + \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@ + \ifnum\innerloopcount>0 + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + &\the\innerloopcount)} + \fi + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + &\csname shade@style\the\loopcount\endcsname)} + \fi + \ifnum\loopcount<\seq@count \repeat +} + +\def\getregion@fromshadingstack@first{% + \expandafter\getregion@fromshadingstack{\the\loopcount} + \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname<\first@@ + \getregion@fromshadingstack@first + \fi + \fi +} + +\def\calc@shading{% + \xdef\shading@style{&} + \loopcount=-1 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname<\first@@ + \getregion@fromshadingstack@first + \else + \xdef\shading@style{\csname shadingstyle\the\loopcount\endcsname} + \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromshadingstack{\the\loopcount} + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat + \loopcount=0 + \loop + \advance\loopcount by 1 + \ifx\shading@style\ampers@nd + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname¤\shading@style)} + \fi + \ifnum\loopcount<\seq@count \repeat +} + +\def\getregion@fromemphstack@first{% + \expandafter\getregion@fromemphstack{\the\loopcount} + \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname emphstop\the\loopcount\endcsname<\first@@ + \getregion@fromemphstack@first + \else + \expandafter\ifx\csname emphall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} + \fi + \fi +} + +\def\calc@regemph{% + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname emphstop\the\loopcount\endcsname<\first@@ + \getregion@fromemphstack@first + \else + \expandafter\ifx\csname emphall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} + \expandafter\ifnum\csname emphstop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromemphstack{\the\loopcount} + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat + \loopcount=0 + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} + \fi + \ifnum\innerloopcount>0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} + \ifnum\loopcount<\seq@count \repeat + \fi +} + +\def\getregion@fromlowerstack@first{% + \expandafter\getregion@fromlowerstack{\the\loopcount} + \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@ + \getregion@fromlowerstack@first + \else + \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y} + \fi + \fi +} + +\def\calc@reglower{% + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@ + \getregion@fromlowerstack@first + \else + \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y} + \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromlowerstack{\the\loopcount} + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat + \loopcount=0 + \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y} + \fi + \ifnum\innerloopcount>0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y} + \ifnum\loopcount<\seq@count \repeat + \fi +} + +\def\getregion@fromtintstack@first{% + \expandafter\getregion@fromtintstack{\the\loopcount} + \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname tintstop\the\loopcount\endcsname<\first@@ + \getregion@fromtintstack@first + \else + \expandafter\ifx\csname tintall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} + \fi + \fi +} + +\def\calc@regtint{% + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname tintstop\the\loopcount\endcsname<\first@@ + \getregion@fromtintstack@first + \else + \expandafter\ifx\csname tintall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} + \expandafter\ifnum\csname tintstop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromtintstack{\the\loopcount} + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat + \loopcount=0 + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} + \fi + \ifnum\innerloopcount>0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} + \ifnum\loopcount<\seq@count \repeat + \fi +} + +\def\getregion@fromframestack@first{% + \expandafter\getregion@fromframestack{\the\loopcount} + \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname framestop\the\loopcount\endcsname<\first@@ + \getregion@fromframestack@first + \else + \ifnum\frame@on=0 + \xdef\frame@on{1} + \xdef\frame@{1} + \expandafter\xdef\csname fr@style\the\loopcount\endcsname{% + \csname framestyle\the\loopcount\endcsname} + \innerloopcount=\pos@count + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;&;} + \xdef\frame@pos{\the\pos@count} + \fi + \expandafter\ifnum\csname framestop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromframestack{\the\loopcount} + \ifnum\frame@on=1 + \xdef\frame@on{0} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \ifnum\pos@count=\res@perline + \ifnum\frame@on=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=\end@num\relax + \ifnum\frame@on=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \fi + \fi +} + +\def\calc@frame{% +% \advance\pos@count by -1 + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname framestart\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname framestop\the\loopcount\endcsname<\first@@ + \getregion@fromframestack@first + \else + \ifnum\frame@on=0 + \xdef\frame@on{1} + \xdef\frame@{1} + \expandafter\xdef\csname fr@style\the\loopcount\endcsname{% + \csname framestyle\the\loopcount\endcsname} + \innerloopcount=\pos@count + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;&;} + \xdef\frame@pos{\the\pos@count} + \fi + \expandafter\ifnum\csname framestop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromframestack{\the\loopcount} + \ifnum\frame@on=1 + \xdef\frame@on{0} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \ifnum\pos@count=\res@perline + \ifnum\frame@on=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=\end@num\relax + \ifnum\frame@on=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat +% \advance\pos@count by 1 +} + +\def\get@nextres#1#2:{% + \xdef\first@{#1} + \xdef\temp@{#2:} + \ifx\first@\gap@char \expandafter\get@nextres\temp@ + \else + \if\first@ @ + \xdef\temp@{} + \else + \xdef\temp@{+\first@} + \expandafter\xdef\csname last@res\bottop@\endcsname{} + \fi + \fi} +\def\get@@nextres#1#2:{% + \xdef\first@{#1} + \xdef\temp@@{#2:} + \ifx\first@\gap@char \expandafter\get@@nextres\temp@@ + \else + \if\first@ @ + \xdef\temp@@{} + \else + \xdef\temp@@{+\first@} + \expandafter\xdef\csname last@res\bottop@\endcsname{} + \fi + \fi} + +\def\char@get#1#2@{\xdef\first@{#1} \xdef\tr@nsl@ted{#2@}} +\def\trans@now#1#2@{% + \xdef\first@{#1} + \xdef\tr@nsl@ted{#2@} + \ifx\first@\ampers@nd + \else + \expandafter\check@char\first@ + \ifletter + \xdef\triplet@{\triplet@\first@} + \advance\triple@count by 1 + \ifnum\triple@count=1 + \xdef\out@{\out@{-}} + \fi + \ifnum\triple@count=3 + \expandafter\ifx\csname @\triplet@\endcsname\relax + \expandafter\xdef\csname @\triplet@\endcsname{?} \fi + \xdef\out@{\out@\csname @\triplet@\endcsname\out@@{-}} + \triple@count=0 + \xdef\triplet@{} + \xdef\out@@{} + \fi + \fi + \if\first@ - + \ifnum\triple@count<2 + \xdef\out@{\out@{-}} + \else + \xdef\out@@{\out@@{-}} + \fi + \fi + \if\first@ + + \expandafter\char@get\tr@nsl@ted + \xdef\triplet@{\triplet@\first@} + \advance\triple@count by 1 + \ifnum\triple@count=3 + \expandafter\ifx\csname @\triplet@\endcsname\relax + \expandafter\xdef\csname @\triplet@\endcsname{?} \fi + \xdef\out@{\out@\csname @\triplet@\endcsname\out@@} + \triple@count=0 + \xdef\triplet@{} + \xdef\out@@{} + \fi + \fi + \if\first@ 2 + \loop + \expandafter\char@get\tr@nsl@ted + \ifx\first@\ampers@nd + \lettertrue + \xdef\tr@nsl@ted{&@} + \else + \expandafter\check@char\first@ + \fi + \ifletter\else\xdef\out@{\out@{-}}\repeat + \xdef\out@{\out@{-}} + \fi + \expandafter\trans@now\tr@nsl@ted + \fi +} + +\def\do@translation{% + \xdef\triplet@{} + \xdef\out@{} + \xdef\out@@{} + \xdef\tr@nsl@ted{\tr@nsl@ted &@} + \triple@count=0 + \expandafter\trans@now\tr@nsl@ted + \xdef\tr@nsl@ted{\out@} +} + +\def\trans@pep#1#2@{% + \xdef\first@{#1} + \xdef\tr@nsl@ted{#2@} + \ifx\first@\ampers@nd + \else + \expandafter\check@char\first@ + \ifletter + \xdef\out@{\out@\csname rev@\first@\endcsname} + \else + \xdef\out@{\out@{-}{-}{-}} + \fi + \expandafter\trans@pep\tr@nsl@ted + \fi +} + +\def\rev@translation{% + \xdef\out@{} + \xdef\tr@nsl@ted{\tr@nsl@ted &@} + \expandafter\trans@pep\tr@nsl@ted + \xdef\tr@nsl@ted{\out@} +} + + +\def\sum@up{% + \advance\innerloopcount by 1 + \xdef\second@@@{\csname res\the\innerloopcount\endcsname} + \xdef\third@@@{\csname cons\first@@@\second@@@\endcsname} + \advance\temp@count by \third@@@ + \ifnum\innerloopcount<\seq@count\sum@up\fi +} + +\def\sum@up@cons{% + \innerloopcount=\outerloopcount + \xdef\first@@@{\csname res\the\outerloopcount\endcsname} + \sum@up + \advance\outerloopcount by 1\relax + \ifnum\outerloopcount<\seq@count + \sum@up@cons + \else + \innerloopcount=\seq@count + \advance\innerloopcount by -1 + \multiply\innerloopcount by \seq@count + \multiply\temp@count by 2 + \multiply\temp@count by \m@trixf@ctor + \divide\temp@count by \innerloopcount + + \ifnum\temp@count>100 \temp@count=100 \fi + \ifnum\temp@count<0 \temp@count=0 \fi + \xdef\cons@val{\the\temp@count} + \ifx\first@\equ@l \xdef\cons@val{N} \fi + + \ifx\T@coffee@bcons\y@ + \xdef\cons@val{\csname TC@num0\endcsname} + \if\cons@val * + \xdef\cons@val{99} + \fi + \fi + \ifx\T@coffee@ccons\y@ + \xdef\cons@val{\csname TC@num0\endcsname} + \if\cons@val * + \xdef\cons@val{99} + \fi + \fi + \fi +} + +\def\collect@cons@res{% + \xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname} + \advance\innerloopcount by 1 + \ifnum\innerloopcount>\seq@count\relax + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \else + \collect@cons@res + \fi +} + +\def\sum@@up{% + \advance\innerloopcount by 1 + \xdef\second@@@{\csname res\the\innerloopcount\endcsname} + + \ifx\first@@@\d@t + \else + \ifx\first@@@\questi@n + \else + \ifx\first@@@\equ@l + \else + \ifx\second@@@\d@t + \else + \ifx\second@@@\questi@n + \else + \ifx\second@@@\equ@l + \else + \xdef\third@@@{\csname poscount\the\outerloopcount @\the\innerloopcount\endcsname} + \temp@@count=\third@@@ + \advance\temp@@count by 1 + \expandafter\xdef\csname poscount\the\outerloopcount @\the\innerloopcount\endcsname{\the\temp@@count} + + \xdef\third@@@{\csname simcount\the\outerloopcount @\the\innerloopcount\endcsname} + \temp@@count=\third@@@ + \xdef\third@@@{\csname simpair\first@@@\second@@@\endcsname} + \advance\temp@@count by \third@@@ + \expandafter\xdef\csname simcount\the\outerloopcount @\the\innerloopcount\endcsname{\the\temp@@count} + + \ifx\first@@@\second@@@ + \xdef\third@@@{\csname identcount\the\outerloopcount @\the\innerloopcount\endcsname} + \temp@@count=\third@@@ + \advance\temp@@count by 1 + \expandafter\xdef\csname identcount\the\outerloopcount @\the\innerloopcount\endcsname{\the\temp@@count} + \fi + \fi + \fi + \fi + \fi + \fi + \fi + + \ifnum\innerloopcount<\seq@count\sum@@up\fi +} + +\def\sum@up@sim{% + \innerloopcount=\outerloopcount + \xdef\first@@@{\csname res\the\outerloopcount\endcsname} + \sum@@up + \advance\outerloopcount by 1\relax + \ifnum\outerloopcount<\seq@count + \sum@up@sim + \fi +} + +\def\collect@similarity{% + \xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname} + \advance\innerloopcount by 1 + \ifnum\innerloopcount>\seq@count\relax + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@sim + \else + \collect@similarity + \fi +} + + +\def\sum@up@bits{% + \ifx\first@@@\second@@@ + \ifx\first@@@\d@t + \temp@count=0\relax + \else + \temp@count=100\relax + \fi + \else + \temp@count=0 +% \xdef\third@@@{\csname cons\first@@@\second@@@\endcsname}\temp@count=\third@@@ %%% or if only identical =0 + \fi + \multiply\temp@count by \last@ + \divide\temp@count by 100 + \expandafter\ifx\csname info@\subfamily@seq @\the\outerloopcount\endcsname\relax + \expandafter\xdef\csname info@\subfamily@seq @\the\outerloopcount\endcsname{0} + \fi + \xdef\third@@@{\csname info@\subfamily@seq @\the\outerloopcount\endcsname} + \advance\temp@count by \third@@@ + \expandafter\xdef\csname info@\subfamily@seq @\the\outerloopcount\endcsname{\the\temp@count} +} +\def\sum@up@info{% + \ifnum\outerloopcount=\subfamily@seq \advance\outerloopcount by 1 \fi + \ifnum\outerloopcount>\seq@count + \else + \xdef\first@@@{\csname res\the\outerloopcount\endcsname} + \sum@up@bits + \advance\outerloopcount by 1\relax + \fi + \ifnum\outerloopcount>\seq@count\else\sum@up@info\fi +} +\def\collect@info{% + \outerloopcount=1\relax + \temp@count=0\relax + \xdef\second@@@{\csname res\subfamily@seq\endcsname} + \sum@up@info +} + +\def\calc@grouping{% + \xdef\second@{\csname res@num\d@t\endcsname} + \innerloopcount=\seq@count + \advance\innerloopcount by -\second@ + \xdef\second@{\the\innerloopcount} + \xdef\seventh@{0} + \innerloopcount=0 + \outerloopcount=65 + \loop + \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} + \xdef\first@{\csname res@num\first@@\endcsname} + \ifnum\first@>0 + \temp@count=\csname log2@\first@\endcsname + \advance\temp@count by -\csname log2@\second@\endcsname + \advance\temp@count by \csname res@corr\first@@\endcsname + \multiply\temp@count by -\first@ + \divide\temp@count by \second@ + \advance\innerloopcount by \temp@count\relax + \temp@count=\second@ %%% + \advance\temp@count by -\first@ %%% + \advance\temp@count by \seventh@ %%% + \xdef\seventh@{\the\temp@count} %%% + \fi + \expandafter\xdef\csname res@num\first@@\endcsname{0} + \advance\outerloopcount by 1 + \ifnum\outerloopcount>90\else\repeat + \expandafter\xdef\csname res@num\d@t\endcsname{0} + \if\seq@type P + \temp@count=\csname log2@20\endcsname + \ifnum\sig@max=100000 \xdef\sig@max{2321} \fi + \else + \temp@count=\csname log2@4\endcsname + \ifnum\sig@max=100000 \xdef\sig@max{1000} \fi + \fi + \xdef\bit@max{\the\temp@count} + \advance\temp@count by -\innerloopcount + \multiply\temp@count by \second@ + \divide\temp@count by \seq@count + \xdef\last@{\the\temp@count} + \expandafter\xdef\csname bit@pos\the\loopcount\endcsname{\last@} + \temp@count=\bit@total + \advance\temp@count by \last@ + \xdef\bit@total{\the\temp@count} + \collect@info +} +\def\do@grouping{% + \ifnum\loopcount>\total@pos + \else + \triple@count=1 + \loop + \xdef\first@{\csname seq\the\triple@count\endcsname} + \expandafter\dis@get\first@ + \ifx\first@\ampers@nd + \else + \innerloopcount=\csname res@num\first@\endcsname + \advance\innerloopcount by 1 + \expandafter\xdef\csname res@num\first@\endcsname{\the\innerloopcount} + \fi + \advance\triple@count by 1\relax + \ifnum\triple@count>\seq@count + \calc@grouping + \advance\loopcount by 1 + \do@grouping + \else + \repeat + \fi +} +\def\total@frequency@correction{% + \innerloopcount=0 + \outerloopcount=65 + \loop + \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} + \xdef\first@{\csname res@corr\first@@\endcsname} + \advance\innerloopcount by \first@\relax + \advance\outerloopcount by 1 + \ifnum\outerloopcount>90\else\repeat + \xdef\res@num@total{\the\innerloopcount} + \outerloopcount=65 + \loop + \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} + \xdef\first@{\csname res@corr\first@@\endcsname} + \innerloopcount=\first@\relax + \ifnum\innerloopcount>0 + \multiply\innerloopcount by 1000\relax + \divide\innerloopcount by \res@num@total\relax + \innerloopcount=\csname log2@\the\innerloopcount\endcsname + \advance\innerloopcount by -5644\relax + \multiply\innerloopcount by -1\relax + \fi + \expandafter\xdef\csname res@corr\first@@\endcsname{\the\innerloopcount} + \ifnum\the\innerloopcount>\corr@max \xdef\corr@max{\the\innerloopcount}\fi + \advance\outerloopcount by 1 + \ifnum\outerloopcount>90\else\repeat +} +\def\calc@total@frequency{% + \ifnum\loopcount>\total@pos + \else + \triple@count=1 + \loop + \xdef\first@{\csname seq\the\triple@count\endcsname} + \expandafter\tot@get\first@ + \ifx\first@\ampers@nd + \else + \innerloopcount=\csname res@corr\first@\endcsname + \advance\innerloopcount by 1 + \expandafter\xdef\csname res@corr\first@\endcsname{\the\innerloopcount} + \fi + \advance\triple@count by 1\relax + \ifnum\triple@count>\seq@count + \advance\loopcount by 1 + \calc@total@frequency + \else + \repeat + \fi +} +\def\prep@logo{% + \if\seq@type P + \ifx\do@freq@correction\y@ + \xdef\do@freq@correction{n} + \loopcount=1 + \loop + \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} + \advance\loopcount by 1 + \ifnum\loopcount>\seq@count\else\repeat + \xdef\corr@max{0} + \loopcount=1 + \calc@total@frequency + \total@frequency@correction + \fi + \fi +} +\def\define@subfamilies{% + \xdef\first@{\csname group@num1\endcsname} + \advance\loopcount by -1 + \xdef\last@{\the\loopcount} + \outerloopcount=\bit@total + \divide\outerloopcount by \last@ + \xdef\bit@mean{\the\outerloopcount} + \multiply\outerloopcount by \subfamily@threshold\relax + \divide\outerloopcount by 100\relax + \xdef\sub@threshold{\the\outerloopcount} + \ifnum\first@=0 + \clear@res@nums{1} + \clear@res@nums{2} + \immediate\write\featurefile{TeXshade subfamily logo data file for \alignfilename} + \immediate\write\featurefile{--} + \immediate\write\featurefile{Average information content [1000*bits per position]: \bit@mean} + \immediate\write\featurefile{Subfamily threshold setting [percent]: \subfamily@threshold} + \immediate\write\featurefile{=> \bit@mean\space * 0.\subfamily@threshold\space = \sub@threshold\space [1000*bits per position]} + \immediate\write\featurefile{} + \expandafter\xdef\csname subfamily@num\subfamily@seq\endcsname{2} + \immediate\write\featurefile{Automatic subfamily assignment around sequence no. \subfamily@seq:} + \immediate\write\featurefile{[sequence pair: average shared information *1000, subfamily number]} + \temp@count=1 + \outerloopcount=1 + \loop + \ifnum\outerloopcount=\subfamily@seq \advance\outerloopcount by 1 \fi + \ifnum\outerloopcount>\seq@count + \else + \xdef\first@{\csname info@\subfamily@seq @\the\outerloopcount\endcsname} + \loopcount=\first@\relax + \divide\loopcount by \last@\relax + \ifnum\loopcount>\sub@threshold + \expandafter\xdef\csname subfamily@num\the\outerloopcount\endcsname{2} + \advance\temp@count by 1\relax + \else + \expandafter\xdef\csname subfamily@num\the\outerloopcount\endcsname{1} + \fi + \xdef\first@@{\csname subfamily@num\the\outerloopcount\endcsname} + \immediate\write\featurefile{\subfamily@seq-\the\outerloopcount:\space\the\loopcount,\space subfamily: \first@@} + \advance\outerloopcount by 1 + \fi + \ifnum\outerloopcount>\seq@count\else\repeat + \immediate\write\featurefile{} + \immediate\write\featurefile{//} + \ifnum\temp@count>0 + \expandafter\xdef\csname group@num2\endcsname{\the\temp@count} + \else + \message{<No subfamilies found (check threshold) - hiding subfamily logo>} + \show@sublogofalse + \immediate\write\featurefile{<No subfamilies found (check threshold) - hiding subfamily logo>} + \fi + \loopcount=\seq@count + \advance\loopcount by -\temp@count + \ifnum\loopcount>0 + \expandafter\xdef\csname group@num1\endcsname{\the\loopcount} + \else + \message{<No subfamilies found (check threshold) - hiding subfamily logo>} + \immediate\write\featurefile{<No subfamilies found (check threshold) - hiding subfamily logo>} + \show@sublogofalse + \fi + \else + \immediate\write\featurefile{TeXshade subfamily logo data file for \alignfilename} + \immediate\write\featurefile{--} + \immediate\write\featurefile{Average information content [1000*bits per position]: \bit@mean} + \immediate\write\featurefile{Subfamily threshold setting [percent]: \subfamily@threshold} + \immediate\write\featurefile{=> \bit@mean\space * 0.\subfamily@threshold\space = \sub@threshold\space [1000*bits per position]} + \immediate\write\featurefile{} + \immediate\write\featurefile{User defined subfamily: \sub@family@setting} + \immediate\write\featurefile{} + \immediate\write\featurefile{//} + \fi +} +\def\prep@sublogo{% + \message{<Calculating subfamily logo...>} + \immediate\openout\featurefile = sublogo.txt + \if\seq@type P + \ifx\do@freq@correction\y@ + \xdef\do@freq@correction{n} + \loopcount=1 + \loop + \xdef\first@{\csname @rd\the\loopcount\endcsname} %%% + \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\first@\endcsname &@} + \advance\loopcount by 1 + \ifnum\loopcount>\seq@count\else\repeat + \xdef\corr@max{0} + \loopcount=1 + \calc@total@frequency + \total@frequency@correction + \fi + \fi + \loopcount=1 + \loop + \xdef\first@{\csname @rd\the\loopcount\endcsname} %%% + \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\first@\endcsname &@} + \advance\loopcount by 1 + \ifnum\loopcount>\seq@count\else\repeat + \loopcount=1 + \do@grouping + \define@subfamilies + \ifshow@sublogo + \loopcount=1 + \loop + \xdef\first@{\csname @rd\the\loopcount\endcsname} %%% + \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\first@\endcsname &@} + \advance\loopcount by 1 + \ifnum\loopcount>\seq@count\else\repeat + \xdef\first@{\csname group@num1\endcsname} + \xdef\first@@{\csname log2@\first@\endcsname} + \xdef\second@{\csname group@num2\endcsname} + \xdef\second@@{\csname log2@\second@\endcsname} + \loopcount=\first@ + \advance\loopcount by \second@ + \xdef\third@{\the\loopcount} + \xdef\third@@{\csname log2@\third@\endcsname} + \loopcount=\first@@ + \advance\loopcount by -\third@@ + \multiply\loopcount by \first@ + \divide\loopcount by \third@ + \xdef\first@@@{\the\loopcount} + \loopcount=\second@@ + \advance\loopcount by -\third@@ + \multiply\loopcount by \second@ + \divide\loopcount by \third@ + \xdef\second@@@{\the\loopcount} + \loopcount=\bit@max + \advance\loopcount by \first@@@ + \advance\loopcount by \second@@@ + \xdef\group@correction{\the\loopcount} + \loopcount=1 \total@count=0 + \do@sublogo + \immediate\closeout\featurefile + \openin\sublogofile = sublogo.txt\relax + \read@header + \else + \immediate\closeout\featurefile + \fi +} +\def\read@header{% + \read\sublogofile to \first@\relax + \xdef\first@{\expandafter\string\first@} + \ifx\first@\par@ \read@header + \else + \xdef\first@{\first@ @} + \expandafter\seq@get\first@ + \ifx\first@\he@derend + \else\read@header + \fi + \fi +} +\def\read@sublogo{% + \xdef\stack@sublogo{}% + \loopcount=1 % + \loop% + \ifeof\sublogofile% + \advance\loopcount by \res@perline% + \else% + \read\sublogofile to \first@\relax% + \xdef\first@{\expandafter\string\first@}% + \ifx\first@\par@% + \advance\loopcount by \res@perline% + \else + \xdef\first@{\first@ @}% + \expandafter\sublogo@get\first@% + \xdef\stack@sublogo{\stack@sublogo\first@}% + \advance\loopcount by 1% + \fi% + \fi% + \ifnum\loopcount=\res@perline\else\repeat% +} +\def\calc@sublogo{% + \xdef\seventh@{\csname res@num.2\endcsname} + \xdef\first@{\csname group@num2\endcsname} + \innerloopcount=\first@ + \advance\innerloopcount by -\seventh@ + \xdef\seventh@{\the\innerloopcount} + \xdef\eighth@{\csname res@num.1\endcsname} + \xdef\first@{\csname group@num1\endcsname} + \innerloopcount=\first@ + \advance\innerloopcount by -\eighth@ + \xdef\eighth@{\the\innerloopcount} + \xdef\nineth@{n} + \xdef\pos@max{0} + \xdef\pos@min{0} + \outerloopcount=65 + \loop + \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} + \xdef\first@{\csname res@num\first@@ 1\endcsname} \xdef\temp@{\first@} + \temp@count=\first@ + \ifnum\seventh@>0 \multiply\temp@count by \seventh@ \fi + \xdef\first@{\the\temp@count} + \xdef\second@{\csname res@num\first@@ 2\endcsname} + \temp@count=\temp@ + \advance\temp@count by \second@\relax + \ifnum\temp@count>0 + \temp@count=\second@ + \ifnum\eighth@>0 \multiply\temp@count by \eighth@ \fi + \advance\temp@count by -\first@ + \xdef\last@{\csname bit@pos\the\loopcount\endcsname} + \multiply\temp@count by \last@ + \ifnum\seventh@>0 \divide\temp@count by \seventh@ \fi + \ifnum\eighth@>0 \divide\temp@count by \eighth@ \fi + \multiply\temp@count by \bit@max + \divide\temp@count by \group@correction + \ifx\hide@negatives\y@ + \ifnum\temp@count>0 \else \temp@count=1 \fi% + \else + \ifnum\temp@count=0 \temp@count=1 \fi% + \fi + \expandafter\xdef\csname res@val\first@@\endcsname{\the\temp@count} + \expandafter\xdef\csname res@num\first@@ 1\endcsname{0} + \expandafter\xdef\csname res@num\first@@ 2\endcsname{0} + \xdef\nineth@{y} + \else + \expandafter\xdef\csname res@val\first@@\endcsname{0} + \expandafter\xdef\csname res@num\first@@ 1\endcsname{0} + \expandafter\xdef\csname res@num\first@@ 2\endcsname{0} + \fi + \ifnum\temp@count>\pos@max \xdef\pos@max{\the\temp@count}\fi + \ifnum\temp@count<\pos@min \xdef\pos@min{\the\temp@count}\fi + \advance\outerloopcount by 1 + \ifnum\outerloopcount>90\else\repeat + \expandafter\xdef\csname res@val\d@t\endcsname{0} + \expandafter\xdef\csname res@num\d@t 1\endcsname{0} + \expandafter\xdef\csname res@num\d@t 2\endcsname{0} + \temp@count=\pos@min\relax + \multiply\temp@count by -1\relax + \xdef\pos@min{\the\temp@count} + \ifnum\pos@min>\pos@max \xdef\pos@max{\pos@min}\fi + \temp@count=\pos@max + \multiply\temp@count by 100 \relax + \divide\temp@count by \bit@max \relax + \xdef\sublogo@num{\sublogo@num\the\temp@count,} + \ifnum\pos@max<\sig@max \xdef\sublogo@sig{\sublogo@sig n} \else \xdef\sublogo@sig{\sublogo@sig y} \fi + \ifx\nineth@\y@ + \xdef\tmpstack{&:&,} + \outerloopcount=65 + \loop + \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} + \xdef\second@@{\csname res@val\first@@\endcsname} + \ifnum\second@@=0 + \else + \xdef\third@{\tmpstack @} \xdef\tmpstack{} + \sort@logostack + \fi + \advance\outerloopcount by 1 + \ifnum\outerloopcount>90 + \immediate\write\featurefile{\expandafter\string\tmpstack&:&,} + \else\repeat + \else + \immediate\write\featurefile{\expandafter\string O:0,&:&,} + \fi +} +\def\do@sublogo{% + \ifnum\loopcount>\total@pos + \xdef\sublogo@sig{\sublogo@sig &@} + \else + \triple@count=1 + \loop + \xdef\first@{\csname seq\the\triple@count\endcsname} + \expandafter\dis@get\first@ + \ifnum\triple@count=\start@seq + \ifx\first@\d@t\else \advance\total@count by 1\relax\fi + \fi + \ifnum\loopcount<\start@number + \else + \ifnum\total@count>\end@num + \else + \ifx\first@\ampers@nd + \else + \xdef\second@{\csname subfamily@num\the\triple@count\endcsname} + \innerloopcount=\csname res@num\first@\second@\endcsname + \advance\innerloopcount by 1 + \expandafter\xdef\csname res@num\first@\second@\endcsname{\the\innerloopcount} + \fi + \fi + \fi + \advance\triple@count by 1\relax + \ifnum\triple@count>\seq@count + \ifnum\loopcount<\start@number + \else + \ifnum\total@count>\end@num + \else + \calc@sublogo + \fi + \fi + \advance\loopcount by 1 + \do@sublogo + \else + \repeat + \fi +} +\def\calc@logo{% + \xdef\second@{\csname res@num\d@t\endcsname} + \innerloopcount=\seq@count + \advance\innerloopcount by -\second@ + \xdef\second@{\the\innerloopcount} + \xdef\seventh@{0} + \innerloopcount=0 + \outerloopcount=65 + \loop + \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} + \xdef\first@{\csname res@num\first@@\endcsname} + \ifnum\first@>0 + \temp@count=\csname log2@\first@\endcsname + \advance\temp@count by -\csname log2@\second@\endcsname + \advance\temp@count by \csname res@corr\first@@\endcsname %%%% correct for background freq. + \multiply\temp@count by -\first@ + \divide\temp@count by \second@ + \advance\innerloopcount by \temp@count\relax + \fi + \advance\outerloopcount by 1 + \ifnum\outerloopcount>90\else\repeat + \if\seq@type P + \temp@count=\csname log2@20\endcsname + \else + \temp@count=\csname log2@4\endcsname + \fi + \advance\temp@count by -\innerloopcount + \multiply\temp@count by \second@ + \divide\temp@count by \seq@count + \xdef\last@{\the\temp@count} + \xdef\nineth@{n} + \outerloopcount=65 + \loop + \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} + \xdef\first@{\csname res@num\first@@\endcsname} + \ifnum\first@>0 + \temp@count=\last@ + \multiply\temp@count by \first@\relax + \divide\temp@count by \second@\relax + \ifnum\temp@count=0 % + \temp@count=1 % + \fi% + \expandafter\xdef\csname res@val\first@@\endcsname{\the\temp@count} + \expandafter\xdef\csname res@num\first@@\endcsname{0} + \xdef\nineth@{y} + \else + \expandafter\xdef\csname res@val\first@@\endcsname{0} + \fi + \advance\outerloopcount by 1 + \ifnum\outerloopcount>90\else\repeat + \expandafter\xdef\csname res@val\d@t\endcsname{0} + \expandafter\xdef\csname res@num\d@t\endcsname{0} + \ifx\nineth@\y@ + \xdef\tmpstack{&:&,} + \outerloopcount=65 + \loop + \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} + \xdef\second@@{\csname res@val\first@@\endcsname} + \ifnum\second@@>0 + \xdef\third@{\tmpstack @} \xdef\tmpstack{} + \sort@logostack + \fi + \advance\outerloopcount by 1 + \ifnum\outerloopcount>90 + \xdef\stack@sequencelogo{\stack@sequencelogo\tmpstack&:&,} + \else\repeat + \else + \xdef\stack@sequencelogo{\stack@sequencelogo O:0,&:&,} + \fi +} +\def\get@fromlogostack#1:#2,#3@{% + \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} +} +\def\sort@logostack{% + \expandafter\get@fromlogostack\third@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\first@@:\second@@,} + \else + \ifnum\second@@<0 + \ifnum\second@>0 + \xdef\tmpstack{\tmpstack\first@@:\second@@,\first@:\second@,\third@} + \else + \temp@count=\second@@\relax \multiply\temp@count by -1\relax + \triple@count=\second@\relax \multiply\triple@count by -1\relax + \ifnum\temp@count<\triple@count + \xdef\tmpstack{\tmpstack\first@@:\second@@,\first@:\second@,\third@} + \else + \xdef\tmpstack{\tmpstack\first@:\second@,} + \xdef\third@@{\third@ .} + \ifx\third@@\d@t + \xdef\third@{&:&,@} + \else + \xdef\third@{\third@ @} + \fi + \sort@logostack + \fi + \fi + \else + \ifnum\second@@<\second@ + \xdef\tmpstack{\tmpstack\first@@:\second@@,\first@:\second@,\third@} + \else + \xdef\tmpstack{\tmpstack\first@:\second@,} + \xdef\third@@{\third@ .} + \ifx\third@@\d@t + \xdef\third@{&:&,@} + \else + \xdef\third@{\third@ @} + \fi + \sort@logostack + \fi + \fi + \fi +} + + +\def\calc@feature{% +% \advance\pos@count by -1 + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname stop\bottop@\the\loopcount\endcsname<\first@@ + \expandafter\getregion@fromfstack{\the\loopcount} + \else + \innerloopcount=\loopcount + \expandafter\ifnum\csname featureon\bottop@\endcsname=0 + \expandafter\xdef\csname featureon\bottop@\endcsname{1} + \expandafter\xdef\csname feature@\bottop@\endcsname{1} + \expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{% + \csname text\bottop@\the\loopcount\endcsname} + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{% + \csname style\bottop@\the\loopcount\endcsname} + \innerloopcount=\pos@count + \advance\innerloopcount by -\csname featurepos\bottop@\endcsname + \expandafter\xdef\csname textfeature\bottop@\endcsname{% + \csname textfeature\bottop@\endcsname% + &\the\innerloopcount;{};} + \expandafter\xdef\csname stylefeature\bottop@\endcsname{% + \csname stylefeature\bottop@\endcsname% + &\the\innerloopcount;&;} + \expandafter\xdef\csname featurepos\bottop@\endcsname{\the\pos@count} + \xdef\temp@@@{n} + \xdef\fourth@{} + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi + \xdef\fourth@{} + \xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi + \ifx\temp@@@\y@ + \ifnum\loopcount=0 + \message{<No translations of the consensus sequence>} + \expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{% + No consensus translations!} + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{% + ///} + \else + \if\seq@type P + \expandafter\xdef\csname collect@res\bottop@\endcsname{yes} + \expandafter\xdef\csname tr@nsseq\bottop@\endcsname{\the\loopcount} + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + \csname res\the\loopcount\endcsname} + \else + \expandafter\xdef\csname collect@res\bottop@\endcsname{yes} + \expandafter\xdef\csname tr@nsseq\bottop@\endcsname{\the\loopcount} + \expandafter\ifx\csname res\the\loopcount\endcsname\gap@char + \expandafter\xdef\csname triple@count\bottop@\endcsname{0} + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{-} + \else + \expandafter\xdef\csname triple@count\bottop@\endcsname{1} + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + \csname res\the\loopcount\endcsname} + \expandafter\xdef\csname last@@res\bottop@\endcsname{% + \csname res\the\loopcount\endcsname} + \fi + \fi + \fi + \fi + \xdef\temp@{plot} + \ifx\temp@\fourth@ + \ifnum\loopcount=0 + \message{<No bar graphs/scales with the consensus sequence>} + \expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{} + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{% + ///} + \else + \expandafter\xdef\csname collect@val\bottop@\endcsname{yes} + \expandafter\xdef\csname v@lseq\bottop@\endcsname{\the\loopcount} + \expandafter\xdef\csname ffourth@\bottop@\endcsname{\ffourth@} + \xdef\temp@{\ffourth@\csname res\the\loopcount\endcsname} + \expandafter\xdef\csname v@l\bottop@\endcsname{\csname \temp@\endcsname} + \fi + \fi + \xdef\temp@{cons} + \ifx\temp@\fourth@ + \expandafter\xdef\csname collect@cons@graph\bottop@\endcsname{yes} + \expandafter\xdef\csname v@lseq\bottop@\endcsname{\the\loopcount} + \expandafter\xdef\csname ffourth@\bottop@\endcsname{\ffourth@} + \innerloopcount=1 + \collect@cons@res + \expandafter\xdef\csname v@l\bottop@\endcsname{\cons@val} + \fi + \else + \ifnum\pos@count=1\relax + \xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname @} + \expandafter\getstyle@right\temp@ + \xdef\temp@@@{n} + \xdef\fourth@{} + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi + \xdef\fourth@{} + \xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi + \ifx\temp@@@\y@ + \if\seq@type P + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + \csname res\the\loopcount\endcsname} + \else + \expandafter\ifnum\csname triple@count\bottop@\endcsname=2 + \expandafter\ifx\csname res\the\loopcount\endcsname\gap@char + \else + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + +\csname last@res\bottop@\endcsname% + \csname tr@nslate\bottop@\endcsname} + \fi + \fi + \expandafter\ifnum\csname triple@count\bottop@\endcsname=1 + \expandafter\xdef\csname last@res\bottop@\endcsname{% + \csname last@@res\bottop@\endcsname} + \expandafter\ifx\csname res\the\loopcount\endcsname\gap@char + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + +\csname last@res\bottop@\endcsname% + \csname tr@nslate\bottop@\endcsname} + \fi + \fi + \fi + \fi + \xdef\temp@{plot} + \ifx\temp@\fourth@ + \expandafter\ifx\csname res\the\loopcount\endcsname\gap@char + \expandafter\xdef\csname v@l\bottop@\endcsname{N} + \else + \xdef\temp@{\ffourth@\csname res\the\loopcount\endcsname} + \expandafter\xdef\csname v@l\bottop@\endcsname{% + \csname \temp@\endcsname} + \fi + \fi + \xdef\temp@{cons} + \ifx\temp@\fourth@ + \innerloopcount=1 + \collect@cons@res + \expandafter\xdef\csname v@l\bottop@\endcsname{\cons@val} + \fi + \fi + \fi + \expandafter\ifnum\csname stop\bottop@\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\temp@@@{n} + \xdef\fourth@{} + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns + \ifx\f@color\comm@ + \xdef\f@color{} \else \xdef\f@color{[\f@color]} + \fi + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \if\seq@type N \do@translation \else \rev@translation \fi + \xdef\temp@{translate:\tr@nsl@ted\f@color} + \xdef\temp@@@{y} + \else + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \fi + \xdef\fourth@{} + \xdef\temp@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \xdef\temp@@{\temp@@[,]:[,][]&}\expandafter\graph@opt@color\temp@@ + \ifx\fourth@\tr@ns + \ifx\f@color\comm@ + \xdef\f@color{} \else \xdef\f@color{[\f@color]} + \fi + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \if\seq@type N \do@translation \else \rev@translation \fi + \xdef\temp@@{translate:\tr@nsl@ted\f@color} + \xdef\temp@@@{y} + \else + \xdef\temp@@{plot} + \ifx\temp@@\fourth@ + \xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]} + \expandafter\xdef\csname collect@val\bottop@\endcsname{no} + \expandafter\xdef\csname v@l\bottop@\endcsname{} + \else + \xdef\temp@@{cons} + \ifx\temp@@\fourth@ + \xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]} + \expandafter\xdef\csname collect@cons@graph\bottop@\endcsname{no} + \expandafter\xdef\csname v@l\bottop@\endcsname{} + \else + \xdef\temp@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \fi + \fi + \fi + \ifx\temp@@@\y@ + \expandafter\xdef\csname collect@res\bottop@\endcsname{no} + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{} + \fi + \expandafter\ifnum\csname featureon\bottop@\endcsname=1 + \expandafter\xdef\csname featureon\bottop@\endcsname{0} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \advance\innerloopcount by -\csname featurepos\bottop@\endcsname + \expandafter\xdef\csname textfeature\bottop@\endcsname{% + \csname textfeature\bottop@\endcsname% + &\the\innerloopcount;\temp@;} + \expandafter\xdef\csname stylefeature\bottop@\endcsname{% + \csname stylefeature\bottop@\endcsname% + &\the\innerloopcount;\temp@@;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \expandafter\xdef\csname % + featurepos\bottop@\endcsname{\the\innerloopcount} + \fi + \fi + \ifnum\pos@count=\res@perline + \expandafter\ifnum\csname featureon\bottop@\endcsname=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\csname featurepos\bottop@\endcsname + \xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname @} + \expandafter\getstyle@left\temp@ + \xdef\temp@@@{n} + \xdef\fourth@{} + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns + \ifx\f@color\comm@ + \xdef\f@color{} \else \xdef\f@color{[\f@color]} + \fi + \expandafter\ifnum\csname triple@count\bottop@\endcsname=2 + \if\seq@type N + \xdef\temp@{\csname sequence\the\loopcount\endcsname:} + \expandafter\get@nextres\temp@ + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname\temp@} + \do@translation + \xdef\temp@@@{2} + \else + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \rev@translation + \xdef\temp@@@{} + \fi + \xdef\temp@{translate:\tr@nsl@ted\f@color} + \else + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \if\seq@type N \do@translation \else \rev@translation \fi + \xdef\temp@{translate:\tr@nsl@ted\f@color} + \xdef\temp@@@{} + \fi + \else \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \fi + \xdef\fourth@{} + \xdef\temp@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \xdef\temp@@{\temp@@[,]:[,][]&}\expandafter\graph@opt@color\temp@@ + \ifx\fourth@\tr@ns + \ifx\f@color\comm@ + \xdef\f@color{} \else \xdef\f@color{[\f@color]} + \fi + \expandafter\ifnum\csname triple@count\bottop@\endcsname=2 + \if\seq@type N + \xdef\temp@@{\csname sequence\the\loopcount\endcsname:} + \expandafter\get@@nextres\temp@@ + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname\temp@@} + \do@translation + \xdef\temp@@@{2} + \else + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \rev@translation + \xdef\temp@@@{} + \fi + \xdef\temp@@{translate:\tr@nsl@ted\f@color} + \else + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \if\seq@type N \do@translation \else \rev@translation \fi + \xdef\temp@@{translate:\tr@nsl@ted\f@color} + \xdef\temp@@@{} + \fi + \else + \xdef\temp@@{plot} + \ifx\temp@@\fourth@ + \xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]} + \else + \xdef\temp@@{cons} + \ifx\temp@@\fourth@ + \xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]} + \else + \xdef\temp@@{\style@@} + \fi + \fi + \fi + \ifx\temp@@@\n@ + \else + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{\temp@@@} + \fi + \expandafter\xdef\csname textfeature\bottop@\endcsname{% + \csname textfeature\bottop@\endcsname% + &\the\innerloopcount;\temp@;} + \expandafter\xdef\csname stylefeature\bottop@\endcsname{% + \csname stylefeature\bottop@\endcsname% + &\the\innerloopcount;\temp@@;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \expandafter\xdef\csname % + featurepos\bottop@\endcsname{\the\innerloopcount} + \fi + \fi + \fi + \fi + \fi + \ifnum\loopcount<\seq@count \repeat +% \advance\pos@count by 1 +} + +\def\add@to@rule@tens{% + \advance\innerloopcount by \ruler@step\relax + \ifnum\innerloopcount=0 + \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi + \fi + \expandafter\ifnum\csname res@count\rule@num\endcsname>\innerloopcount \add@to@rule@tens + \else + \xdef\rule@tens{\the\innerloopcount} + \fi +} + + +\def\c@nsensus{% + \ifnum\pos@count>\res@perline + \else + \loopcount=0 + \ifx\g@p\n@ + \global\advance\cons@count by 1\relax + \fi + \ifnum\cons@count=0\relax + \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi + \fi + \ifT@coffee + \xdef\TC@line{\csname T@coffee0\endcsname} + \expandafter\TC@get\TC@line + \fi + \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} + \loop + \advance\loopcount by 1 + \ifT@coffee + \xdef\TC@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\TC@line + \xdef\TC@first@{\csname TC@num\the\loopcount\endcsname} + \fi + \xdef\seq@line{\csname sequence\the\loopcount\endcsname} + \expandafter\residue@get\seq@line + \xdef\first@{\csname res\the\loopcount\endcsname} + \innerloopcount=\csname res@num\first@\endcsname + \advance\innerloopcount by 1 + \expandafter\xdef\csname res@num\first@\endcsname{\the\innerloopcount} + \expandafter\check@char\first@ + \ifx\dom@in\y@ %%%%%%%%%%%***** + \xdef\temp@{\csname dom@num\the\loopcount\endcsname} + \expandafter\get@dom@count\temp@ + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@} + \fi %%%%%%%%%%%***** + \ifletter + \ifx\dom@in\y@ + \else + \res@count=\csname res@count\the\loopcount\endcsname + \advance\res@count by 1 + \ifnum\res@count=0\relax + \ifx\allow@zero\n@ \advance\res@count by 1 \fi + \fi + \fi + \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count} + \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi + \ifnum\loopcount=\rule@num\relax + \expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens + \innerloopcount=\rule@tens \add@to@rule@tens + \fi + \expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens + \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax + \xdef\temp@{\rule@tens} + \else + \xdef\temp@{\csname alt@ruler\rule@tens\endcsname} + \fi + \xdef\ruler@{\ruler@ !<\temp@>} + \else + \xdef\ruler@{\ruler@ -} + \fi + \xdef\temp@{\csname res@count\rule@num\endcsname} + \expandafter\ifx\csname alt@ruler\temp@\endcsname\relax + \else + \expandafter\xdef\csname alt@ruler\temp@\endcsname{\temp@} + \fi + \fi + \ifx\collect@valtop\yes + \ifnum\v@lseqtop=\loopcount + \xdef\v@ltop{\v@ltop,\csname \ffourth@top\first@\endcsname} + \fi\fi + \ifx\collect@valttop\yes + \ifnum\v@lseqttop=\loopcount + \xdef\v@lttop{\v@lttop,\csname \ffourth@ttop\first@\endcsname} + \fi\fi + \ifx\collect@valtttop\yes + \ifnum\v@lseqtttop=\loopcount + \xdef\v@ltttop{\v@ltttop,\csname \ffourth@tttop\first@\endcsname} + \fi\fi + \ifx\collect@valttttop\yes + \ifnum\v@lseqttttop=\loopcount + \xdef\v@lttttop{\v@lttttop,\csname \ffourth@ttttop\first@\endcsname} + \fi\fi + \ifx\collect@valbottom\yes + \ifnum\v@lseqbottom=\loopcount + \xdef\v@lbottom{\v@lbottom,\csname \ffourth@bottom\first@\endcsname} + \fi\fi + \ifx\collect@valbbottom\yes + \ifnum\v@lseqbbottom=\loopcount + \xdef\v@lbbottom{\v@lbbottom,\csname \ffourth@bbottom\first@\endcsname} + \fi\fi + \ifx\collect@valbbbottom\yes + \ifnum\v@lseqbbbottom=\loopcount + \xdef\v@lbbbottom{\v@lbbbottom,\csname \ffourth@bbbottom\first@\endcsname} + \fi\fi + \ifx\collect@valbbbbottom\yes + \ifnum\v@lseqbbbbottom=\loopcount + \xdef\v@lbbbbottom{\v@lbbbbottom,\csname \ffourth@bbbbottom\first@\endcsname} + \fi\fi + \ifx\collect@restop\yes + \ifnum\tr@nsseqtop=\loopcount + \xdef\last@restop{\last@@restop} + \xdef\last@@restop{\first@} + \xdef\tr@nslatetop{\tr@nslatetop\first@} + \innerloopcount=\triple@counttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@counttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resttop\yes + \ifnum\tr@nsseqttop=\loopcount + \xdef\last@resttop{\last@@resttop} + \xdef\last@@resttop{\first@} + \xdef\tr@nslatettop{\tr@nslatettop\first@} + \innerloopcount=\triple@countttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countttop{\the\innerloopcount} + \fi\fi + \ifx\collect@restttop\yes + \ifnum\tr@nsseqtttop=\loopcount + \xdef\last@restttop{\last@@restttop} + \last@@restttop{\first@} + \xdef\tr@nslatetttop{\tr@nslatetttop\first@} + \innerloopcount=\triple@counttttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@counttttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resttttop\yes + \ifnum\tr@nsseqttttop=\loopcount + \xdef\last@resttttop{\last@@resttttop} + \xdef\last@@resttttop{\first@} + \xdef\tr@nslatettttop{\tr@nslatettttop\first@} + \innerloopcount=\triple@countttttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countttttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resbottom\yes + \ifnum\tr@nsseqbottom=\loopcount + \xdef\last@resbottom{\last@@resbottom} + \xdef\last@@resbottom{\first@} + \xdef\tr@nslatebottom{\tr@nslatebottom\first@} + \innerloopcount=\triple@countbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbottom{\the\innerloopcount} + \fi\fi + \ifx\collect@resbbottom\yes + \ifnum\tr@nsseqbbottom=\loopcount + \xdef\last@resbbottom{\last@@resbbottom} + \xdef\last@@resbbottom{\first@} + \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@} + \innerloopcount=\triple@countbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbottom{\the\innerloopcount} + \fi\fi + \ifx\collect@resbbbottom\yes + \ifnum\tr@nsseqbbbottom=\loopcount + \xdef\last@resbbbottom{\last@@resbbbottom} + \xdef\last@@resbbbottom{\first@} + \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@} + \innerloopcount=\triple@countbbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbbottom{\the\innerloopcount} + \fi\fi + \ifx\collect@resbbbbottom\yes + \ifnum\tr@nsseqbbbbottom=\loopcount + \xdef\last@resbbbbottom{\last@@resbbbbottom} + \xdef\last@@resbbbbottom{\first@} + \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@} + \innerloopcount=\triple@countbbbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbbbottom{\the\innerloopcount} + \fi\fi + \innerloopcount=\csname mol@weight\the\loopcount\endcsname + \advance\innerloopcount by \csname \prefix@ mw\first@\endcsname + \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{% + \the\innerloopcount} + \innerloopcount=\csname ch@rge\the\loopcount\endcsname + \advance\innerloopcount by \csname pepcharge\first@\endcsname + \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{% + \the\innerloopcount} + \else + \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi + \ifx\collect@valtop\yes + \ifnum\v@lseqtop=\loopcount + \xdef\v@ltop{\v@ltop,N} + \fi\fi + \ifx\collect@valttop\yes + \ifnum\v@lseqttop=\loopcount + \xdef\v@lttop{\v@lttop,N} + \fi\fi + \ifx\collect@valtttop\yes + \ifnum\v@lseqtttop=\loopcount + \xdef\v@ltttop{\v@ltttop,N} + \fi\fi + \ifx\collect@valttttop\yes + \ifnum\v@lseqttttop=\loopcount + \xdef\v@lttttop{\v@lttttop,N} + \fi\fi + \ifx\collect@valbottom\yes + \ifnum\v@lseqbottom=\loopcount + \xdef\v@lbottom{\v@lbottom,N} + \fi\fi + \ifx\collect@valbbottom\yes + \ifnum\v@lseqbbottom=\loopcount + \xdef\v@lbbottom{\v@lbbottom,N} + \fi\fi + \ifx\collect@valbbbottom\yes + \ifnum\v@lseqbbbottom=\loopcount + \xdef\v@lbbbottom{\v@lbbbottom,N} + \fi\fi + \ifx\collect@valbbbbottom\yes + \ifnum\v@lseqbbbbottom=\loopcount + \xdef\v@lbbbbottom{\v@lbbbbottom,N} + \fi\fi + \ifx\collect@restop\yes + \ifnum\tr@nsseqtop=\loopcount + \xdef\tr@nslatetop{\tr@nslatetop -} + \fi\fi + \ifx\collect@resttop\yes + \ifnum\tr@nsseqttop=\loopcount + \xdef\tr@nslatettop{\tr@nslatettop -} + \fi\fi + \ifx\collect@restttop\yes + \ifnum\tr@nsseqtttop=\loopcount + \xdef\tr@nslatetttop{\tr@nslatetttop -} + \fi\fi + \ifx\collect@resttttop\yes + \ifnum\tr@nsseqttttop=\loopcount + \xdef\tr@nslatettttop{\tr@nslatettttop -} + \fi\fi + \ifx\collect@resbottom\yes + \ifnum\tr@nsseqbottom=\loopcount + \xdef\tr@nslatebottom{\tr@nslatebottom -} + \fi\fi + \ifx\collect@resbbottom\yes + \ifnum\tr@nsseqbbottom=\loopcount + \xdef\tr@nslatebbottom{\tr@nslatebbottom -} + \fi\fi + \ifx\collect@resbbbottom\yes + \ifnum\tr@nsseqbbbottom=\loopcount + \xdef\tr@nslatebbbottom{\tr@nslatebbbottom -} + \fi\fi + \ifx\collect@resbbbbottom\yes + \ifnum\tr@nsseqbbbbottom=\loopcount + \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom -} + \fi\fi + \fi + \ifnum\loopcount<\seq@count \repeat + \ifx\collect@cons@graphtop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@ltop{\v@ltop,\cons@val} + \fi + \ifx\collect@cons@graphttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lttop{\v@lttop,\cons@val} + \fi + \ifx\collect@cons@graphtttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@ltttop{\v@ltttop,\cons@val} + \fi + \ifx\collect@cons@graphttttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lttttop{\v@lttttop,\cons@val} + \fi + \ifx\collect@cons@graphbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbottom{\v@lbottom,\cons@val} + \fi + \ifx\collect@cons@graphbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbottom{\v@lbbottom,\cons@val} + \fi + \ifx\collect@cons@graphbbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbbottom{\v@lbbbottom,\cons@val} + \fi + \ifx\collect@cons@graphbbbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbbbottom{\v@lbbbbottom,\cons@val} + \fi + \ifx\collect@cons@colors\y@ + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \outerloopcount=\cons@val + \advance\outerloopcount by 4 + \divide\outerloopcount by 5 + \multiply\outerloopcount by 5 + \ifnum\outerloopcount<5\relax\outerloopcount=5\fi + \xdef\c@nscol{\c@nscol\the\outerloopcount,} + \fi + \ifx\exp@rt\y@ + \ifx\seventh@\y@ + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \outerloopcount=\cons@val + \advance\outerloopcount by 4 + \divide\outerloopcount by 5 + \multiply\outerloopcount by 5 + \ifnum\outerloopcount<5\relax\outerloopcount=5\fi + \xdef\seventh@{n} + \immediate\write\exp@rtfile{\string color col\the\outerloopcount, resi \sixth@} + \fi + \fi + + \xdef\g@p{n} + \ifregionalshadenow \calc@regshade \fi + \ifregionaltintnow \calc@regtint \fi + \ifregionalemphnow \calc@regemph \fi + \ifregionallowernow \calc@reglower \fi + \ifframenow \calc@frame \fi + \ifshadingnow\iffuncmode\else\ifT@coffee\else \calc@shading \fi\fi\fi + \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi + \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi + \iftttopfeaturenow \xdef\bottop@{tttop} \calc@feature \fi + \ifttttopfeaturenow \xdef\bottop@{ttttop} \calc@feature \fi + \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \ifbbbottomfeaturenow \xdef\bottop@{bbbottom} \calc@feature \fi + \ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi + \ifnum\seq@count>1 \innerloopcount=1 \collect@similarity \fi + \advance\pos@count by 1 + \ifshow@logo \calc@logo \fi + \ifall@fshade \all@funcshade + \else + \ifT@coffee \T@coffee@shade + \else + \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi + \xdef\match@case{0} \xdef\m@x{1} + \iffuncmode + \xdef\prfx{\prefix@} \xdef\prefix@{func} \xdef\c@se{3} \check@sim + \xdef\prefix@{\prfx} + \else \xdef\c@se{1} \check@ident \fi + \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi + \fi + \fi + \ifnum\rule@num=0 + \ifx\g@p\y@ + \xdef\ruler@{\ruler@ -} + \else + \ifnum\cons@count=\rule@tens + \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax + \xdef\temp@{\rule@tens} + \else + \xdef\temp@{\csname alt@ruler\rule@tens\endcsname} + \fi + \xdef\ruler@{\ruler@ !<\temp@>} + \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax + \ifnum\innerloopcount=0 + \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi + \fi + \xdef\rule@tens{\the\innerloopcount} + \else + \xdef\ruler@{\ruler@ -} + \fi + \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax + \else + \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count} + \fi + \fi + \fi + \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax + \c@nsensus + \else + \global\stop@true + \loopcount=\pos@count \advance\loopcount by -1 \relax + \res@perline=\loopcount + \iftopfeature \xdef\bottop@{top} \calc@feature \fi + \ifttopfeature \xdef\bottop@{ttop} \calc@feature \fi + \iftttopfeature \xdef\bottop@{tttop} \calc@feature \fi + \ifttttopfeature \xdef\bottop@{ttttop} \calc@feature \fi + \ifbottomfeature \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeature \xdef\bottop@{bbottom} \calc@feature \fi + \ifbbbottomfeature \xdef\bottop@{bbbottom} \calc@feature \fi + \ifbbbbottomfeature \xdef\bottop@{bbbbottom} \calc@feature \fi + \pos@count=0 + \fi + \fi} + +\def\prep@reexp@rtfile{ + \loopcount=0 + \loop + \advance\loopcount by 5 + \immediate\write\exp@rtfile{\string set_color col\the\loopcount, \csname\c@nsc@l\the\loopcount\endcsname} + \ifnum\loopcount>95\else\repeat +} + +\def\c@unt{% + \advance\loopcount by 1 + \ifT@coffee + \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\seq@line + \fi + \xdef\seq@line{\csname sequence\the\loopcount\endcsname} + \expandafter\residue@get\seq@line + \xdef\first@{\csname res\the\loopcount\endcsname} + \expandafter\check@char\first@ + \ifletter + \res@count=\csname res@count\the\loopcount\endcsname + \advance\res@count by 1 + \ifnum\res@count=0 + \ifx\allow@zero\n@ \advance\res@count by 1 \fi + \fi + \ifx\dom@in\y@ + \xdef\temp@{\csname dom@num\the\loopcount\endcsname} + \expandafter\get@dom@count\temp@ + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@} + \fi %%%%%%%%%%%***** + \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count} + \ifnum\rule@num=\loopcount + \temp@count=\csname res@count\the\loopcount\endcsname + \advance\temp@count by \ruler@step + \divide\temp@count by \ruler@step + \multiply\temp@count by \ruler@step + \xdef\rule@tens{\the\temp@count} + \fi + \fi + \ifnum\loopcount<\seq@count \c@unt\fi} +\def\count@first{% + \advance\end@count by 1 + \ifnum\end@count<\start@number + \loopcount=0 + \ifT@coffee + \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\seq@line + \fi + \c@unt + \count@first + \fi} +\def\findc@nsensus{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname sequence\the\loopcount\endcsname{% + \csname sequence\the\loopcount\endcsname @} + \ifnum\loopcount<\seq@count \repeat + \end@count=0 \count@first \end@count=0 \xdef\start@number{0} + \topfeaturenowfalse \bottomfeaturenowfalse + \ttopfeaturenowfalse \bbottomfeaturenowfalse + \tttopfeaturenowfalse \bbbottomfeaturenowfalse + \ttttopfeaturenowfalse \bbbbottomfeaturenowfalse + \innerloopcount=\cons@count + \advance\innerloopcount by \res@perline \advance\innerloopcount by 1 + \loopcount=0 + \ifregionalshade + \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\the\loopcount\endcsname>% + \innerloopcount + \else + \regionalshadenowtrue + \fi + \fi + \fi + \ifregionaltint + \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionaltintnowtrue + \fi + \fi + \fi + \ifregionalemph + \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionalemphnowtrue + \fi + \fi + \fi + \ifregionallower + \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionallowernowtrue + \fi + \fi + \fi + \ifframe@ + \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname framestart\the\loopcount\endcsname>% + \innerloopcount + \else + \framenowtrue + \fi + \fi + \fi + \ifshading@ + \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>% + \innerloopcount + \else + \shadingnowtrue + \fi + \fi + \fi + \iftopfeature + \xdef\bottop@{top} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \topfeaturenowtrue + \fi + \fi + \fi + \ifttopfeature + \xdef\bottop@{ttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttopfeaturenowtrue + \fi + \fi + \fi + \iftttopfeature + \xdef\bottop@{tttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \tttopfeaturenowtrue + \fi + \fi + \fi + \ifttttopfeature + \xdef\bottop@{ttttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttttopfeaturenowtrue + \fi + \fi + \fi + \ifbottomfeature + \xdef\bottop@{bottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bottomfeaturenowtrue + \fi + \fi + \fi + \ifbbottomfeature + \xdef\bottop@{bbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbottomfeature + \xdef\bottop@{bbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbbottomfeature + \xdef\bottop@{bbbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbbottomfeaturenowtrue + \fi + \fi + \fi +\loop + \advance\loopcount by 1 + \ifnumbers@left + \innerloopcount=\csname seq@len\the\loopcount\endcsname\relax + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=% + \innerloopcount + \res@count=\innerloopcount + \else + \res@count=\csname res@count\the\loopcount\endcsname + \advance\res@count by 1 + \ifnum\res@count=0 + \ifx\allow@zero\n@ \advance\res@count by 1 \fi + \fi + \fi + \ifx\dom@in\y@ + \xdef\temp@{\csname dom@num\the\loopcount\endcsname} + \expandafter\get@dom@count\temp@ + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\the\res@count,\temp@} + \fi %%%%%%%%%%***** + \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count} + \ifnames@right + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname res@count\the\loopcount\endcsname)} + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + <\csname newseqname\the\loopcount\endcsname> + \csname res@count\the\loopcount\endcsname)} + \fi + \ifx\dom@in\y@ + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=% + \innerloopcount + \else + \res@count=\csname res@count\the\loopcount\endcsname + \advance\res@count by -1 + \ifnum\res@count=0 + \ifx\allow@zero\n@ \advance\res@count by -1 \fi + \fi + \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count} + \fi + \fi + \else + \ifnames@right + \expandafter\xdef\csname seq\the\loopcount\endcsname{} + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + <\csname newseqname\the\loopcount\endcsname>} + \fi + \fi + \ifx\dom@in\y@ + \xdef\temp@{\csname dom@num@break\the\loopcount\endcsname} + \expandafter\get@dom@count\temp@ + \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{\temp@} + \innerloopcount=\res@count + \else + \innerloopcount=\csname res@count\the\loopcount\endcsname + \advance\innerloopcount by \res@perline + \fi + \advance\innerloopcount by 1 + \ifregionalshade + \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\the\loopcount\endcsname>% + \innerloopcount + \else + \regionalshadenowtrue + \fi + \fi + \fi + \ifregionaltint + \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionaltintnowtrue + \fi + \fi + \fi + \ifregionalemph + \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionalemphnowtrue + \fi + \fi + \fi + \ifregionallower + \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionallowernowtrue + \fi + \fi + \fi + \ifframe@ + \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname framestart\the\loopcount\endcsname>% + \innerloopcount + \else + \framenowtrue + \fi + \fi + \fi + \ifshading@ + \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>% + \innerloopcount + \else + \shadingnowtrue + \fi + \fi + \fi + \iftopfeature + \xdef\bottop@{top} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \topfeaturenowtrue + \fi + \fi + \fi + \ifttopfeature + \xdef\bottop@{ttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttopfeaturenowtrue + \fi + \fi + \fi + \iftttopfeature + \xdef\bottop@{tttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \tttopfeaturenowtrue + \fi + \fi + \fi + \ifttttopfeature + \xdef\bottop@{ttttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttttopfeaturenowtrue + \fi + \fi + \fi + \ifbottomfeature + \xdef\bottop@{bottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bottomfeaturenowtrue + \fi + \fi + \fi + \ifbbottomfeature + \xdef\bottop@{bbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbottomfeature + \xdef\bottop@{bbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbbottomfeature + \xdef\bottop@{bbbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbbottomfeaturenowtrue + \fi + \fi + \fi +\ifnum\loopcount<\seq@count \repeat + \c@nsensus} + +%%%%% Output routines + +\def\white@box{% + \bgroup + \fboxsep-0.5pt\fboxrule0.5pt + \fcolorbox{Black}{White}{\box@hstrut\box@wstrut}\egroup} +\def\box@rule{\vrule depth\box@depth height\box@height width\box@width} +\def\box@hstrut{\vrule depth\box@depth height\box@height width 0pt} +\def\box@wstrut{\vrule depth 0pt height 0pt width\box@width} +\def\do@legend{% + \baselineskip=1.2\baselineskip + \xdef\first@{White} + \fontfamily{\legend@family}% + \fontseries{\legend@series}% + \fontshape{\legend@shape}% + \ifT@coffee + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \def\res@@style{\csname no@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}% + \expandafter\ifx\csname n@m@tch\the\loopcount\endcsname\low@up% + \def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \textcolor{TC0}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{schlecht}% + \else\ifsp@nish\kern2ex\legend@size{mala}% + \else\kern2ex\legend@size{bad}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC1}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC2}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC3}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC4}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{Grad der}% + \else\ifsp@nish\kern2ex\legend@size{conservaci\'on}% + \else\kern2ex\legend@size{level of}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC5}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{Konservierung}% + \else\ifsp@nish\kern2ex\legend@size{}% + \else\kern2ex\legend@size{conservation}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC6}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC7}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC8}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC9}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{gut}% + \else\ifsp@nish\kern2ex\legend@size{buena}% + \else\kern2ex\legend@size{good}\fi\fi} + \newline\hbox{}% + \else + \iffuncmode + \ifnum\fgroup@num>0 + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\third@{\csname fg@color\the\loopcount\endcsname}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi% + \xdef\third@{\csname fg@textcolor\the\loopcount\endcsname}% + \def\res@@style{\csname func@style\the\loopcount\endcsname}% + \def\temp@{X}\xdef\low@up{lower}% + \expandafter\ifx\csname funcm@tch\the\loopcount\endcsname\low@up% + \def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\third@}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \legend@size{\csname fgroup@name\the\loopcount\endcsname}} + \newline\hbox{}% + \ifnum\loopcount<\fgroup@num \repeat + \fi + \else + \noindent + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \ifx\Nomatch\first@\white@box\else\textcolor{\Nomatch}{\box@rule}\fi% + \def\res@@style{\csname no@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}\ifx\resn@m@tch\low@up\def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\TextNomatch}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{nicht konserviert}% + \else\ifsp@nish\kern2ex\legend@size{no conservado}% + \else\kern2ex\legend@size{non-conserved}\fi\fi} + \newline\hbox{}\noindent% + \ifsimmode% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi + \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi + \hbox to \hspace@legend{\hss}% + \ifx\Similar\first@\white@box\else\textcolor{\Similar}{\box@rule}\fi + \def\res@@style{\csname sim@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}\ifx\ressimm@tch\low@up\def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\TextSimilar}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{\"ahnlich}% + \else\ifsp@nish\kern2ex\legend@size{similar}% + \else\kern2ex\legend@size{similar}\fi\fi} + \newline\hbox{}\noindent% + \fi% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi + \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi + \hbox to \hspace@legend{\hss}% + \ifx\Identical\first@\white@box\else\textcolor{\Identical}{\box@rule}\fi + \def\res@@style{\csname id@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}\ifx\resm@tch\low@up\def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\TextIdentical}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{$\ge$\,\thresh@ld\% konserviert}% + \else\ifsp@nish\kern2ex\legend@size{$\ge$\,\thresh@ld\% conservado}% + \else\kern2ex\legend@size{$\ge$\,\thresh@ld\% conserved}\fi\fi} + \newline\hbox{}\noindent% + \ifall@shade% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi + \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi + \hbox to \hspace@legend{\hss}% + \ifx\Allmatch\first@\white@box\else\textcolor{\Allmatch}{\box@rule}\fi + \def\res@@style{\csname all@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}\ifx\res@llm@tch\low@up\def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\TextAllmatch}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \ifnum\all@thresh@ld=100 + \textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{alle identisch}% + \else\ifsp@nish\kern2ex\legend@size{todos id\'enticos}% + \else\kern2ex\legend@size{all match}\fi\fi} + \else + \textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% konserviert}% + \else\ifsp@nish\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% conservado}% + \else\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% conserved}\fi\fi} + \fi + \newline\hbox{}\noindent + \fi + \fi + \fi +} +\def\put@name<#1>#2@{% + \ifnames@% + \expandafter\ifx\csname hide@name\the\loopcount\endcsname\yes% + \xdef\temp@{}\else\xdef\temp@{#1}\fi% + \expandafter\ifx\csname name@col\the\loopcount\endcsname\yes% + \def\second@{\names@fg}% + \else\def\second@{\csname name@col\the\loopcount\endcsname}\fi% + \fontfamily{\namestext@family}% + \fontseries{\namestext@series}% + \fontshape{\namestext@shape}% + \selectfont% + \textcolor{\second@}{% + \hbox to \name@width{\@kern\namestext@size{\temp@}\hss}}\fi% + \xdef\first@{#2@}% +} +\def\put@number#1)#2@{% + \ifnumbers@% + \expandafter\ifx\csname hide@number\the\loopcount\endcsname\yes% + \xdef\temp@{}\else\xdef\temp@{#1}\fi% + \expandafter\ifx\csname number@col\the\loopcount\endcsname\yes% + \def\second@{\numbering@fg}% + \else\def\second@{\csname number@col\the\loopcount\endcsname}\fi% + \fontfamily{\numbertext@family}% + \fontseries{\numbertext@series}% + \fontshape{\numbertext@shape}% + \selectfont% + \textcolor{\second@}{% + \hbox to \number@width{\hss\numbertext@size{\temp@}\@kern}}\fi% + \xdef\first@{#2@}% +} +\def\special@shading#1)#2#3#4@{% + \xdef\second@{@\second@#1}% + \xdef\third@{\second@}% + \xdef\first@{#4@}% + \xdef\second@{#3}% + \xdef\last@{#2}% + \def\res@@style{\csname relax\endcsname}% +} +\def\special@shade#1)#2#3#4@{% + \xdef\second@{\second@#1}% + \xdef\boxc@l@r{\csname bgseqregion\second@\endcsname}% + \xdef\textc@l@r{\csname fgseqregion\second@\endcsname}% + \xdef\first@{#4@}% + \xdef\second@{#3}% + \def\res@@style{\csname relax\endcsname}% +} +\def\get@second@#1#2@{\xdef\second@{#1}\xdef\first@{#2@}} +\def\next@char#1#2#3@{% + \xdef\first@{#3@}% + \xdef\second@{#2}% + \xdef\last@{#1}% + \xdef\temp@@{}% + \xdef\third@{}% + \ifx\last@\p@r@gr@ph\expandafter\special@shading\first@\fi% + \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% + \else% + \ifT@coffee% + \xdef\boxc@l@r{\csname fg@color#1\endcsname}% + \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% + \def\res@@style{\csname func@style#1\endcsname}% + \if\last@ *\def\last@{0}\fi + \if\last@ /\def\last@{10}\fi + \if\last@ !\def\last@{11}\fi + \else% + \iffuncmode% + \xdef\boxc@l@r{\csname fg@color#1\endcsname}% + \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% + \def\res@@style{\csname func@style#1\endcsname}% + \if\last@ *\def\last@{0}\fi + \if\last@ /\def\last@{10}\fi + \if\last@ !\def\last@{11}\fi + \else% + \ifcase\last@\xdef\boxc@l@r{\csname Allmatch\third@\endcsname}% + \xdef\textc@l@r{\csname TextAllmatch\third@\endcsname}% + \def\res@@style{\all@style}% + \or\xdef\boxc@l@r{\csname Identical\third@\endcsname}% + \xdef\textc@l@r{\csname TextIdentical\third@\endcsname}% + \def\res@@style{\id@style}% + \or\xdef\boxc@l@r{\csname Similar\third@\endcsname}% + \xdef\textc@l@r{\csname TextSimilar\third@\endcsname}% + \def\res@@style{\sim@style}% + \or\xdef\boxc@l@r{\csname Nomatch\third@\endcsname}% + \xdef\textc@l@r{\csname TextNomatch\third@\endcsname}% + \def\res@@style{\no@style}% + \or\xdef\boxc@l@r{\csname ConsNomatch\third@\endcsname}% + \xdef\textc@l@r{\csname ConsTextNomatch\third@\endcsname}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\csname ConsMatch\third@\endcsname}% + \xdef\textc@l@r{\csnam ConsTextMatch\third@\endcsname}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\csname ConsAllmatch\third@\endcsname}% + \xdef\textc@l@r{\csname ConsTextAllmatch\third@\endcsname}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\csname gap@bg\third@\endcsname}% + \xdef\textc@l@r{\csname gap@fg\third@\endcsname}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \def\res@@style{\csname relax\endcsname}% + \else\xdef\boxc@l@r{\csname domgap@bg\endcsname}% + \xdef\textc@l@r{\csname domgap@fg\endcsname}% + \def\res@@style{\csname relax\endcsname}% + \fi\fi\fi\fi% + \ifx\second@\comm@% + \def\temp@{\res@style}% + \expandafter\get@second@\first@% + \else% + \def\temp@{\csname relax\endcsname}% + \fi% + \ifx\second@\equ@l% + \xdef\temp@@{\light@}% + \expandafter\get@second@\first@% + \fi% + \ifx\second@\semic@n% + \expandafter\get@second@\first@% + \xdef\first@@{\first@}% + \xdef\first@{\second@}% + \make@lower% + \xdef\second@{\first@}% + \xdef\first@{\first@@}% + \fi% + \textcolor{\temp@@\boxc@l@r}{\box@rule}% + \ifhidechar% + \ifx\second@\o@% + \def\second@{\gap@rule}% + \hbox to -\box@width{\hss\textcolor{\temp@@\textc@l@r}% + {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% + \kern\box@width% + \fi% + \else% + \ifx\second@\o@\def\second@{\gap@rule}\fi% + \hbox to -\box@width{\hss\textcolor{\temp@@\textc@l@r}% + {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% + \kern\box@width\fi% +} +\def\put@char{% + \ifnum\innerloopcount>\res@perline + \else + \expandafter\next@char\first@ + \advance\innerloopcount by 1 + \put@char% + \fi} +\def\next@cons#1#2#3@{% + \xdef\last@{#1}% + \xdef\third@{}% + \ifx\last@\p@r@gr@ph\expandafter\special@shading\first@\fi% + \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% + \else% + \ifx\collect@cons@colors\y@% + \if\last@ *% + \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% + \else% + \if\last@ !% + \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}% + \else% + \if\last@ /% + \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \else% + \expandafter\get@item\first@@@% + \xdef\first@@@{\first@}% + \ifx\box@scale\y@% + \xdef\boxc@l@r{\c@nssc@le\fourth@}% + \else% + \xdef\first@{T-Coffee}% + \ifx\first@\c@nssc@le% + \xdef\boxc@l@r{TC\last@}% + \else + \xdef\boxc@l@r{\c@nssc@le}% + \fi% + \fi% + \ifx\text@scale\y@% + \xdef\textc@l@r{\c@nsc@l\fourth@}% + \else% + \xdef\first@{T-Coffee}% + \ifx\first@\c@nsc@l% + \xdef\textc@l@r{TC\last@}% + \else + \xdef\textc@l@r{\c@nsc@l}% + \fi% + \fi\fi\fi\fi% + \def\res@@style{\csname relax\endcsname}% + \else% + \ifT@coffee% + \if\last@ *% + \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% + \else% + \if\last@ !% + \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}% + \else% + \if\last@ /% + \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \else% + \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}% + \def\res@@style{\csname relax\endcsname}% + \fi + \fi% + \fi% + \else% + \ifcase#1\xdef\boxc@l@r{\csname Allmatch\third@\endcsname}% + \xdef\textc@l@r{\csname TextAllmatch\third@\endcsname}% + \def\res@@style{\all@style}% + \or\xdef\boxc@l@r{\csname Identical\third@\endcsname}% + \xdef\textc@l@r{\csname TextIdentical\third@\endcsname}% + \def\res@@style{\id@style}% + \or\xdef\boxc@l@r{\csname Similar\third@\endcsname}% + \xdef\textc@l@r{\csname TextSimilar\third@\endcsname}% + \def\res@@style{\sim@style}% + \or\xdef\boxc@l@r{\csname Nomatch\third@\endcsname}% + \xdef\textc@l@r{\csname TextNomatch\third@\endcsname}% + \def\res@@style{\no@style}% + \or\xdef\boxc@l@r{\ConsNomatch}\xdef\textc@l@r{\ConsTextNomatch}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\ConsMatch}\xdef\textc@l@r{\ConsTextMatch}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\ConsAllmatch}\xdef\textc@l@r{\ConsTextAllmatch}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \def\res@@style{\csname relax\endcsname}% + \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}% + \def\res@@style{\csname relax\endcsname}% + \fi\fi\fi\fi% + \xdef\first@{#3@}% + \xdef\second@{#2}% + \ifx\second@\comm@% + \def\temp@{\res@style}% + \expandafter\get@second@\first@% + \else% + \def\temp@{\csname relax\endcsname}% + \fi% + \ifx\second@\semic@n% + \expandafter\get@second@\first@% + \xdef\first@@{\first@}% + \xdef\first@{\second@}% + \make@lower% + \xdef\second@{\first@}% + \xdef\first@{\first@@}% + \fi% + \textcolor{\boxc@l@r}{\box@rule}% + \ifhidechar% + \ifx\second@\o@% + \def\second@{\gap@rule}% + \hbox to -\box@width{\hss\textcolor{\textc@l@r}% + {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% + \kern\box@width% + \fi% + \else% + \ifx\second@\o@\def\second@{\gap@rule}\fi% + \hbox to -\box@width{\hss\textcolor{\textc@l@r}% + {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% + \kern\box@width\fi% +} +\def\put@cons{% + \ifnum\innerloopcount>\res@perline + \else + \expandafter\next@cons\first@ + \advance\innerloopcount by 1 + \put@cons% + \fi} +\def\put@line{% + \ifnames@right\else\def\@kern{\kern0em}\expandafter\put@name\first@\fi + \ifnumbers@left\def\@kern{\kern1em}\expandafter\put@number\first@\fi + \fontfamily{\residues@family}% + \fontseries{\residues@series}% + \fontshape{\residues@shape}% + \selectfont% + \ifx\cons@now\y@% + \innerloopcount=1\relax\put@cons% + \else + \innerloopcount=1\relax\put@char% + \fi + \ifnumbers@right\def\@kern{\kern0em}\expandafter\put@number\first@\fi + \ifnames@right\def\@kern{\kern1em}\expandafter\put@name\first@\fi + \newline\hbox{}% +} + +\def\set@consensus{% + \ifnames@right + \ifnumbers@left + \ifnumbers@right + \xdef\consensus{)\consensus)<\cons@name>}% + \else + \xdef\consensus{)\consensus<\cons@name>}% + \fi + \else + \xdef\consensus{\consensus)<\cons@name>}% + \fi + \else + \ifnumbers@left + \ifnumbers@right + \xdef\consensus{<\cons@name>)\consensus)}% + \else + \xdef\consensus{<\cons@name>)\consensus}% + \fi + \else + \xdef\consensus{<\cons@name>\consensus)}% + \fi + \fi} + +\def\get@rulenum<#1>#2@{% + \xdef\first@{#2@}% + \xdef\fill@char{#1[,]&}% + \expandafter\opt@color\fill@char% + \ifx\f@color\comm@\xdef\f@color{\ruler@fg}\fi% + \ifcase\rule@top + \ifnum\ruler@rot=0 % + \xdef\temp@{tt}% + \ifx\ruler@family\temp@% + \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\mathtt{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% + \else + \xdef\temp@{sf}% + \ifx\ruler@family\temp@% + \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\mathsf{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% + \else + \xdef\temp@{rm}% + \ifx\ruler@family\temp@% + \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\mathrm{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% + \fi\fi\fi + \else + \xdef\temp@{tt}% + \ifx\ruler@family\temp@% + \def\third@{\tt\bottomruler@size\,\,\,\,% + \begin{rotopo}{90}\hbox to \ruler@width{\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}\,\fourth@\hss}\end{rotopo}}% + \else + \xdef\temp@{sf}% + \ifx\ruler@family\temp@% + \def\third@{\sf\bottomruler@size\,\,\,\,% + \begin{rotopo}{90}\hbox to \ruler@width{\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}\,\fourth@\hss}\end{rotopo}}% + \else + \xdef\temp@{rm}% + \ifx\ruler@family\temp@% + \def\third@{\rm\bottomruler@size\,\,\,\,% + \begin{rotopo}{90}\hbox to \ruler@width{\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}\,\fourth@\hss}\end{rotopo}}% + \fi\fi\fi + \fi + \else + \ifnum\ruler@rot=0 % + \xdef\temp@{tt}% + \ifx\ruler@family\temp@% + \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\textcolor{\ruler@fg}{.}}{\mathtt{\fourth@}}}}% + \else + \xdef\temp@{sf}% + \ifx\ruler@family\temp@% + \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\textcolor{\ruler@fg}{.}}{\mathsf{\fourth@}}}}% + \else + \xdef\temp@{rm}% + \ifx\ruler@family\temp@% + \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\textcolor{\ruler@fg}{.}}{\mathrm{\fourth@}}}}% + \fi\fi\fi + \else + \xdef\temp@{tt}% + \ifx\ruler@family\temp@% + \def\third@{\tt\bottomruler@size\,\,\,\,% + \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}% + \else + \xdef\temp@{sf}% + \ifx\ruler@family\temp@% + \def\third@{\sf\bottomruler@size\,\,\,\,% + \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}% + \else + \xdef\temp@{rm}% + \ifx\ruler@family\temp@% + \def\third@{\rm\bottomruler@size\,\,\,\,% + \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}% + \fi\fi\fi + \fi + \fi} + +\def\next@rulechar#1#2@{% + \xdef\third@{#1}% + \xdef\first@{#2@}% + \xdef\second@{!}% + \ifx\third@\second@ \expandafter\get@rulenum\first@% + \else \xdef\third@{}\xdef\f@color{Black}\fi + \textcolor{\f@color}{\hbox to \box@width{\hss\third@\hss}}% + } + +\def\put@rulechar{% + \ifnum\innerloopcount>\res@perline + \else + \expandafter\next@rulechar\first@ + \advance\innerloopcount by 1 + \put@rulechar% + \fi} + +\def\put@ruler{% + \ifnames@right% + \ifnumbers@left% + \ifnumbers@right% + \xdef\ruler@{)\ruler@)<>}% + \else% + \xdef\ruler@{)\ruler@<>}% + \fi% + \else% + \xdef\ruler@{\ruler@)<>}% + \fi% + \else% + \ifnumbers@left% + \ifnumbers@right% + \xdef\ruler@{<>)\ruler@)}% + \else% + \xdef\ruler@{<>)\ruler@}% + \fi% + \else% + \xdef\ruler@{<>\ruler@)}% + \fi% + \fi% + \xdef\first@{\ruler@ @}% + \ifnum\rule@top=1% + \vspace{\ruler@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \fi% + \ifnames@right\else\def\@kern{\kern0em}\expandafter\put@name\first@\fi% + \ifnumbers@left\def\@kern{\kern1em}\expandafter\put@number\first@\fi% + \vspace{-0.25\baselineskip}% + \ifnum\rule@top=0% + \vspace{\ruler@sp@ce}% + \fi% + \fontfamily{\ruler@family}% + \fontseries{m}% + \fontshape{n}% + \selectfont% + \innerloopcount=1\relax\put@rulechar% + \newline\hbox{}% +} +\def\get@firstfill#1#2&{\xdef\second@@{#1}\xdef\fill@char{#2&}} +\def\get@firstv@l#1,#2&{\xdef\second@@{#1}\xdef\fill@char{#2&}} +\def\get@tripletfill#1#2#3#4&{% + \multiply\temp@count by -1% + \def\second@@{#1}\def\second@@@{#2}\def\second@@@@{#3}\def\fill@char{#4&}} + + +\def\putfeature@style#1{% + \residues@size% + \setbox1=\hbox{\ensuremath{\overrightarrow{\hbox{}}}}% + \arrow@height=\ht1% + \arrow@width=\wd1% + \xdef\second@@{#1}% + \xdef\last@{\second@@::&}\expandafter\test@fill\last@% + \xdef\last@{empty}% + \ifx\second@@\last@% + \hbox to \second@\box@width{\hss}% + \else% + \xdef\last@{translate}% + \ifx\second@@\last@% + \fontfamily{\featurestyles@family}% + \fontseries{\featurestyles@series}% + \fontshape{\featurestyles@shape}% + \selectfont% + \xdef\fill@char{\fill@char &}% + \if\seq@type N% + \loop% + \expandafter\get@firstfill\fill@char% + \if\second@@ -\def\second@@{\hss}\fi% + \hbox to \box@width{\hss\textcolor{\f@color}{\featurestyles@size{\second@@}}\hss}% + \ifx\fill@char\ampers@nd\else\repeat% + \else% + \temp@count=1% + \loop% + \expandafter\get@tripletfill\fill@char% + \if\second@@ -\ifnum\tr@nsstyle>0\hbox to \box@width{\hss}\fi% + \else% + \ifcase\tr@nsstyle% + \hbox{\trans@size\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\,\hss}}% + \or% + \ifnum\temp@count=1% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% + \else% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}}% + \fi% + \or% + \ifnum\temp@count=1% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss}}}% + \else% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\hss}}% + \hbox to \box@width{\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\hss}}}% + \fi% + \or% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% + \or% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@\hss}}}% + \fi% + \fi% + \ifx\fill@char\ampers@nd\else\repeat% + \fi% + \else% + \xdef\last@{brace}% + \ifx\second@@\last@% + \xdef\last@{top}% + \textcolor{\f@color}{% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \xdef\last@{ttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \xdef\last@{tttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \xdef\last@{ttttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \raisebox{1.75\arrow@height}{\ensuremath{\underbrace{\hbox to % + \second@\box@width{}}}}% + \fi\fi\fi\fi}% + \else% + \xdef\last@{fill}% + \ifx\second@@\last@% + \fontfamily{\featurestyles@family}% + \fontseries{\featurestyles@series}% + \fontshape{\featurestyles@shape}% + \selectfont% + \xdef\last@{bottom}% + \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi% + \kern0.15\box@width% + \loopcount=0\relax% + \loop% + \advance\loopcount by 1\relax% + \raisebox{\last@\arrow@height}{% + \hbox to \box@width{\hss{\textcolor{\f@color}{\featurestyles@size\fill@char}}\hss}}% + \ifnum\loopcount<\second@ \repeat% + \else% + \xdef\last@{bar}% + \ifx\second@@\last@% + \setlength\arrow@width{\pm@shift\box@height}% + \setlength\arrow@width{\b@r@stretch\arrow@width}% + \ifx\fill@char\N@% + \raisebox{\pm@shift\box@height}{\vrule width\box@width}% + \else% + \kern-0.6\box@width% + \ifx\frame@color\back@color% + \else% + \setlength\arrow@height{\box@height}% + \advance\arrow@height by -\pm@shift\box@height% + \setlength\arrow@height{\b@r@stretch\arrow@height}% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\back@color}{\vrule depth\arrow@width% + height\arrow@height width\box@width}}\hss}}% + \kern-\box@width% + \fi% + \setlength\arrow@height{\fill@char\box@height}% + \setlength\arrow@height{\b@r@stretch\arrow@height}% + \divide\arrow@height by 100\relax% + \ifdim\arrow@height<0pt% + \arrow@height=-\arrow@height% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\frame@color}{\vrule depth\arrow@height width0.8\box@width}}\hss}}% + \else% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\frame@color}{\vrule height\arrow@height width0.8\box@width}}\hss}}\fi% + \kern-\box@width% + \raisebox{\arrow@width}{\textcolor{Black}{\vrule height0.25pt depth0.25pt width\box@width}}% + \fi% + \else% + \xdef\last@{color}% + \ifx\second@@\last@% + \setlength\arrow@height{\fill@char\box@height}% + \setlength\arrow@height{\sc@le@stretch\arrow@height}% + \divide\arrow@height by 100\relax% + \raisebox{0.2\box@height}{% + \hbox to \box@width{\hss{\textcolor{\f@color}{\vrule height\arrow@height width\box@width}}\hss}}% + \else% + \xdef\last@{plotcolor}% + \ifx\second@@\last@% + \xdef\fill@char{\fill@char,&}% + \loop% + \expandafter\get@firstv@l\fill@char% + \ifx\second@@\N@\hbox to \box@width{\hss}% + \else + \loopcount=\second@@% + \ifx\T@coffee@ccons\y@% + \else% + \advance\loopcount by -\pm@shift% + \advance\loopcount by 4% + \divide\loopcount by 5% + \multiply\loopcount by 5% + \ifnum\loopcount>100\loopcount=100\fi% + \ifnum\loopcount<5\loopcount=5\fi% + \fi% + \setlength\arrow@height{50\box@height}% + \divide\arrow@height by 100\relax% + \setlength\arrow@height{\sc@le@stretch\arrow@height}% + \raisebox{0.2\box@height}{% + \hbox to \box@width{\hss{\textcolor{\f@color\the\loopcount}{\vrule height\arrow@height width\box@width}}\hss}}% + \fi + \ifx\fill@char\ampers@nd\else\repeat% + \else% + \xdef\last@{plotbar}% + \ifx\second@@\last@% + \xdef\fill@char{\fill@char,&}% + \ifnum\pm@shift>0% + \setlength\arrow@width{0pt}% + \else + \setlength\arrow@width{-\pm@shift\box@height}% + \divide\arrow@width by 100% + \setlength\arrow@width{\b@r@stretch\arrow@width}% + \fi% + \loop% + \expandafter\get@firstv@l\fill@char% + \ifx\second@@\N@\hbox to \box@width{\hss}% + \else\relax% + \ifx\frame@color\back@color% + \else% + \setlength\arrow@height{\b@r@stretch\box@height}% + \hbox to \box@width{\hss{\textcolor{\back@color}% + {\vrule height\arrow@height width\box@width}}\hss}% + \kern-\box@width% + \fi% + \ifx\T@coffee@bcons\y@% + \ifnum\second@@=99 \xdef\second@@{0}\fi% + \fi + \setlength\arrow@height{\second@@\box@height}% + \ifx\T@coffee@bcons\y@% + \setlength\arrow@height{11\arrow@height}% + \fi + \divide\arrow@height by 100\relax% + \setlength\arrow@height{\b@r@stretch\arrow@height}% + \ifdim\arrow@height<0pt% + \arrow@height=-\arrow@height% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\frame@color}% + {\vrule depth\arrow@height width0.8\box@width}}\hss}}% + \else% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\frame@color}% + {\vrule height\arrow@height width0.8\box@width}}\hss}}\fi% + \kern-\box@width% + \raisebox{\arrow@width}{\textcolor{Black}% + {\vrule height0.25pt depth0.25pt width\box@width}}% + \fi + \ifx\fill@char\ampers@nd\else\repeat% + \else% + \xdef\last@{helix}% + \ifx\second@@\last@% + \fontfamily{cmr}% + \fontseries{m}% + \fontshape{it}% + \selectfont% + \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi% + \kern0.15\box@width% + \setbox1=\hbox{\ensuremath{\helixhook}\kern-1.13exo\kern-1.02ex}% + \arrow@width=\second@\box@width% + \divide\arrow@width by \wd1% + \arrow@width=2\wd1% + \loop% + \textcolor{\f@color}{\raisebox{-0.25ex}{\ensuremath{\helixhook}}% + \kern-1.13ex\raisebox{0.3ex}{o}}\kern-1.02ex% + \advance\arrow@width by \wd1\relax% + \ifdim\arrow@width<\second@\box@width \repeat% + \textcolor{\f@color}{\raisebox{-0.25ex}{\ensuremath{\helixhook}}}% + \else% + \xdef\last@{box}% + \ifx\second@@\last@% + \fontfamily{\featurestyles@family}% + \fontseries{\featurestyles@series}% + \fontshape{\featurestyles@shape}% + \selectfont% + \kern-\second@\box@width% + \bgroup% + \textcolor{\back@color}{% + \vrule width\second@\box@width height\box@height depth\box@depth}% + \kern-\second@\box@width% + \fboxsep-\rule@@thick\fboxrule\rule@@thick% + \textcolor{\frame@color}{% + \fbox{\makebox[\second@\box@width]% + {\vrule\@height\box@height\@depth\box@depth \@width\z@}}}% + \egroup% + \setbox1=\hbox{\residues@size{\fill@char}}% + \temp@count=\wd1 \xdef\wd@{\the\temp@count}% + \width@tmp=\second@\box@width% + \temp@count=\width@tmp% + \xdef\sb@{\the\temp@count}% + \ifnum\wd@>\sb@ \xdef\fill@char{}\fi% + \hbox to -\second@\box@width{\hss\textcolor{\f@color}% + {\residues@size{\fill@char}}\hss}% + \else% + \expandafter\get@shape\second@@% + \xdef\last@{arrow}% + \ifx\second@@\last@% + \kern-0.75\box@width% + \ifx\bottop@\temp@ \xdef\last@{0.35}\else\xdef\last@{-0.55}\fi% + \textcolor{\f@color}{% + \raisebox{\last@\arrow@height}{% + \if\first@@ b \xdef\first@@{,}\fi% + \if\first@@ ,% + \rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height% + \else% + \if\first@@ |% + \rule{0.1\arrow@height}{2\arrow@height}\kern-0.35\arrow@height% + \else% + \if\first@@ `\xdef\first@@{'}\fi% + \if\first@@ '% + \rule[\arrow@height]% + {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height% + \else% + \if\first@@ '% + \rule[\arrow@height]% + {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height% + \else% + \if\first@@ -% + \rule{0pt}{0pt}\kern-0.35\arrow@height% + \fi% + \fi% + \fi% + \fi% + \fi% + \if\third@@ v% + \if\first@@ v% + \ensuremath{\overleftarrow{\hbox to % + \second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% + \kern-\arrow@width% + \ensuremath{\overrightarrow{\hbox% + {\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \ensuremath{\overrightarrow{\hbox to % + \second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% + \fi% + \else% + \if\first@@ v% + \ensuremath{\overleftarrow{\hbox to % + \second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% + \else + \kern0.35\arrow@height% + \rule[0.9\arrow@height]{\second@\box@width}{0.1\arrow@height}% + \kern0.35\arrow@height% + \fi + \if\third@@ ,% + \kern-0.4\arrow@height\rule{0.1\arrow@height}{\arrow@height}% + \else% + \if\third@@ |% + \kern-0.4\arrow@height\rule{0.1\arrow@height}{2\arrow@height}% + \else% + \if\third@@ `\xdef\third@@{'}\fi% + \if\third@@ '% + \kern-0.4\arrow@height% + \rule[\arrow@height]{0.1\arrow@height}{\arrow@height}% + \fi% + \fi% + \fi% + \fi}}% + \else% + \xdef\last@{doublearrow}% + \ifx\second@@\last@% + \setbox1=\hbox{\ensuremath{\Rightarrow}}% + \arrow@height=\ht1% + \arrow@width=\wd1% + \setbox1=\hbox to \second@\box@width{}% + \width@tmp=\wd1% + \kern-0.75\box@width% + \xdef\temp@{top}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\temp@{ttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\temp@{tttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\temp@{ttttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\last@{-0.25}\fi\fi\fi\fi% + \textcolor{\f@color}{% + \raisebox{\last@\arrow@height}{% + \if\first@@ b \xdef\first@@{,}\fi% + \if\first@@ ,% + \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% + \kern-0.1\arrow@height% + \else% + \if\first@@ |% + \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}% + \kern-0.1\arrow@height% + \else% + \if\first@@ a \xdef\first@@{'}\fi% + \if\first@@ ` \xdef\first@@{'}\fi% + \if\first@@ '% + \rule[0.4\arrow@height]% + {0.1\arrow@height}{1.5\arrow@height}% + \kern-0.1\arrow@height% + \else% + \if\first@@ <% + \ensuremath{\Leftarrow}\kern-0.5\arrow@width% + \advance\width@tmp by -0.5\arrow@width + \else + \rule{0pt}{0pt}% + \fi% + \fi% + \fi% + \fi% + \if\third@@ >% + \advance\width@tmp by -0.5\arrow@width% + \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}% + \kern-\width@tmp% + \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}% + \kern-0.5\arrow@width\ensuremath{\Rightarrow}% + \else% + \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}% + \kern-\width@tmp% + \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}% + \if\first@@ b \xdef\first@@{,}\fi% + \if\third@@ ,% + \kern-0.05\arrow@height% + \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% + \else% + \if\third@@ |% + \kern-0.05\arrow@height% + \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}% + \else% + \if\first@@ a \xdef\first@@{'}\fi% + \if\third@@ ` \xdef\third@@{'}\fi% + \if\third@@ '% + \kern-0.05\arrow@height% + \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% + \else% + \if\third@@ a% + \kern-0.05\arrow@height% + \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% + \fi% + \fi% + \fi% + \fi% + \fi}}% + \else + \loopcount=0\relax% + \width@tmp=\arrow@height% + \temp@@length=\rule@@thick% + \advance\width@tmp by -0.5\temp@@length% + \if\first@@ o\xdef\first@@{O}\fi% + \if\third@@ o\xdef\third@@{O}\fi% + \xdef\last@{bottom}% + \ifx\fe@turep@s\last@% + \vspace{-20pt}\message{(((-20pt)))}% + \fi% + \textcolor{\f@color}{% + \if\first@@ ,% + \rule{\temp@@length}{\arrow@height}\kern-\temp@@length% + \else% + \if\first@@ b% + \xdef\last@{bottom}% + \ifx\fe@turep@s\last@% + \rule{\temp@@length}{\arrow@height}\kern-\temp@@length% + \else + \xdef\shift@feature{y}% + \kern-\temp@@length% + \rule[-\bar@length]{\temp@@length}{\bar@length}% + \kern-\temp@@length% + \rule{\temp@@length}{\arrow@height}\kern-\temp@@length% + \fi + \else% + \if\first@@ |% + \rule{\temp@@length}{2\arrow@height}\kern-\temp@@length% + \else% + \if\first@@ O% + \raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex% + \rule[\width@tmp]{0.65ex}{\temp@@length}% + \else% + \if\first@@ S% + \xdef\last@{bottom}% + \ifx\fe@turep@s\last@% + \advance\width@tmp by 0.5\temp@@length% + \kern0.5\box@width% + \kern-2\temp@@length% + \rule[\width@tmp]{\temp@@length}{\arrow@height}% + \advance\width@tmp by -0.5\temp@@length% + \kern-\temp@@length% + \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% + \rule[\width@tmp]{0.5\box@width}{\temp@@length}% + \else% + \kern0.5\box@width% + \kern-2\temp@@length% + \rule{\temp@@length}{\arrow@height}% + \kern-\temp@@length% + \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% + \rule[\width@tmp]{0.5\box@width}{\temp@@length}% + \fi% + \else% + \if\first@@ c% + \xdef\last@{bottom}% + \ifx\fe@turep@s\last@% + \advance\width@tmp by 0.5\temp@@length% + \raisebox{\arrow@height}{\rule[\box@height]{0pt}{\bar@length}}%%%%%%%%%%%%%%%%%%%%%%% + \kern0.5\box@width% + \kern-2\temp@@length% + \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%% + \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%% + \rule[\width@tmp]{\temp@@length}{\arrow@height}% + \advance\width@tmp by -0.5\temp@@length% + \kern-\temp@@length% + \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% + \rule[\width@tmp]{0.5\box@width}{\temp@@length}% + \else% + \xdef\shift@feature{y}% + \kern0.5\box@width% + \kern-2\temp@@length% + \rule[-\bar@length]{\temp@@length}{\bar@length}% + \kern-\temp@@length% + \rule{\temp@@length}{\arrow@height}% + \kern-\temp@@length% + \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% + \rule[\width@tmp]{0.5\box@width}{\temp@@length}% + \fi% + \else% + \if\first@@ <% + \raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex% + \else + \if\first@@ `\xdef\first@@{'}\fi% + \if\first@@ '% + \advance\width@tmp by 0.5\temp@@length% + \rule[\width@tmp]{\temp@@length}{\arrow@height}\kern-\temp@@length% + \advance\width@tmp by -0.5\temp@@length% + \fi% + \fi% + \fi% + \fi% + \fi% + \fi% + \fi% + \fi% + \loopcount=\second@% + \if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\first@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\third@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\first@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\third@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \xdef\second@{\the\loopcount}% + \rule[\width@tmp]{\second@\box@width}{\temp@@length}% + \setbox1=\hbox{\residues@size{\fill@char}}% + \kern-\second@\box@width% + \hbox to \second@\box@width{\textcolor{\backtext@color}{\hss\rule[\width@tmp]{1.2\wd1}{\temp@@length}\hss}}% + \kern-\second@\box@width% + \hbox to \second@\box@width{\textcolor{\frame@color}{\residues@size{\hss\fill@char\hss}}}% + \if\third@@ ,% + \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% + \else% + \if\third@@ b% + \xdef\last@{bottom}% + \ifx\fe@turep@s\last@% + \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% + \else + \xdef\shift@feature{y}% + \kern-\temp@@length% + \rule[-\bar@length]{\temp@@length}{\bar@length}% + \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% + \fi + \else% + \if\third@@ |% + \kern-\temp@@length\rule{\temp@@length}{2\arrow@height}% + \else% + \if\third@@ O% + \rule[\width@tmp]{0.65ex}{\temp@@length}% + \kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}% + \else% + \if\third@@ S% + \rule[\width@tmp]{0.5\box@width}{\temp@@length}% + \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% + \xdef\last@{bottom}% + \ifx\fe@turep@s\last@% + \advance\width@tmp by 0.5\temp@@length% + \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}% + \else + \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% + \fi% + \else% + \if\third@@ c% + \xdef\shift@feature{y}% + \rule[\width@tmp]{0.5\box@width}{\temp@@length}% + \xdef\last@{bottom}% + \ifx\fe@turep@s\last@% + \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%% + \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%% + \advance\width@tmp by 0.5\temp@@length% + \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}% + \else + \kern-\temp@@length\rule[-\bar@length]{\temp@@length}{\bar@length}% + \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% + \fi% + \else% + \if\third@@ >% + \kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}% + \else + \if\third@@ `\xdef\third@@{'}\fi% + \if\third@@ '% + \advance\width@tmp by 0.5\temp@@length% + \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}% + \fi% + \fi% + \fi% + \fi% + \fi% + \fi% + \fi% + \fi}% + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi +} +\def\next@featuretext#2;#3@{% + \xdef\first@{#3@}% + \xdef\last@{fill:#2:&}\expandafter\test@fill\last@% + \ifx\f@color\comm@\xdef\f@color{Black}\fi% + \fontfamily{\featuretext@family}% + \fontseries{\featuretext@series}% + \fontshape{\featuretext@shape}% + \selectfont% + \xdef\last@{translate}% + \ifx\last@\second@@% + \xdef\fill@char{\fill@char &}% + \if\seq@type N + \loop% + \expandafter\get@firstfill\fill@char% + \if\second@@ -\def\second@@{\hss}\fi% + \hbox to \box@width{\hss\textcolor{\f@color}{% + \featuretext@size{\strut\second@@}}\hss}% + \ifx\fill@char\ampers@nd\else\repeat% + \else + \hbox to #1\box@width{\hss% + \temp@count=1% + \loop% + \expandafter\get@tripletfill\fill@char% + \if\second@@ -\ifnum\tr@nstextstyle>0\hbox to \box@width{\hss}\fi% + \else% + \ifcase\tr@nstextstyle% + \hbox{\transtext@size\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\,\hss}}% + \or% + \ifnum\temp@count=1% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% + \else% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}}% + \fi% + \or% + \ifnum\temp@count=1% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss}}}% + \else% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\hss}}% + \hbox to \box@width{\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\hss}}}% + \fi% + \or% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% + \or% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@\hss}}}% + \fi% + \fi% + \ifx\fill@char\ampers@nd\else\repeat% + \hss} + \fi% + \else% + \textcolor{\f@color}{% + \hbox to #1\box@width{\hss\featuretext@size{\strut\fourth@}\hss}}% + \fi% + \advance\loopcount by -#1% +} +\def\put@featuretext{% + \if\first@ @% + \else + \expandafter\next@featuretext\first@% + \put@featuretext% + \fi} +\def\next@featurestyle#2;#3@{% + \xdef\first@{#2}% + \xdef\second@{#1}% + \ifx\first@\ampers@nd \hbox to \second@\box@width{\hss}% + \else% + \hbox to \second@\box@width% + {\hss\expandafter\putfeature@style{\first@}\hss}\fi% + \xdef\first@{#3@}% + \advance\loopcount by -\second@% +} +\def\put@featurestyle{% + \if\first@ @% + \else + \expandafter\next@featurestyle\first@% + \put@featurestyle% + \fi +} +\def\put@feature{% + \vspace{-\baselineskip}% + \newline\hbox{}% + \xdef\temp@{ttttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else% + \xdef\temp@{tttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else% + \xdef\temp@{ttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else% + \xdef\temp@{top}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \fi\fi\fi\fi% + \newline\hbox{}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else% + \xdef\temp@{ttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \xdef\temp@{tttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \xdef\temp@{ttttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \fi\fi\fi\fi% + \newline\hbox{}% +} +\def\put@@@frame#1{% + \xdef\last@{#1[,]&}\expandafter\opt@color\last@% + \xdef\second@@{\fourth@}% + \ifx\f@color\comm@% + \xdef\third@@{0.2\box@width}% + \else% + \xdef\third@@{\f@color}% + \fi% + \setlength\arrow@width{\temp@@length}% + \advance\arrow@width by -\third@@% + \textcolor{\second@@}{% + \rule{\second@\box@width}{\third@@}% + \kern-\second@\box@width% + \rule{\third@@}{\arrow@width}% + \kern-\third@@% + \rule[\arrow@width]{\second@\box@width}{\third@@}% + \kern-\third@@% + \rule{\third@@}{\arrow@width}}% +} +\def\next@frame#2;#3@{% + \xdef\first@{#2}% + \xdef\second@{#1}% + \ifx\first@\ampers@nd \hbox to \second@\box@width{\hss}% + \else% + \expandafter\put@@@frame{\first@}% + \fi% + \xdef\first@{#3@}% +} +\def\put@@frame{% + \if\first@ @% + \else + \expandafter\next@frame\first@% + \put@@frame% + \fi% +} +\def\put@frame{% + \ifx\hide@seqs\n@% + \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi% + \temp@count=\seq@count% + \ifx\hide@seqs\y@ + \advance\temp@count by -1 + \else + \loopcount=1% + \xdef\first@{true}% + \loop% + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@% + \advance\temp@count by -1\fi% + \advance\loopcount by 1% + \ifnum\loopcount>\seq@count\else\repeat% + \fi + \ifnum\temp@count>0% + \setlength\temp@@length{\box@height}% + \advance\temp@@length by \box@depth% + \setlength\arrow@height{0.5\temp@@length}% + \setlength\temp@@length{\temp@count\temp@@length}% + \advance\temp@@length by \arrow@height% + \setlength\arrow@width{\sep@space}% + \setlength\arrow@width{\seq@gap@num\arrow@width}% + \advance\temp@@length by \arrow@width% + \vspace{\arrow@height}% + \vspace{-\temp@@length}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\styleframe @}% + \put@@frame% + \vspace{-\arrow@height}% + \ifshow@cons\ifnum\cons@top=1 \vspace{\baselineskip}\fi\fi% + \newline\hbox{}% + \fi% + \fi% +} +\def\decimal@A#1#2@{% + \def\decimal@AB##1##2@{\xdef\temp@{##1.##2}}% + \xdef\temp@@{#1}% + \xdef\temp@{#2@}% + \expandafter\decimal@AB\temp@% + \xdef\temp@{\temp@@\temp@}% +} +\def\decimal@B#1#2@{\xdef\temp@{#1.#2}} +\def\decimal@C#1#2@{\xdef\temp@{0.#1#2}} +\def\decimal@D#1#2@{\xdef\temp@{0.0#1#2}} +\def\decimal@E#1#2@{\xdef\temp@{0.00#1#2}} +\def\correct@CGSO{% + \setlength\temp@@length{0.12\logo@height}% + \multiply\temp@@length by \third@ % + \if\seq@type P % + \divide\temp@@length by 4322 % + \else% + \divide\temp@@length by 4000 % + \fi% + \loopcount=\third@% + \multiply\loopcount by 94 % + \divide\loopcount by 100 % + \xdef\third@{\the\loopcount}% +} +\def\correct@Q{% + \setlength\temp@@length{0.063\logo@height}% + \multiply\temp@@length by \third@% + \if\seq@type P % + \divide\temp@@length by 4322 % + \else% + \divide\temp@@length by 4000 % + \fi% + \multiply\temp@@length by 10 % + \loopcount=\third@% + \multiply\loopcount by 83 % + \divide\loopcount by 100 % + \xdef\third@{\the\loopcount}% +} +\def\correct@JUV{% + \setlength\temp@@length{0.12\logo@height}% + \multiply\temp@@length by \third@ % + \if\seq@type P % + \divide\temp@@length by 4322 % + \else% + \divide\temp@@length by 4000 % + \fi% + \loopcount=\third@% + \multiply\loopcount by 97 % + \divide\loopcount by 100 % + \xdef\third@{\the\loopcount}% +} +\def\next@logo#1:#2,#3@{% + \xdef\first@{#1}\xdef\second@{#2}\xdef\last@{#3}% + \ifx\first@\ampers@nd% + \ifx\clear@logo\n@% + \ifx\hide@sig\n@% + \expandafter\firstchar@get\sublogo@sig% + \xdef\sublogo@sig{\third@}% + \ifx\first@\y@% + \loopcount=\temp@count% + \ifnum\loopcount<0 \loopcount=0\fi% + \xdef\fourth@{\the\loopcount @}% + \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% + \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% + \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% + \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% + \expandafter\decimal@E\fourth@% + \fi\fi\fi\fi% + \raisebox{\temp@\logo@height}{% + \hbox to \box@width{\textcolor{\sig@color}{\hss\residues@size{\sig@char}\hss}}}% + \kern-\box@width% + \fi% + \fi% + \fi% + \temp@count=0% + \kern\box@width% + \advance\outerloopcount by 1 % + \else% + \ifnum#2=1% + \temp@count=0% + \else% + \if\seq@type N% + \loopcount=\second@% + \multiply\loopcount by 2% + \xdef\second@{\the\loopcount}% + \fi% + \xdef\third@{\second@}% + \if\first@ C\correct@CGSO \else% + \if\first@ G\correct@CGSO \else% + \if\first@ S\correct@CGSO \else% + \if\first@ O\correct@CGSO \else% + \if\first@ Q\correct@Q \else% + \if\first@ J\correct@JUV \else% + \if\first@ U\correct@JUV \else% + \if\first@ V\correct@JUV \else% + \setlength\temp@@length{0pt}% + \fi\fi\fi\fi\fi\fi\fi\fi% + \loopcount=\third@ + \multiply\loopcount by \logo@stretch@IOOO% + \ifnum\loopcount>0 % + \divide\loopcount by 1000 \xdef\fl@g{}% + \xdef\tint@{}% + \else% + \divide\loopcount by -1000 \xdef\fl@g{-}% + \xdef\tint@{\sublogo@tint}% + \fi% + \ifnum\loopcount=0\relax\loopcount=1\relax\fi + \xdef\third@{\the\loopcount @}% + \ifnum\loopcount>9999 \expandafter\decimal@A\third@ \else% + \ifnum\loopcount>999 \expandafter\decimal@B\third@ \else% + \ifnum\loopcount>99 \expandafter\decimal@C\third@ \else% + \ifnum\loopcount>9 \expandafter\decimal@D\third@ \else% + \expandafter\decimal@E\third@% + \fi\fi\fi\fi% + \xdef\third@{\fl@g\temp@}% + \ifnum\temp@count<0 % + \ifnum\second@<0 \else\temp@count=0 \fi% + \fi% + \ifnum\temp@count>0 % + \loopcount=\temp@count \xdef\fl@g{}% + \else + \loopcount=-\temp@count \xdef\fl@g{-}% + \fi% + \xdef\fourth@{\the\loopcount @}% + \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% + \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% + \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% + \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% + \expandafter\decimal@E\fourth@% + \fi\fi\fi\fi% + \xdef\fourth@{\fl@g\temp@}% + \if\first@ W% + \hbox to \box@width{\hss% + \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch@W}[\third@]% + {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{W}\hss}}}}}\hss}% + \kern-\box@width% + \else% + \hbox to \box@width{\hss% + \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch}[\third@]% + {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}\hss}% + \kern-\box@width% + \fi% + \advance\temp@count by \second@% + \fi% + \fi% + \xdef\temp@{\last@.}% + \ifx\temp@\d@t% + \else% + \xdef\last@{#3@}% + \ifnum\outerloopcount>\res@perline% + \else + \expandafter\next@logo\last@% + \fi% + \fi% +} + +\def\put@logo{% + \ifx\clear@logo\y@% + \ifnum\logo@top=1 % + \vspace{-0.5\baselineskip}% + \else + \vspace{-0.75\baselineskip}% + \fi% + \else% + \ifnum\sublogo@top=1 % + \vspace{-0.5\baselineskip}% + \else + \vspace{-0.75\baselineskip}% + \fi% + \fi% + \newline\hbox{}% + \ifnames@right% + \else% + \fontfamily{\namestext@family}\fontseries{\namestext@series}\fontshape{\namestext@shape}% + \selectfont% + \ifnames@ + \textcolor{\names@fg}{% + \raisebox{2\logo@height}{\hbox to \name@width{\namestext@size{\logo@name}\hss}}% + \ifx\clear@logo\n@ + \ifx\hide@negatives\n@% + \kern-\name@width\raisebox{-3\logo@height}{\hbox to \name@width{\namestext@size{\sublogo@name@neg}\hss}}% + \fi% + \fi}% + \fi% + \fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \fontfamily{cmss}\fontseries{m}\fontshape{n}\selectfont% + \ifx\show@logoscale\n@% + \if\seq@type P% + \ifnum\corr@max>600\relax% + \rule[5.4\logo@height]{0pt}{0pt}% + \else% + \rule[4.4\logo@height]{0pt}{0pt}% + \fi% + \else% + \rule[4.0688\logo@height]{0pt}{0pt}% + \fi% + \else% + \xdef\first@{right}% + \ifx\show@logoscale\first@% + \else% + \textcolor{\logo@scalecol}{% + \kern-0.7\box@width% + \rule[-0.05\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[2\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[4\logo@height]{0.4\box@width}{0.1\box@width}% + \if\seq@type P% + \kern-0.4\box@width% + \rule[1\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[3\logo@height]{0.4\box@width}{0.1\box@width}% + \ifnum\corr@max>600\relax% + \kern-0.4\box@width\rule[5\logo@height]{0.4\box@width}{0.1\box@width}\fi% + \setbox1=\hbox{\bottomruler@size 2}% + \kern-1.2\box@width% + \ifdim\logo@height>1.25\ht1 \relax% + \raisebox{-0.5\ht1}{\raisebox{1\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 1}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{3\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 3}}}% + \kern-0.6\box@width% + \ifnum\corr@max>600\relax% + \raisebox{-0.5\ht1}{\raisebox{5\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 5}}}% + \kern-0.6\box@width% + \fi + \fi + \raisebox{-0.5\ht1}{\raisebox{2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 2}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 4}}}% + \kern0.6\box@width% + \ifnum\corr@max>600\relax% + \rule[5.4\logo@height]{0pt}{0pt}% + \else + \rule[4.4\logo@height]{0pt}{0pt}% + \fi + \else% + \setbox1=\hbox{\bottomruler@size 2}% + \kern-1.2\box@width% + \raisebox{-0.5\ht1}{\raisebox{2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 1}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 2}}}% + \kern0.6\box@width% + \rule[4.0688\logo@height]{0pt}{0pt}% + \fi% + \kern-0.1\box@width% + \ifnum\corr@max>600\relax% + \rule{0.1\box@width}{5\logo@height}% + \else% + \rule{0.1\box@width}{4\logo@height}% + \fi% + \ifx\clear@logo\n@% + \ifx\hide@negatives\n@% + \kern-0.4\box@width% + \rule[-2\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[-4\logo@height]{0.4\box@width}{0.1\box@width}% + \if\seq@type P% + \kern-0.4\box@width% + \rule[-\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[-3\logo@height]{0.4\box@width}{0.1\box@width}% + \ifnum\corr@max>600\relax% + \kern-0.4\box@width\rule[-5\logo@height]{0.4\box@width}{0.1\box@width}\fi% + \setbox1=\hbox{\bottomruler@size 2}% + \kern-1.2\box@width% + \ifdim\logo@height>1.25\ht1 \relax% + \raisebox{-0.5\ht1}{\raisebox{-\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -1}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{-3\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -3}}}% + \kern-0.6\box@width% + \ifnum\corr@max>600\relax% + \raisebox{-0.5\ht1}{\raisebox{-5\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -5}}}% + \kern-0.6\box@width% + \fi + \fi + \raisebox{-0.5\ht1}{\raisebox{-2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -2}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{-4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -4}}}% + \kern0.6\box@width% + \ifnum\corr@max>600\relax% + \rule[-5.4\logo@height]{0pt}{0pt}% + \else + \rule[-4.4\logo@height]{0pt}{0pt}% + \fi + \else% + \setbox1=\hbox{\bottomruler@size 2}% + \kern-1.2\box@width% + \raisebox{-0.5\ht1}{\raisebox{-2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -1}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{-4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -2}}}% + \kern0.6\box@width% + \rule[-4.0688\logo@height]{0pt}{0pt}% + \fi% + \kern-0.1\box@width% + \ifnum\corr@max>600\relax% + \rule[-5\logo@height]{0.1\box@width}{5\logo@height}% + \else% + \rule[-4\logo@height]{0.1\box@width}{4\logo@height}% + \fi% + \fi% + \fi + \kern0.3\box@width}% + \fi% + \fi% + \temp@count=0% + \outerloopcount=1 \expandafter\next@logo\last@% + \ifx\clear@logo\n@% + \ifx\hide@negatives\n@% + \textcolor{\logo@scalecol}{% + \kern-\res@perline\box@width\rule[-0.03\box@width]{\res@perline\box@width}{0.06\box@width}}% + \fi% + \fi% + \def\@kern{\kern1em}% + \ifx\show@logoscale\n@% + \else% + \xdef\first@{left}% + \ifx\show@logoscale\first@% + \kern0.1\box@width% + \else% + \def\@kern{\kern2em}% + \textcolor{\logo@scalecol}{% + \kern0.3\box@width% + \rule[-0.05\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[2\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[4\logo@height]{0.4\box@width}{0.1\box@width}% + \if\seq@type P% + \kern-0.4\box@width% + \rule[1\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[3\logo@height]{0.4\box@width}{0.1\box@width}% + \ifnum\corr@max>600\relax% + \kern-0.4\box@width\rule[5\logo@height]{0.4\box@width}{0.1\box@width}\fi% + \setbox1=\hbox{\bottomruler@size 2}% + \kern0.2\box@width% + \ifdim\logo@height>1.25\ht1 \relax% + \raisebox{-0.5\ht1}{\raisebox{1\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 1 \hss}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{3\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 3 \hss}}}% + \kern-0.6\box@width% + \ifnum\corr@max>600\relax% + \raisebox{-0.5\ht1}{\raisebox{5\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 5 \hss}}}% + \kern-0.6\box@width% + \fi + \fi + \raisebox{-0.5\ht1}{\raisebox{2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 2 \hss}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 4 \hss}}}% + \kern-0.8\box@width% + \ifnum\corr@max>600\relax% + \rule[5.4\logo@height]{0pt}{0pt}% + \else + \rule[4.4\logo@height]{0pt}{0pt}% + \fi + \else% + \setbox1=\hbox{\bottomruler@size 2}% + \kern0.2\box@width% + \raisebox{-0.5\ht1}{\raisebox{2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 1 \hss}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 2 \hss}}}% + \kern-0.8\box@width% + \rule[4.0688\logo@height]{0pt}{0pt}% + \fi% + \kern-0.4\box@width% + \ifnum\corr@max>600\relax% + \rule{0.1\box@width}{5\logo@height}% + \else% + \rule{0.1\box@width}{4\logo@height}% + \fi% + \ifx\clear@logo\n@% + \ifx\hide@negatives\n@% + \kern-0.1\box@width% + \rule[-2\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[-4\logo@height]{0.4\box@width}{0.1\box@width}% + \if\seq@type P% + \kern-0.4\box@width% + \rule[-\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% + \rule[-3\logo@height]{0.4\box@width}{0.1\box@width}% + \ifnum\corr@max>600\relax% + \kern-0.4\box@width\rule[-5\logo@height]{0.4\box@width}{0.1\box@width}\fi% + \setbox1=\hbox{\bottomruler@size 2}% + \kern0.2\box@width% + \ifdim\logo@height>1.25\ht1 \relax% + \raisebox{-0.5\ht1}{\raisebox{-\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -1 \hss}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{-3\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -3 \hss}}}% + \kern-0.6\box@width% + \ifnum\corr@max>600\relax% + \raisebox{-0.5\ht1}{\raisebox{-5\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -5 \hss}}}% + \kern-0.6\box@width% + \fi + \fi + \raisebox{-0.5\ht1}{\raisebox{-2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -2 \hss}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{-4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -4 \hss}}}% + \kern-0.8\box@width% + \ifnum\corr@max>600\relax% + \rule[-5.4\logo@height]{0pt}{0pt}% + \else + \rule[-4.4\logo@height]{0pt}{0pt}% + \fi + \else% + \setbox1=\hbox{\bottomruler@size 2}% + \kern0.2\box@width% + \raisebox{-0.5\ht1}{\raisebox{-2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -1 \hss}}}% + \kern-0.6\box@width% + \raisebox{-0.5\ht1}{\raisebox{-4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -2 \hss}}}% + \kern-0.8\box@width% + \rule[-4.0688\logo@height]{0pt}{0pt}% + \fi% + \kern-0.4\box@width% + \ifnum\corr@max>600\relax% + \rule[-5\logo@height]{0.1\box@width}{5\logo@height}% + \else% + \rule[-4\logo@height]{0.1\box@width}{4\logo@height}% + \fi% + \fi% + \fi% + \kern-0.3\box@width}% + \fi% + \fi% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\def\@kern{\kern1em}\fi\fi% + \ifnames@right% + \fontfamily{\namestext@family}\fontseries{\namestext@series}\fontshape{\namestext@shape}% + \selectfont% + \ifnames@ + \textcolor{\names@fg}{% + \raisebox{2\logo@height}{\hbox to \name@width{\namestext@size{\@kern\logo@name}\hss}}% + \ifx\clear@logo\n@ + \ifx\hide@negatives\n@% + \kern-\name@width\raisebox{-3\logo@height}{\hbox to \name@width{\namestext@size{\@kern\sublogo@name@neg}\hss}}% + \fi% + \fi}% + \fi% + \fi% + \ifx\clear@logo\y@\xdef\stack@sequencelogo{}% + \else% + \ifx\hide@negatives\n@ \newline\hbox{}\fi% + \fi% + \newline\hbox{}% +} + +\def\set@lines{% + \pos@count=1 + \xdef\frame@pos{1}\xdef\bar@pos{0}% + \xdef\featurepostop{1} \xdef\featureposbottom{1}% + \xdef\featureposttop{1} \xdef\featureposbbottom{1}% + \xdef\featurepostttop{1} \xdef\featureposbbbottom{1}% + \xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}% + \findc@nsensus% + \noindent% + \setlength{\bar@length}{0pt}% + \xdef\fe@turep@s{top}% + \ifnum\feature@ttttop=1 + \advance\bar@length by \feature@tttop\baselineskip% + \advance\bar@length by \feature@ttop\baselineskip% + \advance\bar@length by \feature@top\baselineskip% + \multiply\bar@length by 2% + \advance\bar@length by \tttt@sp@ce% + \advance\bar@length by \ttt@sp@ce% + \advance\bar@length by \tt@sp@ce% + \ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi + \xdef\bottop@{ttttop}% + \xdef\shift@feature{n}% + \put@feature% + \advance\bar@length by -\baselineskip% + \ifx\shift@feature\y@ \vspace{-\bar@length}\fi% + \setlength{\bar@length}{0pt}% + \vspace{\tttt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi + \ifnum\feature@tttop=1 + \advance\bar@length by \feature@ttop\baselineskip% + \advance\bar@length by \feature@top\baselineskip% + \multiply\bar@length by 2% + \advance\bar@length by \ttt@sp@ce% + \advance\bar@length by \tt@sp@ce% + \ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi + \xdef\bottop@{tttop}% + \xdef\shift@feature{n}% + \put@feature% + \advance\bar@length by -\baselineskip% + \ifx\shift@feature\y@ \vspace{-\bar@length}\fi% + \setlength{\bar@length}{0pt}% + \vspace{\ttt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi + \ifnum\feature@ttop=1 + \advance\bar@length by \feature@top\baselineskip% + \multiply\bar@length by 2% + \advance\bar@length by \tt@sp@ce\message{tt\the\bar@length tt}% + \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi + \xdef\bottop@{ttop}% + \xdef\shift@feature{n}% + \put@feature% + \advance\bar@length by -\baselineskip% + \ifx\shift@feature\y@ \vspace{-\bar@length}\fi% + \setlength{\bar@length}{0pt}% + \vspace{\tt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\ifttopfeature \vspace{\tt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi + \ifnum\feature@top=1 + \ifnum\featureontop=0 \xdef\feature@top{0} \fi + \xdef\bottop@{top}% + \put@feature% + \vspace{\t@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\iftopfeature \vspace{\t@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi + \ifnum\rule@num<0 \else \ifnum\rule@top=0 \loopcount=0 \put@ruler \fi\fi + \ifshow@logo\ifnum\logo@top=0 + \xdef\last@{\stack@sequencelogo @}% + \ifx\logo@name@user\ampers@nd\xdef\logo@name{logo}\else\xdef\logo@name{\logo@name@user}\fi + \xdef\clear@logo{y}% + \put@logo% + \xdef\clear@logo{n}% + \fi\fi + \ifshow@sublogo\ifnum\sublogo@top=0 + \read@sublogo% + \xdef\last@{\stack@sublogo @}% + \ifx\sublogo@name@user\ampers@nd\xdef\logo@name{subfamily}\else\xdef\logo@name{\sublogo@name@user}\fi + \put@logo% + \fi\fi + \set@consensus + \ifshow@cons\ifnum\cons@top=0 + \xdef\cons@now{y}% + \xdef\first@{\consensus @}% + \xdef\first@@@{\c@nscol @}% + \loopcount=0\relax% + \put@line% + \xdef\c@nscol{}% + \xdef\cons@now{no}% + \fi\fi + \ifx\hide@seqs\n@% + \loopcount=0 % + \loop + \advance\loopcount by 1 % + \xdef\second@{\csname hide@seq\the\loopcount\endcsname}% + \xdef\first@{noshade}\nosh@defalse% + \ifx\second@\first@ \nosh@detrue \xdef\second@{false}\fi + \xdef\first@{false}% + \ifx\second@\first@ + \ifnames@right + \ifnumbers@right + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + \csname res@count\the\loopcount\endcsname)% + <\csname newseqname\the\loopcount\endcsname>}% + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + <\csname newseqname\the\loopcount\endcsname>}% + \fi + \else + \ifnumbers@right + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + \csname res@count\the\loopcount\endcsname)}% + \fi + \fi + \xdef\first@{\csname seq\the\loopcount\endcsname @}% + \expandafter\ifx\csname seq@gap\the\loopcount\endcsname\yes% + \ifnum\finger@linenum=0\seq@skip% + \else% + \ifnum\loopcount<\seq@count\seq@skip\fi% + \fi% + \fi% + \put@line% + \fi% + \ifnum\loopcount<\seq@count\repeat% + \fi% + \ifshow@cons\ifnum\cons@top=1 % + \xdef\cons@now{y}% + \xdef\first@{\consensus @}% + \xdef\first@@@{\c@nscol @}% + \loopcount=0\relax% + \put@line% + \xdef\c@nscol{}% + \xdef\cons@now{no}% + \fi\fi% + \ifnum\frame@=1 % + \ifnum\frame@on=0 \xdef\frame@{0}\fi% + \put@frame% + \fi% + \ifshow@logo\ifnum\logo@top=1 % + \xdef\last@{\stack@sequencelogo @}% + \ifx\logo@name@user\ampers@nd\xdef\logo@name{logo}\else\xdef\logo@name{\logo@name@user}\fi + \xdef\clear@logo{y}% + \put@logo% + \xdef\clear@logo{n}% + \fi\fi% + \ifshow@sublogo\ifnum\sublogo@top=1 + \read@sublogo% + \xdef\last@{\stack@sublogo @} + \ifx\sublogo@name@user\ampers@nd\xdef\logo@name{subfamily}\else\xdef\logo@name{\sublogo@name@user}\fi + \put@logo% + \fi\fi% + \ifnum\rule@num<0 % + \else% + \ifnum\rule@top=1 % + \loopcount=0\relax% + \ifnum\ruler@rot=0 % + \else \vspace{\ruler@width}\vspace{-1.75\baselineskip}\newline\hbox{}% + \fi + \put@ruler% + \ifnum\ruler@rot=0 \vspace{0.25\baselineskip}\fi% + \fi% + \fi% + \xdef\fe@turep@s{bottom}% + \setlength{\bar@length}{0pt}% + \xdef\b@feature@count{0} + \ifnum\feature@bottom=1 % + \ifnum\featureonbottom=0 \xdef\feature@bottom{0}\fi% + \xdef\bottop@{bottom}% + \vspace{\b@sp@ce}% + \if\bottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature% + \temp@@count=\b@feature@count% + \advance\temp@@count by 1% + \xdef\b@feature@count{\the\temp@@count}% + \else + \iffix@ + \if\bottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbottomfeature% + \vspace{\b@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi% + \fi% + \fi% + \ifnum\feature@bbottom=1 % + \advance\bar@length by \b@feature@count \baselineskip% + \multiply\bar@length by \b@r@stretch% + \multiply\bar@length by 2% + \advance\bar@length by \bb@sp@ce\message{bb\the\bar@length bb}% + \ifnum\featureonbbottom=0 \xdef\feature@bbottom{0}\fi% + \xdef\bottop@{bbottom}% + \vspace{\bb@sp@ce}% + \if\bbottom@stretch y% + \advance\bar@length by -\box@height% + \advance\bar@length by \b@r@stretch\box@height% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% +% \vspace{-\bar@length}%%%%%%%%%%%%%%%%%%%%%%% + \setlength{\bar@length}{0pt}%%%%%%%%%%%%%%%%%%%%%%% + \put@feature% + \temp@@count=\b@feature@count% + \advance\temp@@count by 1% + \xdef\b@feature@count{\the\temp@@count}% + \else + \iffix@ + \if\bbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbottomfeature + \vspace{\bb@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi + \fi + \fi + \ifnum\feature@bbbottom=1 % + \advance\bar@length by \b@feature@count\baselineskip% + \multiply\bar@length by \b@r@stretch% + \multiply\bar@length by 2% + \advance\bar@length by \bbb@sp@ce\message{bbb\the\bar@length bbb}% + \ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi% + \xdef\bottop@{bbbottom}% + \vspace{\bbb@sp@ce}% + \if\bbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature% + \temp@@count=\b@feature@count% + \advance\temp@@count by 1% + \xdef\b@feature@count{\the\temp@@count}% + \else + \iffix@ + \if\bbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbbottomfeature + \vspace{\bbb@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi + \fi + \fi + \ifnum\feature@bbbbottom=1 % + \advance\bar@length by \b@feature@count\baselineskip% + \multiply\bar@length by \b@r@stretch% + \multiply\bar@length by 2% + \advance\bar@length by \bbbb@sp@ce\message{bbbb\the\bar@length bbbb}% + \ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi% + \xdef\bottop@{bbbbottom}% + \vspace{\bbbb@sp@ce}% + \if\bbbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature% + \else + \iffix@ + \if\bbbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbbbottomfeature + \vspace{\bbbb@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi + \fi + \fi + \xdef\consensus{} \xdef\ruler@{} + \xdef\styleframe{} + \xdef\textfeaturetop{} \xdef\textfeaturebottom{} + \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} + \xdef\textfeaturetttop{} \xdef\textfeaturebbbottom{} + \xdef\textfeaturettttop{} \xdef\textfeaturebbbbottom{} + \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} + \xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{} + \xdef\stylefeaturetttop{} \xdef\stylefeaturebbbottom{} + \xdef\stylefeaturettttop{} \xdef\stylefeaturebbbbottom{} + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\seq@line{\csname sequence\the\loopcount\endcsname} + \expandafter\remove@fromseq\seq@line + \ifnum\loopcount<\seq@count \repeat} + +\def\block@output{% + \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax + \message{.} + \ifx\out@put\y@ + \vbox{\set@lines}\par + \block@skip + \else + \pos@count=1 + \findc@nsensus + \loopcount=0 + \loop + \advance\loopcount by 1\relax + \xdef\seq@line{\csname sequence\the\loopcount\endcsname} + \expandafter\remove@fromseq\seq@line + \ifT@coffee + \xdef\TC@cons{\csname TC0\endcsname} + \expandafter\remove@fromTC\TC@cons + \fi + \ifnum\loopcount<\seq@count \repeat + \fi + \ifstop@ + \else + \advance\seq@pointer by -\res@perline + \ifnum\seq@pointer>\res@perline \block@output \fi + \fi + \fi} + +%%%%% Basic input routines + +\def\savedseqlength#1#2#3{% + \expandafter\xdef\csname savelength#1seq#2\endcsname{#3}} + +\def\set@savedseqlength{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\ifx% + \csname savelength\@lign@count seq\the\loopcount\endcsname\relax + \else + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{% + \csname savelength\@lign@count seq\the\loopcount\endcsname} + \fi + \ifnum\loopcount<\seq@count\repeat +} + +\def\save@lengths{% + \loopcount=0 + \loop + \advance\loopcount by 1\relax + \immediate\write\@auxout{% + \string\savedseqlength{\@lign@count}{\the\loopcount}% + {\csname res@count\the\loopcount\endcsname}} + \ifnum\loopcount<\seq@count \repeat +} + +\def\do@cleanup{% + \expandafter\firstchar@get\third@ + \expandafter\check@char\first@ + \ifletter + \xdef\second@{\second@\first@} + \else + \ifnumber + \ifx\first@\gre@ter + \xdef\second@{\second@{$>$}} + \else + \ifx\first@\sm@ller + \xdef\second@{\second@{$<$}} + \else + \xdef\second@{\second@\first@} + \fi\fi + \else + \ifnum\code@num=6 + \xdef\second@{\second@\#} + \else + \ifnum\code@num=14 + \xdef\second@{\second@\%} + \else + \xdef\second@{\second@\noexpand\string\first@} + \fi\fi + \fi + \fi + \ifx\third@\@t \else \do@cleanup \fi +} + +\def\cleanup@name{% + \xdef\third@{\csname seqname\the\loopcount\endcsname @} + \xdef\second@{} + \do@cleanup + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{\second@} +} + +\def\clear@seq{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\def\csname sequence\the\loopcount\endcsname{} + \ifnum\loopcount<\seq@count \repeat + \xdef\consensus{} + \xdef\constopo{} + \xdef\frame@on{0} + \xdef\textfeaturetop{} \xdef\featureontop{0} + \xdef\textfeaturettop{} \xdef\featureonttop{0} + \xdef\textfeaturetttop{} \xdef\featureontttop{0} + \xdef\textfeaturettttop{} \xdef\featureonttttop{0} + \xdef\textfeaturebottom{} \xdef\featureonbottom{0} + \xdef\textfeaturebbottom{} \xdef\featureonbbottom{0} + \xdef\textfeaturebbbottom{} \xdef\featureonbbbottom{0} + \xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0} + \xdef\styleframe{} + \xdef\stylefeaturetop{} + \xdef\stylefeaturettop{} + \xdef\stylefeaturetttop{} + \xdef\stylefeaturettttop{} + \xdef\stylefeaturebottom{} + \xdef\stylefeaturebbottom{} + \xdef\stylefeaturebbbottom{} + \xdef\stylefeaturebbbbottom{}} +\def\guess@protein{\seqtype{P}\message{<Seqtype guess: protein>}} +\def\guess@DNA{\seqtype{N}\message{<Seqtype guess: nucleotide>}} +\def\allmatch@out{% + \xdef\leave@in{n} + \loopcount=1 + \xdef\seq@line{\csname seq\the\loopcount\endcsname} + \expandafter\res@get\seq@line + \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line} + \ifnum\loopcount=\start@seq\relax + \expandafter\check@char\first@ + \ifletter + \advance\temp@@count by 1 + \ifnum\temp@@count=\end@num\relax + \advance\temp@count by 1 + \xdef\second@{\the\temp@count} + \advance\temp@count by -1 + \fi + \fi + \fi + \ifx\first@\ampers@nd + \ifx\domain@active\y@ + \xdef\stack@dom{\stack@dom\the\temp@count;} + \fi + \xdef\stack@dom{\stack@dom &;&;@} + \else + \xdef\first@@{\first@} + \advance\temp@count by 1 + \loop + \advance\loopcount by 1 + \xdef\seq@line{\csname seq\the\loopcount\endcsname} + \expandafter\res@get\seq@line + \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line} + \ifx\first@@\first@\else\xdef\leave@in{y}\fi + \ifnum\loopcount=\start@seq\relax + \expandafter\check@char\first@ + \ifletter + \advance\temp@@count by 1 + \ifnum\temp@@count=\end@num\relax \xdef\second@{\the\temp@count}\fi + \fi + \fi + \ifnum\loopcount<\seq@count\repeat + \ifx\leave@in\y@ + \ifx\domain@active\n@ + \ifnum\start@seq=0 + \xdef\domain@active{y} + \xdef\stack@dom{\stack@dom\the\temp@count;} + \else + \ifnum\temp@@count<\start@num\relax + \else + \ifnum\temp@@count>\end@num\relax + \else + \xdef\domain@active{y} + \xdef\stack@dom{\stack@dom\the\temp@count;} + \fi + \fi + \fi + \else + \ifnum\start@seq>0 + \ifnum\temp@@count<\end@num\relax + \else + \xdef\domain@active{n} + \xdef\stack@dom{\stack@dom\second@;} + \fi + \fi + \fi + \else + \ifx\domain@active\y@ + \xdef\domain@active{n} + \advance\temp@count by -1 + \xdef\stack@dom{\stack@dom\the\temp@count;} + \advance\temp@count by 1 + \fi + \fi + \allmatch@out + \fi +} +\def\domain@count{% + \xdef\@ddg@p{n} + \loopcount=0 + \ifT@coffee + \xdef\seq@line{\csname T@cof\the\loopcount\endcsname} + \expandafter\res@get\seq@line + \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@} + \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line} + \fi + \loop + \advance\loopcount by 1 + \xdef\seq@line{\csname seq\the\loopcount\endcsname} + \expandafter\res@get\seq@line + \expandafter\xdef\csname res\the\loopcount\endcsname{\first@} + \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line} + \ifT@coffee + \xdef\seq@line{\csname T@cof\the\loopcount\endcsname} + \expandafter\res@get\seq@line + \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@} + \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line} + \fi + \ifnum\loopcount<\seq@count\repeat + \ifx\first@\ampers@nd + \else + \ifnum\next@domain@num>-99999\relax + \ifnum\domain@seq=0 + \temp@count=\csname dom@count0\endcsname + \advance\temp@count by 1 + \expandafter\xdef\csname dom@count0\endcsname{\the\temp@count} + \fi + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{\csname res\the\loopcount\endcsname} + \expandafter\check@char\first@ + \ifletter + \temp@count=\csname dom@count\the\loopcount\endcsname + \advance\temp@count by 1 + \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\the\temp@count} + \if\seq@type A \relax + \temp@count=\char@num + \ifnum\temp@count>96 \advance\temp@count by -32 \fi + \ifnum\temp@count=69 \guess@protein + \else + \ifnum\temp@count=70 \guess@protein + \else + \ifnum\temp@count=73 \guess@protein + \else + \ifnum\temp@count=76 \guess@protein + \else + \ifnum\temp@count=80 \guess@protein + \else + \ifnum\temp@count=81 \guess@protein + \fi\fi\fi\fi\fi\fi + \fi + \else + \ifx\d@m@in\y@ + \ifnum\loopcount=\domain@seq \xdef\@ddg@p{y} \fi + \fi + \fi + \ifnum\loopcount<\seq@count\repeat + \ifx\@ddg@p\y@ + \ifx\g@p\n@ + \loopcount=0 + \loop + \advance\loopcount by 1 + \ifT@coffee + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% + \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} + \fi + \expandafter\xdef\csname sequence\the\loopcount\endcsname{% + \csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname} + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{% + \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} + \ifnum\loopcount<\seq@count\repeat + \advance\total@count by 1 + \advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi + \fi + \fi + \expandafter\ifnum\csname dom@count\domain@seq\endcsname=\next@domain@num + \xdef\d@m@in{y} + \advance\total@count by 1 + \advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi + \loopcount=0 + \ifx\g@p\y@ + \ifT@coffee + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% + \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} + \fi + \fi + \ifT@coffee + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% + \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} + \fi + \loop + \advance\loopcount by 1 + \ifx\g@p\y@ + \ifT@coffee + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% + \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} + \fi + \expandafter\xdef\csname sequence\the\loopcount\endcsname{% + \csname sequence\the\loopcount\endcsname\equ@l} + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{% + \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} + \ifnum\outerloopcount=0 + \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% + \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} + \fi + \fi + \ifT@coffee + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% + \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} + \fi + \expandafter\xdef\csname sequence\the\loopcount\endcsname{% + \csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname} + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{% + \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} + \ifnum\outerloopcount=0 + \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% + \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} + \fi + \ifnum\loopcount<\seq@count\repeat + \ifx\@ddg@p\n@ + \expandafter\get@item\domain@num@list + \xdef\domain@num@list{\first@} + \fi + \ifx\fourth@\ampers@nd \xdef\next@domain@num{-99999} + \else + \loopcount=\next@domain@num + \advance\loopcount by 1 + \ifnum\loopcount=\fourth@ + \xdef\g@p{n} + \else + \xdef\g@p{y} + \advance\total@count by 1 + \advance\outerloopcount by 1 + \ifnum\outerloopcount=\res@perline + \outerloopcount=0 + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% + \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} + \ifnum\loopcount<\seq@count\repeat + \fi + \fi + \xdef\next@domain@num{\fourth@} \xdef\end@num{\fourth@} + \fi + \fi + \domain@count + \fi + \fi +} +\def\residue@count{% + \expandafter\res@get\seq@line + \if\first@\ampers@nd + \else + \advance\total@count by 1 + \advance\innerloopcount by 1 + \ifstart@ \advance\res@count by 1 \fi + \ifnum\start@seq=0 + \advance\end@count by 1 +%%%%%%%%%% + \ifnum\end@count=\start@num\relax + \xdef\start@number{\the\innerloopcount} + \start@true \res@count=1 + \fi +%%%%%%%%%% + \else + \expandafter\check@char\first@ + \ifletter + \advance\end@count by 1 + \if\seq@type A \relax + \temp@count=\char@num + \ifnum\temp@count>96 \advance\temp@count by -32 \fi + \ifnum\temp@count=69 \guess@protein + \else + \ifnum\temp@count=70 \guess@protein + \else + \ifnum\temp@count=73 \guess@protein + \else + \ifnum\temp@count=76 \guess@protein + \else + \ifnum\temp@count=80 \guess@protein + \else + \ifnum\temp@count=81 \guess@protein + \fi\fi\fi\fi\fi\fi + \fi + \fi + \ifnum\end@count=\start@num\relax + \xdef\start@number{\the\innerloopcount} + \start@true \res@count=1 + \fi + \fi + \residue@count + \fi} +\def\clean@seq{% + \expandafter\res@get\seq@line + \if\first@\ampers@nd \xdef\seq@line{\seq@@line} + \else + \expandafter\check@char\first@ + \ifnum\char@num>64 + \ifnum\char@num>96 \make@upper \fi + \xdef\seq@@line{\seq@@line\first@} + \else + \ifnum\char@num=46 + \xdef\seq@@line{\seq@@line\d@t} + \else + \ifnum\char@num=45 + \xdef\seq@@line{\seq@@line\d@t} + \else + \ifnum\char@num=42 + \xdef\seq@@line{\seq@@line\questi@n} + \fi + \fi + \fi + \fi + \clean@seq + \fi} +\def\read@loop{% + \read\alignfile to \inline + \xdef\last@{\expandafter\string\inline} + \ifx\last@\par@ + \else + \xdef\inline{\inline @} + \expandafter\seq@get\inline + \ifstop@ + \else + \innerloopcount=\csname @rd\the\loopcount\endcsname\relax + \expandafter\ifx\csname seq@name\the\loopcount\endcsname\first@ + \xdef\seq@@line{} \xdef\seq@line{\seq@line &@} \clean@seq + \expandafter\xdef\csname sequence\the\innerloopcount\endcsname{% + \csname sequence\the\innerloopcount\endcsname\seq@line} + \advance\loopcount by 1 + \ifnum\loopcount>\seq@count + \loopcount=1 + \fi + \fi + \fi + \fi + \ifeof\alignfile + \ifx\all@out\y@ + \xdef\domain@seq{0} + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} + \ifnum\loopcount<\seq@count\repeat + \xdef\domain@active{n} + \xdef\stack@dom{} + \temp@count=0 + \temp@@count=0 + \allmatch@out + \xdef\dom@in{y} + \fi + \ifx\dom@in\y@ + \loopcount=0 + \ifT@coffee + \xdef\temp@{\csname T@coffee\the\loopcount\endcsname} + \expandafter\get@temp\temp@ + \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@} + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} + \fi + \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0} + \loop + \advance\loopcount by 1 + \ifT@coffee + \xdef\temp@{\csname T@coffee\the\loopcount\endcsname} + \expandafter\get@temp\temp@ + \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@} + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} + \fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} + \expandafter\xdef\csname sequence\the\loopcount\endcsname{} + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{} + \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{} + \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname} + \ifnum\loopcount<\seq@count\repeat + \xdef\domain@num@list{} + \xdef\last@{\stack@dom} + \get@domain + \xdef\domain@num@list{\domain@num@list &,@} + \expandafter\get@item\domain@num@list + \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@} + \xdef\d@m@in{n} + \domain@count + \loopcount=0 + \ifT@coffee + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} + \fi + \loop + \advance\loopcount by 1 + \ifT@coffee + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} + \fi + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @} + \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% + \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@} + \ifnum\loopcount<\seq@count\repeat + \if\seq@type A \guess@DNA \fi + \advance\seq@pointer by \total@count\relax + \xdef\total@pos{\the\total@count} + + \else + + \ifnum\start@seq=0 + \xdef\seq@line{\csname sequence1\endcsname &@} + \else + \xdef\seq@line{\csname sequence\start@seq\endcsname &@} + \fi + \res@count=0 + \innerloopcount=0 + \residue@count + \if\seq@type A \guess@DNA \fi + \advance\seq@pointer by \res@count\relax + \xdef\total@pos{\the\total@count} + \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi + \total@count=\end@count\relax + \xdef\first@{\csname res@count\start@seq\endcsname} + \advance\total@count by \first@\relax + \xdef\first@{\the\total@count} + \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi + \fi + \ifshow@sublogo \prep@sublogo \fi + \ifshow@logo \prep@logo \fi + \ifx\label@motif\y@ \prep@motif \fi + \ifnum\seq@pointer>\res@perline \block@output \fi + \else \read@loop + \fi} +\def\read@fasta{% + \read\alignfile to \inline + \xdef\last@{\expandafter\string\inline} + \ifx\last@\par@ + \else + \xdef\seq@line{\inline} + \xdef\inline{\inline @} + \expandafter\firstchar@get\inline + \ifstop@ + \else + \ifx\first@\gre@ter + \advance\loopcount by 1\relax + \expandafter\seq@get\third@ + \xdef\seq@name{\first@} + \xdef\second@{\first@ &} + \ifx\second@\ampers@nd \xdef\seq@name{seq\the\loopcount}\fi + \innerloopcount=\csname @rd\the\loopcount\endcsname\relax + \else + \expandafter\ifx\csname seq@name\the\loopcount\endcsname\seq@name + \xdef\seq@@line{} \xdef\seq@line{\seq@line &@} \clean@seq + \expandafter\xdef\csname sequence\the\innerloopcount\endcsname{% + \csname sequence\the\innerloopcount\endcsname\seq@line} + \fi + \fi + \fi + \fi + \ifeof\alignfile + \ifx\all@out\y@ + \xdef\domain@seq{0} + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} + \ifnum\loopcount<\seq@count\repeat + \xdef\domain@active{n} + \xdef\stack@dom{} + \temp@count=0 + \temp@@count=0 + \allmatch@out + \xdef\dom@in{y} + \fi + \ifx\dom@in\y@ + \loopcount=0 + \ifT@coffee + \xdef\temp@{\csname T@coffee\the\loopcount\endcsname} + \expandafter\get@temp\temp@ + \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@} + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} + \fi + \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0} + \loop + \advance\loopcount by 1 + \ifT@coffee + \xdef\temp@{\csname T@coffee\the\loopcount\endcsname} + \expandafter\get@temp\temp@ + \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@} + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} + \fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} + \expandafter\xdef\csname sequence\the\loopcount\endcsname{} + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{} + \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{} + \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname} + \ifnum\loopcount<\seq@count\repeat + \xdef\domain@num@list{} + \xdef\last@{\stack@dom} + \get@domain + \xdef\domain@num@list{\domain@num@list &,@} + \expandafter\get@item\domain@num@list + \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@} + \xdef\d@m@in{n} + \domain@count + \loopcount=0 + \ifT@coffee + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} + \fi + \loop + \advance\loopcount by 1 + \ifT@coffee + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} + \fi + \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @} + \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% + \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@} + \ifnum\loopcount<\seq@count\repeat + \if\seq@type A \guess@DNA \fi + \advance\seq@pointer by \total@count\relax + \xdef\total@pos{\the\total@count} + + \else + + \ifnum\start@seq=0 + \xdef\seq@line{\csname sequence1\endcsname &@} + \else + \xdef\seq@line{\csname sequence\start@seq\endcsname &@} + \fi + \res@count=0 + \innerloopcount=0 + \residue@count + \if\seq@type A \guess@DNA \fi + \advance\seq@pointer by \res@count + \xdef\total@pos{\the\total@count} + \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi + \total@count=\end@count\relax + \xdef\first@{\csname res@count\start@seq\endcsname} + \advance\total@count by \first@\relax + \xdef\first@{\the\total@count} + \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi + \fi + \ifshow@sublogo \prep@sublogo \fi + \ifshow@logo \prep@logo \fi + \ifx\label@motif\y@ \prep@motif \fi + \ifnum\seq@pointer>\res@perline \block@output \fi + \else + \read@fasta + \fi} +\def\read@lines{% + \openin\alignfile = \alignfilename + \clear@seq + \ifnum\start@seq>0 + \xdef\start@seq{\csname @rd\start@seq\endcsname} \fi + \loopcount=\start@num + \advance\loopcount by -\csname res@count\start@seq\endcsname\relax + \expandafter\ifnum\csname res@count\start@seq\endcsname<\start@num\relax + \xdef\start@num{\the\loopcount} + \else \start@true \fi + \res@count=0 \seq@pointer=0 \end@count=0 \total@count=0 + \xdef\start@number{0} + \ifx\exp@rt\y@ \prep@reexp@rtfile \fi + \ifx\f@st@\y@ + \loopcount=0 + \read@fasta + \else + \loopcount=1 + \read@loop + \fi + \ifnum\seq@pointer>0 + \ifstop@ + \else + \res@count=\res@perline + \res@perline=\seq@pointer + \block@output + \fi + \fi + \ifshow@sublogo \closein\sublogofile \fi + \ifx\exp@rt\y@ \closeout\exp@rtfile \fi + \closein\alignfile + \message{)} +} + + +%%%%% Read alignment, decide whether MSF or ALN, interpret + +\def\readalignfile#1{% + \def\alignfilename{#1} + \xdef\first@{byhand} + \ifx\alignfilename\first@ + \else + \openin\alignfile = #1 + \ifeof\alignfile + \PackageError{TeXshade} + {File `#1' not found} + {\MessageBreak + The alignment file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + Stop here, otherwise you're likely getting in trouble. \MessageBreak + Type X <return> to quit. \MessageBreak +} + \else + \message{(\alignfilename :} + \xdef\seq@type{A} \xdef\he@der{no} \xdef\f@st@{no} + \xdef\first@line{y} + \seq@count=0 \loopcount=0 \innerloopcount=0 \temp@count=0 + \loop + \read\alignfile to \inline + \xdef\test@{\expandafter\string\inline} + \ifx\test@\par@ \innerloopcount=0 + \else + \xdef\msfline{\inline & & & & @} + \expandafter\inf@@get\msfline + \ifx\first@\@msf \expandafter\type@get\msfline \fi + \ifx\second@\@msf \expandafter\type@get\msfline \fi + \ifx\third@\@msf \expandafter\type@get\msfline \fi + \ifx\first@\n@me \advance\loopcount by 1\relax + \expandafter\xdef\csname seqname\the\loopcount\endcsname{\second@} + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{\fourth@} + \fi + \ifx\first@\he@derend + \ifnum\loopcount>0 \xdef\he@der{yes} \fi + \fi + \xdef\alnline{\inline @} + \expandafter\check@letter\alnline + \ifletter + \expandafter\seq@get\alnline + \advance\innerloopcount by 1\relax + \seq@count=\innerloopcount + \expandafter\xdef\csname newseqname\the\seq@count\endcsname{\first@} + \else + \expandafter\firstchar@get\alnline + \ifx\first@\gre@ter + \ifx\first@line\y@ \xdef\f@st@{y}\fi + \expandafter\seq@get\third@ + \advance\temp@count by 1\relax + \xdef\second@{\first@ &} + \ifx\second@\ampers@nd \xdef\first@{seq\the\temp@count}\fi + \expandafter\xdef\csname seq@name\the\temp@count\endcsname{\first@} + \fi + \fi + \fi + \xdef\first@line{n} + \ifeof\alignfile \else\repeat + \closein\alignfile + \xdef\first@{no} + \ifx\he@der\first@ + \loopcount=0 + \ifx\f@st@\y@ + \seq@count=\temp@count \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname seqname\the\loopcount\endcsname{% + \csname seq@name\the\loopcount\endcsname} + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% + \csname seq@name\the\loopcount\endcsname} + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999} + \ifnum\loopcount<\seq@count \repeat + \else + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname seqname\the\loopcount\endcsname{% + \csname newseqname\the\loopcount\endcsname} + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999} + \ifnum\loopcount<\seq@count \repeat + \fi + \else + \seq@count=\loopcount \loopcount=0 \box@width=0pt + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% + \csname seqname\the\loopcount\endcsname} + \ifnum\loopcount<\seq@count \repeat + \fi + \set@savedseqlength + \loopcount=0 \xdef\seq@order{} + \expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} + \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} + \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes} + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname @rd\the\loopcount\endcsname{\the\loopcount} + \expandafter\xdef\csname res@count\the\loopcount\endcsname{0} + \cleanup@name + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} + \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{false} + \expandafter\xdef\csname hide@@@seq\the\loopcount\endcsname{false} + \expandafter\xdef\csname hide@name\the\loopcount\endcsname{no} + \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} + \expandafter\xdef\csname hide@number\the\loopcount\endcsname{no} + \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes} + \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{no} + \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} + \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{0} + \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{0} + \ifnum\loopcount=1 \xdef\seq@order{\the\loopcount} + \else \xdef\seq@order{\seq@order,\the\loopcount}\fi + \ifnum\loopcount<\seq@count \repeat + \xdef\seq@order{\seq@order,@} + \killseq@count=\seq@count +% \seq@percent=100 +% \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi + \fi + \fi +} + +%%%%% TeXshade + +\def\calc@widths{% + \fontfamily{cmss}\fontseries{m}\fontshape{n} + \selectfont + \setbox1=\hbox{\residues@size{A}}\logo@height=\ht1 + \setlength\logo@height{\logo@stretch\logo@height} + \fontfamily{\residues@family} + \fontseries{\residues@series} + \fontshape{\residues@shape} + \selectfont + \setbox1=\hbox{\residues@size{W}}\box@width=1.15\wd1 + \global\setlength\box@width{\char@stretch\box@width} + \box@height=1.2\ht1 + \setbox1=\hbox{\residues@size{g}}\box@depth=1.1\dp1 + \global\setlength\box@height{\line@stretch\box@height} + \global\setlength\box@depth{\line@stretch\box@depth} + \baselineskip=\box@height \advance\baselineskip by \box@depth + \lineskip=0pt + \ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi + \loopcount=0 + \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\getregion@fromtintstack{\the\loopcount} + \expandafter\getregion@fromemphstack{\the\loopcount} + \expandafter\getregion@fromlowerstack{\the\loopcount} + \expandafter\getregion@fromframestack{\the\loopcount} + \expandafter\getregion@fromshadingstack{\the\loopcount} + \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \fontfamily{\namestext@family} + \fontseries{\namestext@series} + \fontshape{\namestext@shape} + \selectfont + \ifshow@logo + \ifx\logo@name@user\ampers@nd + \setbox1=\hbox{\namestext@size logo\kern1em} + \else + \setbox1=\hbox{\namestext@size\logo@name@user\kern1em} + \fi + \ifnum\wd1>\name@width \name@width=\wd1 \fi + \fi + \ifshow@sublogo + \ifx\sublogo@name@user\ampers@nd + \setbox1=\hbox{\namestext@size family\kern1em} + \else + \setbox1=\hbox{\namestext@size\sublogo@name@user\kern1em} + \fi + \ifnum\wd1>\name@width \name@width=\wd1 \fi + \ifx\hide@negatives\n@ + \setbox1=\hbox{\namestext@size\sublogo@name@neg\kern1em} + \fi + \ifnum\wd1>\name@width \name@width=\wd1 \fi + \fi + \loopcount=1 + \loop + \setbox1=\hbox{\namestext@size\csname newseqname\the\loopcount\endcsname} + \ifnum\wd1>\name@width \name@width=\wd1 \fi + \ifnum\ht1>\box@height + \box@height=1.1\ht1 + \global\setlength\box@height{\line@stretch\box@height} + \baselineskip=\box@height \advance\baselineskip by \box@depth + \fi + \ifnum\dp1>\box@depth + \box@depth=1.1\dp1 + \global\setlength\box@depth{\line@stretch\box@depth} + \baselineskip=\box@height \advance\baselineskip by \box@depth + \fi + \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\getregion@fromtintstack{\the\loopcount} + \expandafter\getregion@fromemphstack{\the\loopcount} + \expandafter\getregion@fromlowerstack{\the\loopcount} + \expandafter\getregion@fromframestack{\the\loopcount} + \expandafter\getregion@fromshadingstack{\the\loopcount} + \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \innerloopcount = \csname seq@len\the\loopcount\endcsname + \advance\innerloopcount by \csname seq@start\the\loopcount\endcsname + \advance\innerloopcount by -1 + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{\the\innerloopcount} + \advance\loopcount by 1 + \ifnum\loopcount>\seq@count \else \repeat + \advance\name@width by -2em + \global\xdef\name@@width{\the\name@width} + \advance\name@width by 3em + \fontfamily{\numbertext@family} + \fontseries{\numbertext@series} + \fontshape{\numbertext@shape} + \selectfont + \setbox1=\hbox{\bottomruler@size\num@width\,-} + \xdef\ruler@width{\the\wd1} + \setbox1=\hbox{\numbertext@size\num@width} + \number@width=\wd1 + \advance\number@width by 1em + \loopcount=\linewidth + \ifnames@ \advance\loopcount by -\name@width \fi + \width@tmp=1.6\box@width + \ifnumbers@ + \ifnumbers@left + \advance\loopcount by -\number@width + \else + \xdef\first@{left} + \ifx\show@logoscale\first@ + \advance\loopcount by -\width@tmp + \fi + \fi + \ifnumbers@right + \advance\loopcount by -\number@width + \else + \xdef\first@{right} + \ifx\show@logoscale\first@ + \advance\loopcount by -\width@tmp + \fi + \fi + \else + \xdef\first@{left} + \ifx\show@logoscale\first@ + \advance\loopcount by -\width@tmp + \fi + \xdef\first@{right} + \ifx\show@logoscale\first@ + \advance\loopcount by -\width@tmp + \fi + \xdef\first@{leftright} + \ifx\show@logoscale\first@ + \advance\loopcount by -\width@tmp + \advance\loopcount by -\width@tmp + \fi + \fi + \divide\loopcount by \box@width + \divide\loopcount by 5 \multiply\loopcount by 5 + \ifrpl@fix\else + \ifnum\res@perline>\loopcount \res@perline=\loopcount\fi\fi + \ifnum\finger@linenum>0 + \width@tmp=\linewidth + \ifnames@ \advance\width@tmp by -\name@width \fi + \ifnumbers@ \advance\width@tmp by -\number@width \fi + \divide\width@tmp by \finger@linenum + \global\setlength\box@width{\width@tmp} + \fi + \center@fill=\linewidth + \ifnames@ \advance\center@fill by -\name@width \fi + \ifnumbers@ \advance\center@fill by -\number@width \fi + \width@tmp=\box@width \multiply\width@tmp by \res@perline + \advance\center@fill by -\width@tmp + \ifx\out@put\y@\leftskip\c@factor\center@fill\fi + \ifx\logo@colors@set\n@ + \if\seq@type N + \clearlogocolors[Yellow] + \logocolor{G}{Black} + \logocolor{A}{Green} + \logocolor{TU}{Red} + \logocolor{C}{Blue} + \else + \clearlogocolors + \logocolor{DE}{Red} + \logocolor{CM}{Yellow} + \logocolor{KR}{Blue} + \logocolor{ST}{Orange} + \logocolor{FY}{MidnightBlue} + \logocolor{NQ}{Cyan} + \logocolor{G}{LightGray} + \logocolor{LVI}{Green} + \logocolor{A}{DarkGray} + \logocolor{W}{CarnationPink} + \logocolor{H}{CornflowerBlue} + \logocolor{P}{Apricot} + \logocolor{BZ}{LightMagenta} + \fi + \fi +} + +\def\multiple@dssp{% + \advance\loopcount by 1 + \include@DSSP + \ifnum\loopcount<\dssp@num\multiple@dssp\fi} + +\def\multiple@stride{% + \advance\loopcount by 1 + \include@stride + \ifnum\loopcount<\stride@num\multiple@stride\fi} + +\def\multiple@PHD{% + \advance\loopcount by 1 + \include@PHD + \ifnum\loopcount<\PHD@num\multiple@PHD\fi} + +\def\multiple@HMMTOP{% + \advance\loopcount by 1 + \include@HMMTOP + \ifnum\loopcount<\HMMTOP@num\multiple@HMMTOP\fi} + +\newenvironment{texshade}[2][&]% + {\standarddefinitions + \c@d@ns + \xdef\first@{#1}\ifx\first@\ampers@nd\else\input{#1}\fi + \readalignfile{#2} + }% + {\ifnum\seq@count>0 + \loopcount=0 + \ifnum\loopcount<\dssp@num \multiple@dssp\fi + \loopcount=0 + \ifnum\loopcount<\stride@num \multiple@stride\fi + \loopcount=0 + \ifnum\loopcount<\PHD@num \multiple@PHD\fi + \loopcount=0 + \ifnum\loopcount<\HMMTOP@num \multiple@HMMTOP\fi + \loopcount=1 \kill@seqnow + \reorder@seqs\seq@order \seq@count=\killseq@count + \global\xdef\seq@num{\the\seq@count} + \clear@sim@count + \ifnum\csname res@count\start@seq\endcsname<0 + \ifnum\start@num>0 + \loopcount=\start@num + \advance\loopcount by -1 + \xdef\start@num{\the\loopcount} + \fi + \fi + \ifnum\rule@num>0 + \loopcount=\csname res@count\rule@num\endcsname + \divide\loopcount by \ruler@step + \multiply\loopcount by \ruler@step + \ifnum\loopcount<0 + \ifnum\ruler@step<3 + \advance\loopcount by \ruler@step + \fi + \else + \advance\loopcount by \ruler@step + \fi + \xdef\rule@tens{\the\loopcount} + \else + \loopcount=\cons@count + \divide\loopcount by \ruler@step + \multiply\loopcount by \ruler@step + \ifnum\loopcount<0 + \ifnum\ruler@step<3 + \advance\loopcount by \ruler@step + \fi + \else + \advance\loopcount by \ruler@step + \fi + \xdef\rule@tens{\the\loopcount} + \fi + \xdef\first@{top} + \ifx\cap@pos\first@ + \xdef\@captype{figure} + \ifx\c@pshort\n@ + \caption{\c@p} + \else + \caption[\c@pshort]{\c@p} + \fi + \fi + \loopcount = \thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100 + \xdef\thresh@ld@{\the\loopcount} + \loopcount = \all@thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100 + \xdef\all@thresh@ld@{\the\loopcount} + \bgroup + \ifx\out@put\y@\bigskip\fi + \iffuncmode \show@consfalse \fi + \ifall@fshade \iffuncmode \else \all@fshadefalse \fi\fi + \ifnum\finger@linenum>0 + \show@consfalse + \hidechartrue + \message{<Fingerprinting---please wait>} + \fi + \calc@widths + \read@lines + \save@lengths + \iflegend@ + \vspace{\vspace@legend} + \setbox1=\vbox{\do@legend} + \vbox{\do@legend}\par + \ifnum\ht1<-\vspace@legend + \vspace{-\ht1}\vspace{-\vspace@legend} + \fi + \fi + \egroup + \xdef\first@{bottom} + \ifx\cap@pos\first@ + \vspace{-\baselineskip} + \xdef\@captype{figure} + \ifx\c@pshort\n@ + \caption{\c@p} + \else + \caption[\c@pshort]{\c@p} + \fi + \fi + \fi} + +\def\standarddefinitions{% +\xdef\prfx{pep}\clear@groups\clear@sims +\xdef\prfx{DNA}\clear@groups\clear@sims +\clearfuncgroups +\clear@simpairs +\shadingcolors{blues} +\shadingcolors{reds} +\shadingcolors{greens} +\shadingcolors{grays} +\shadingcolors{black} +\loopcount=\@lign@count +\advance\loopcount by 1\relax +\xdef\@lign@count{\the\loopcount} +\start@true \xdef\start@num{1} \xdef\start@seq{0} +\stop@false \xdef\end@num{n} \xdef\seq@regions{0} +\cons@count=0 +\expandafter\xdef\csname res@count0\endcsname{0} +\xdef\allow@zero{n} \xdef\c@ns@shift{0} +\regionalshadefalse\regionalemphfalse\regionallowerfalse\regionaltintfalse +\frame@false\shading@false +\xdef\ruler@rot{0} +\topfeaturefalse \bottomfeaturefalse +\ttopfeaturefalse \bbottomfeaturefalse +\tttopfeaturefalse \bbbottomfeaturefalse +\ttttopfeaturefalse \bbbbottomfeaturefalse +\all@fshadefalse\hidecharfalse +\xdef\finger@linenum{0} +\xdef\hide@seqs{n} +\xdef\dssp@num{0} \xdef\stride@num{0} \xdef\PHD@num{0} \xdef\HMMTOP@num{0} +\xdef\bottop@{top} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{ttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{tttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{ttttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbbbottom}\expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\frame@{0} +\xdef\show@Hdssp{no} \xdef\show@Gdssp{no} \xdef\show@Idssp{no} +\xdef\show@Edssp{no} \xdef\show@Bdssp{no} \xdef\show@Tdssp{no} +\xdef\show@Sdssp{no} +\xdef\show@Hstride{no} \xdef\show@Gstride{no} \xdef\show@Istride{no} +\xdef\show@Estride{no} \xdef\show@Bstride{no} \xdef\show@Tstride{no} +\xdef\show@itop{no} \xdef\show@etop{no} \xdef\show@TMtop{no} +\xdef\show@i@HMMTOP{no} \xdef\show@e@HMMTOP{no} \xdef\show@TM@HMMTOP{no} +\xdef\show@Hsec{no} \xdef\show@Esec{no} +\xdef\collect@restop{no} \xdef\collect@resttop{no} +\xdef\collect@restttop{no} \xdef\collect@resttttop{no} +\xdef\collect@resbottom{no} \xdef\collect@resbbottom{no} +\xdef\collect@resbbbottom{no}\xdef\collect@resbbbbottom{no} +\xdef\tr@nslatetop{} \xdef\tr@nslatettop{} +\xdef\tr@nslatetttop{} \xdef\tr@nslatettttop{} +\xdef\tr@nslatebottom{} \xdef\tr@nslatebbottom{} +\xdef\tr@nslatebbbottom{} \xdef\tr@nslatebbbbottom{} +\xdef\tr@nsseqtop{0} \xdef\tr@nsseqttop{0} +\xdef\tr@nsseqtttop{0} \xdef\tr@nsseqttttop{0} +\xdef\tr@nsseqbottom{0} \xdef\tr@nsseqbbottom{0} +\xdef\tr@nsseqbbbottom{0} \xdef\tr@nsseqbbbbottom{0} +\xdef\triple@counttop{0} \xdef\triple@countttop{0} +\xdef\triple@counttttop{0} \xdef\triple@countttttop{0} +\xdef\triple@countbottom{0} \xdef\triple@countbbottom{0} +\xdef\triple@countbbbottom{0}\xdef\triple@countbbbbottom{0} +\xdef\last@@restop{} \xdef\last@@resttop{} +\xdef\last@@restttop{} \xdef\last@@resttttop{} +\xdef\last@@resbottom{} \xdef\last@@resbbottom{} +\xdef\last@@resbbbottom{} \xdef\last@@resbbbbottom{} +\xdef\out@put{y} \xdef\m@p{no} +\xdef\t@sp@ce{0mm} \xdef\tt@sp@ce{0mm} +\xdef\ttt@sp@ce{0mm} \xdef\tttt@sp@ce{0mm} +\xdef\b@sp@ce{0mm} \xdef\bb@sp@ce{0mm} +\xdef\bbb@sp@ce{0mm} \xdef\bbbb@sp@ce{0mm} +\xdef\ruler@sp@ce{0mm} +\xdef\seq@gap@num{0} +\xdef\h@ndalign{no} \xdef\sep@space{0pt} +\xdef\c@pshort{n} +\xdef\bottom@stretch{n} \xdef\bbottom@stretch{n} +\xdef\bbbottom@stretch{n} \xdef\bbbbottom@stretch{n} +\xdef\c@nscol{} \xdef\c@nssc@le{ColdHot} +\xdef\collect@cons@colors{no} \xdef\cons@now{no} +\xdef\res@numA{0} \xdef\res@numB{0} +\xdef\res@numC{0} \xdef\res@numD{0} +\xdef\res@numE{0} \xdef\res@numF{0} +\xdef\res@numG{0} \xdef\res@numH{0} +\xdef\res@numI{0} \xdef\res@numJ{0} +\xdef\res@numK{0} \xdef\res@numL{0} +\xdef\res@numM{0} \xdef\res@numN{0} +\xdef\res@numO{0} \xdef\res@numP{0} +\xdef\res@numQ{0} \xdef\res@numR{0} +\xdef\res@numS{0} \xdef\res@numT{0} +\xdef\res@numU{0} \xdef\res@numV{0} +\xdef\res@numW{0} \xdef\res@numX{0} +\xdef\res@numY{0} \xdef\res@numZ{0} +\expandafter\xdef\csname res@num\questi@n\endcsname{0} +\expandafter\xdef\csname res@num\d@t\endcsname{0} +\expandafter\xdef\csname res@num\equ@l\endcsname{0} +\xdef\res@corrA{0} \xdef\res@corrB{0} +\xdef\res@corrC{0} \xdef\res@corrD{0} +\xdef\res@corrE{0} \xdef\res@corrF{0} +\xdef\res@corrG{0} \xdef\res@corrH{0} +\xdef\res@corrI{0} \xdef\res@corrJ{0} +\xdef\res@corrK{0} \xdef\res@corrL{0} +\xdef\res@corrM{0} \xdef\res@corrN{0} +\xdef\res@corrO{0} \xdef\res@corrP{0} +\xdef\res@corrQ{0} \xdef\res@corrR{0} +\xdef\res@corrS{0} \xdef\res@corrT{0} +\xdef\res@corrU{0} \xdef\res@corrV{0} +\xdef\res@corrW{0} \xdef\res@corrX{0} +\xdef\res@corrY{0} \xdef\res@corrZ{0} +\expandafter\xdef\csname res@corr\questi@n\endcsname{0} +\expandafter\xdef\csname res@corr\d@t\endcsname{0} +\expandafter\xdef\csname res@corr\equ@l\endcsname{0} +\xdef\corr@max{0} \xdef\do@freq@correction{n} +\xdef\res@total{0} +\xdef\stack@sequencelogo{} \xdef\bit@total{0} +\clearlogocolors \xdef\logo@colors@set{n} +\show@sublogofalse \xdef\stack@sublogo{} +\xdef\clear@logo{n} \xdef\subfamily@threshold{50} +\xdef\subfamily@seq{1} \xdef\sig@max{100000} +\xdef\sublogo@num{} \xdef\sublogo@sig{} +\xdef\subfamily@count{0} \xdef\sublogo@name@neg{} +\xdef\logo@name@user{&} \xdef\sublogo@name@user{&} +\expandafter\xdef\csname group@num1\endcsname{0} +\expandafter\xdef\csname group@num2\endcsname{0} +\xdef\exp@rt@num{0} \xdef\exp@rt{n} +\xdef\divref@{0} +\xdef\all@thresh@ld{100} \all@shadefalse +\hidefeaturenames \hidefeaturestylenames +\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n} +\xdef\dom@in{no} \xdef\label@motif{no} +\xdef\motif@num{0} \xdef\all@out{n} +\hfuzz9999pt + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% Under any circumstances: %%%%% +%%%%% %%%%% +%%%%% DO NOT CHANGE ANY SETTINGS HERE !!! %%%%% +%%%%% %%%%% +%%%%% Please define your personal parameter file! Store your new file %%%%% +%%%%% together with this style-file in the same directory and load the %%%%% +%%%%% file by naming it as an optional parameter in the `texshade' en- %%%%% +%%%%% vironment. The file `texshade.def' can be used as a template for %%%%% +%%%%% the new creation. See the manual for further help. %%%%% +%%%%% %%%%% +%%%%% THANK YOU !!! %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +\shadingmode{identical} % Shade identical residues only +\shadingcolors{blues} % Select the blue color scheme for shading +\constoallseqs % Calculate consensus considering all seqs +\threshold{50} % Consensus threshold percentage is 50 +\residuesperline{999} % As many residues as possible per line +\numberingwidth{9999} % Assign space for 4 digit numbering +\charstretch{1} % Do not stretch character width +\linestretch{1} % Do not stretch lines vertically +\gapchar{.} % . is printed in sequence gaps +\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt +\gapcolors{Black}{White} % Gap symbols appear `Black on White' +\domaingaprule{1pt} % If a rule is set between domains use 1 pt +\domaingapcolors{Red}{White} % Domain separation line appears `Red on White' +\numberingcolor{Black} % Numbering color is `Black' +\shownumbering{right} % Show sequence numbering on the left +\namescolor{Black} % Names' color is `Black' +\featurenamescolor{Black} % Feature names' color is `Black' +\featurestylenamescolor{Black} % Feature names' color is `Black' +\shownames{left} % Show sequence names on the right +\consensuscolors{Black}{White} % All consensus symbols/letters + {Black}{White} % appear `Black on White' + {Black}{White} % +\showconsensus{bottom} % Show consensus line at bottom with +\hidesequencelogo % Do not show a sequence logo as consensus +\showlogoscale{leftright} % Show vertical scale bar if logo is on +\logostretch{1} % Do not stretch sequence logo vertically +\hidesubfamilylogo % Do not show a subfamily logo +\subfamilythreshold{50} % Set subfamily threshold to 50% +\shownegatives % Show negative values in subfamily logo +\showrelevance[Black]{*} % Label relevant subfamily deviations +\defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match +\showleadinggaps % Show gap symbols before sequence start +\rulercolor{Black} % Ruler's color is `Black' +\hideruler % Do not show the ruler +\rulersteps{10} % Ruler ticks every 10 residues +\legendcolor{Black} % Legend text color is `Black' +\hidelegend % Do not show the legend +\alignment{center} % Center alignment on page +\medsepline % Medium height if separation line is on +\medblockskip % Medium skip between sequence blocks +\flexblockspace % Use optimized space between blocks +\featurerule{0.5ex} % Set feature rule thickness to 1/2 ex +\bargraphstretch{1} % Do not stretch bars in feature graphs +\colorscalestretch{1} % Do not stretch color scales in features +\backtranstext{horizontal} % Horizontal triplets in feature texts +\backtranslabel{alternating} % Alternating triplets in feature styles +\setfamily{residues}{tt} % Use typewriter family for residues +\setseries{residues}{md} % Use normal series for residues +\setshape {residues}{up} % Use upright shape for residues +\setsize {residues}{normalsize} % Use normal size for residues +\setfamily{numbering}{tt} % Use typewriter family for numbering +\setseries{numbering}{md} % Use normal series for numbering +\setshape {numbering}{up} % Use upright shape for numbering +\setsize {numbering}{normalsize} % Use normal size for numbering +\setfamily{names}{tt} % Use typewriter family for names +\setseries{names}{md} % Use normal series for names +\setshape {names}{up} % Use upright shape for names +\setsize {names}{normalsize} % Use normal size for names +\setfamily{featurenames}{tt} % Use typewriter family for feature names +\setseries{featurenames}{md} % Use normal series for feature names +\setshape {featurenames}{up} % Use upright shape for feature names +\setsize {featurenames}{normalsize}% Use normal size for feature names +\setfamily{featurestylenames}{tt} % Use typewriter family for feature style names +\setseries{featurestylenames}{md} % Use normal series for feature style names +\setshape {featurestylenames}{up} % Use upright shape for feature style names +\setsize {featurestylenames}{normalsize}% Use normal size for feature style names +\setfamily{features}{rm} % Use roman family for feature texts +\setseries{features}{md} % Use normal series for feature texts +\setshape {features}{it} % Use italics shape for feature texts +\setsize {features}{normalsize} % Use normal size for feature texts +\setfamily{featurestyles}{tt} % Use typewriter family for feature styles +\setseries{featurestyles}{md} % Use normal series for feature styles +\setshape {featurestyles}{up} % Use upright shape for feature styles +\setsize {featurestyles}{normalsize}% Use normal size for feature styles +\setfamily{legend}{tt} % Use typewriter family for legend texts +\setseries{legend}{md} % Use normal series for legend texts +\setshape {legend}{up} % Use upright shape for legend texts +\setsize {legend}{normalsize} % Use normal size for legend texts +\setfamily{ruler}{sf} % Use sans serif font for ruler numbers +\tintdefault{medium} % Use medium tint intensity +\emphdefault{it} % Use italics to emphasize regions +\showonPHDsec{alpha,beta} % Show helices and strands (PHD input) +\showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input) +\showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input) +\showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input) +\showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input) +\secondcolumnDSSP % Use numbering from 2. column in DSSP +\appearance{PHDtopo}{internal} % \ + {bottom}{'-'} % \ + {int.\ \Alphacount} % | +\appearance{PHDtopo}{external} % | + {top}{,-,} % | + {ext.\ \Alphacount} % | +\appearance{PHDtopo}{TM}{top} % | + {box[LightGray]:TM\numcount}{} % | +\appearance{HMMTOP}{internal} % | + {bottom}{'-'} % | + {int.\ \Alphacount} % | +\appearance{HMMTOP}{external} % | + {top}{,-,} % | + {ext.\ \Alphacount} % | +\appearance{HMMTOP}{TM}{top} % | + {helix}{TM\numcount} % | +\appearance{PHDsec}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{PHDsec}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | Definitions for the appearance of +\appearance{STRIDE}{3-10}{top} % \ + {fill:$\circ$}{3$_{10}$} % > secondary structures included from| +\appearance{STRIDE}{pi} % / + {top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files. +\appearance{STRIDE}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{STRIDE}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{DSSP}{3-10}{top} % | + {fill:$\circ$}{3$_{10}$} % | +\appearance{DSSP}{pi} % | + {top}{---}{$\pi$} % | +\appearance{DSSP}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{DSSP}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{DSSP}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{bend}{top} % / + {fill:$\diamond$}{} % / + +\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity + +\pepsims{F}{YW} % Y and W are similar to F +\pepsims{Y}{WF} % W and F are similar to Y +\pepsims{W}{YF} % Y and F are similar to W + +\pepsims{I}{LVM} % L, V and M are similar to I +\pepsims{L}{VMI} % V, M and I are similar to L +\pepsims{V}{MIL} % M, I and L are similar to V + +\pepsims{R}{KH} % K and H are similar to R +\pepsims{K}{HR} % H and R are similar to K +\pepsims{H}{RK} % R and K are similar to H + +\pepsims{A}{GS} % G and S are similar to A +\pepsims{G}{A} % A (but not S) is similar to G + +\pepsims{S}{TA} % T and A are similar to S +\pepsims{T}{S} % S (but not A) is similar to T + +\pepsims{D}{EN} % E and N (but not Q) are similar to D +\pepsims{E}{DQ} % D and Q (but not N) are similar to E +\pepsims{N}{QD} % Q and D (but not E) are similar to N +\pepsims{Q}{NE} % N and E (but not D) are similar to Q + +\DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity + +\DNAsims{A}{GR} % G and R are similar to A +\DNAsims{G}{AR} % A and R are similar to G +\DNAsims{R}{AG} % A and G are similar to R + +\DNAsims{C}{TY} % T and Y are similar to C +\DNAsims{T}{CY} % C and Y are similar to T +\DNAsims{Y}{CT} % C and T are similar to Y + +} +\catcode`\@=12 +%</texshade> +% \end{macrocode} +% \subsection{\file{texshade.def}} +% \begin{macrocode} +%<*definitions> +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% This example file contains all standard settings of the TeXshade %%%%% +%%%%% package. It can be used as a template for the creation of perso- %%%%% +%%%%% nal parameter files. All TeXshade user commands are allowed and %%%%% +%%%%% functional when specified here. %%%%% +%%%%% %%%%% +%%%%% To activate these settings for your alignment load this file by %%%%% +%%%%% naming it as optional parameter at the beginning of the texshade %%%%% +%%%%% environment, e.g. %%%%% +%%%%% %%%%% +%%%%% \begin{texshade}[myparameterfile]{alignmentfile} %%%%% +%%%%% . %%%%% +%%%%% . %%%%% +%%%%% \end{texshade} %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +\shadingmode{identical} % Shade identical residues only +\shadingcolors{blues} % Select the blue color scheme for shading +\constoallseqs % Calculate consensus considering all seqs +\threshold{50} % Consensus threshold percentage is 50 +\residuesperline{999} % As many residues as possible per line +\numberingwidth{9999} % Assign space for 4 digit numbering +\charstretch{1} % Do not stretch character width +\linestretch{1} % Do not stretch lines vertically +\gapchar{.} % . is printed in sequence gaps +\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt +\gapcolors{Black}{White} % Gap symbols appear `Black on White' +\domaingaprule{1pt} % If a rule is set between domains use 1 pt +\domaingapcolors{Red}{White} % Domain separation line appears `Red on White' +\numberingcolor{Black} % Numbering color is `Black' +\shownumbering{right} % Show sequence numbering on the left +\namescolor{Black} % Names' color is `Black' +\featurenamescolor{Black} % Feature names' color is `Black' +\featurestylenamescolor{Black} % Feature names' color is `Black' +\shownames{left} % Show sequence names on the right +\consensuscolors{Black}{White} % All consensus symbols/letters + {Black}{White} % appear `Black on White' + {Black}{White} % +\showconsensus{bottom} % Show consensus line at bottom with +\hidesequencelogo % Do not show a sequence logo as consensus +\showlogoscale{leftright} % Show vertical scale bar if logo is on +\logostretch{1} % Do not stretch sequence logo vertically +\hidesubfamilylogo % Do not show a subfamily logo +\subfamilythreshold{50} % Set subfamily threshold to 50% +\shownegatives % Show negative values in subfamily logo +\showrelevance[Black]{*} % Label relevant subfamily deviations +\defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match +\showleadinggaps % Show gap symbols before sequence start +\rulercolor{Black} % Ruler's color is `Black' +\hideruler % Do not show the ruler +\rulersteps{10} % Ruler ticks every 10 residues +\legendcolor{Black} % Legend text color is `Black' +\hidelegend % Do not show the legend +\alignment{center} % Center alignment on page +\medsepline % Medium height if separation line is on +\medblockskip % Medium skip between sequence blocks +\flexblockspace % Use optimized space between blocks +\featurerule{0.5ex} % Set feature rule thickness to 1/2 ex +\bargraphstretch{1} % Do not stretch bars in feature graphs +\colorscalestretch{1} % Do not stretch color scales in features +\backtranstext{horizontal} % Horizontal triplets in feature texts +\backtranslabel{alternating} % Alternating triplets in feature styles +\setfamily{residues}{tt} % Use typewriter family for residues +\setseries{residues}{md} % Use normal series for residues +\setshape {residues}{up} % Use upright shape for residues +\setsize {residues}{normalsize} % Use normal size for residues +\setfamily{numbering}{tt} % Use typewriter family for numbering +\setseries{numbering}{md} % Use normal series for numbering +\setshape {numbering}{up} % Use upright shape for numbering +\setsize {numbering}{normalsize} % Use normal size for numbering +\setfamily{names}{tt} % Use typewriter family for names +\setseries{names}{md} % Use normal series for names +\setshape {names}{up} % Use upright shape for names +\setsize {names}{normalsize} % Use normal size for names +\setfamily{featurenames}{tt} % Use typewriter family for feature names +\setseries{featurenames}{md} % Use normal series for feature names +\setshape {featurenames}{up} % Use upright shape for feature names +\setsize {featurenames}{normalsize}% Use normal size for feature names +\setfamily{featurestylenames}{tt} % Use typewriter family for feature style names +\setseries{featurestylenames}{md} % Use normal series for feature style names +\setshape {featurestylenames}{up} % Use upright shape for feature style names +\setsize {featurestylenames}{normalsize}% Use normal size for feature style names +\setfamily{features}{rm} % Use roman family for feature texts +\setseries{features}{md} % Use normal series for feature texts +\setshape {features}{it} % Use italics shape for feature texts +\setsize {features}{normalsize} % Use normal size for feature texts +\setfamily{featurestyles}{tt} % Use typewriter family for feature styles +\setseries{featurestyles}{md} % Use normal series for feature styles +\setshape {featurestyles}{up} % Use upright shape for feature styles +\setsize {featurestyles}{normalsize}% Use normal size for feature styles +\setfamily{legend}{tt} % Use typewriter family for legend texts +\setseries{legend}{md} % Use normal series for legend texts +\setshape {legend}{up} % Use upright shape for legend texts +\setsize {legend}{normalsize} % Use normal size for legend texts +\setfamily{ruler}{sf} % Use sans serif font for ruler numbers +\tintdefault{medium} % Use medium tint intensity +\emphdefault{it} % Use italics to emphasize regions +\showonPHDsec{alpha,beta} % Show helices and strands (PHD input) +\showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input) +\showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input) +\showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input) +\showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input) +\secondcolumnDSSP % Use numbering from 2. column in DSSP +\appearance{PHDtopo}{internal} % \ + {bottom}{'-'} % \ + {int.\ \Alphacount} % | +\appearance{PHDtopo}{external} % | + {top}{,-,} % | + {ext.\ \Alphacount} % | +\appearance{PHDtopo}{TM}{top} % | + {box[LightGray]:TM\numcount}{} % | +\appearance{HMMTOP}{internal} % | + {bottom}{'-'} % | + {int.\ \Alphacount} % | +\appearance{HMMTOP}{external} % | + {top}{,-,} % | + {ext.\ \Alphacount} % | +\appearance{HMMTOP}{TM}{top} % | + {helix}{TM\numcount} % | +\appearance{PHDsec}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{PHDsec}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | Definitions for the appearance of +\appearance{STRIDE}{3-10}{top} % \ + {fill:$\circ$}{3$_{10}$} % > secondary structures included from| +\appearance{STRIDE}{pi} % / + {top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files. +\appearance{STRIDE}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{STRIDE}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{DSSP}{3-10}{top} % | + {fill:$\circ$}{3$_{10}$} % | +\appearance{DSSP}{pi} % | + {top}{---}{$\pi$} % | +\appearance{DSSP}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{DSSP}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{DSSP}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{bend}{top} % / + {fill:$\diamond$}{} % / + +\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity + +\pepsims{F}{YW} % Y and W are similar to F +\pepsims{Y}{WF} % W and F are similar to Y +\pepsims{W}{YF} % Y and F are similar to W + +\pepsims{I}{LVM} % L, V and M are similar to I +\pepsims{L}{VMI} % V, M and I are similar to L +\pepsims{V}{MIL} % M, I and L are similar to V + +\pepsims{R}{KH} % K and H are similar to R +\pepsims{K}{HR} % H and R are similar to K +\pepsims{H}{RK} % R and K are similar to H + +\pepsims{A}{GS} % G and S are similar to A +\pepsims{G}{A} % A (but not S) is similar to G + +\pepsims{S}{TA} % T and A are similar to S +\pepsims{T}{S} % S (but not A) is similar to T + +\pepsims{D}{EN} % E and N (but not Q) are similar to D +\pepsims{E}{DQ} % D and Q (but not N) are similar to E +\pepsims{N}{QD} % Q and D (but not E) are similar to N +\pepsims{Q}{NE} % N and E (but not D) are similar to Q + +\DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity + +\DNAsims{A}{GR} % G and R are similar to A +\DNAsims{G}{AR} % A and R are similar to G +\DNAsims{R}{AG} % A and G are similar to R + +\DNAsims{C}{TY} % T and Y are similar to C +\DNAsims{T}{CY} % C and Y are similar to T +\DNAsims{Y}{CT} % C and T are similar to Y +%</definitions> +% \end{macrocode} +% \begin{macrocode} +%<*AQPDNA> +AQPDNA.MSF MSF: 979 Type: N Freitag, 12. Februar 1999 Check: 2594 .. +Name: AQP1nuc.SEQ Len: 807 Check: 8330 Weight: 1.00 +Name: AQP2nuc.SEQ Len: 813 Check: 7220 Weight: 1.00 +Name: AQP3nuc.SEQ Len: 855 Check: 7590 Weight: 1.00 +Name: AQP4nuc.SEQ Len: 960 Check: 8696 Weight: 1.00 +Name: AQP5nuc.SEQ Len: 795 Check: 758 Weight: 1.00 +// + 1 60 +AQP1nuc.SEQ ATGGCCAGCGAAATCAAGAAGAAGC.................TCTTCT........GGAG +AQP2nuc.SEQ ATGTG....GGAACTCAG.........................ATCCAT........... +AQP3nuc.SEQ ATG........AACC........GTTGCGGGG.AGATG.....CTCC............. +AQP4nuc.SEQ ATGAGTGACGGAGCTGCAGCGAGGCGGTGGGGTAAGTGTGGACCTCCCTGCAGCAGAGAG +AQP5nuc.SEQ ATGAAAAA.GGAGGTGTG.........................CTCCCT........... + + 61 120 +AQP1nuc.SEQ GGC..TGTGGTGGCT.....GAGTTCCTGGCCATGA.CCCTCTTCG.............. +AQP2nuc.SEQ ...................................AGCCTTCTCCCGAGCAGTGCTGGCT +AQP3nuc.SEQ .ACATCC.....GCTACCGG......CTG.........CTTCGCCA....GGCTCTGGCG +AQP4nuc.SEQ AGCATCATGGTGGCTTTCAAAGGCGTCTGGACTCAAGCCTTCTGGAAGGCGGTCACAGCA +AQP5nuc.SEQ ...................................TGCCTTCTTCAAGGCGGTGTTCGCA + + 121 180 +AQP1nuc.SEQ ....TCTTCATCAGCATCGGTTCTGCCCTA...GGCTT.....CAATTACCCACTGGAGA +AQP2nuc.SEQ GAGTTCTTGGCCACGCTCCTTTTTGTCTTCTTTGGCCTTGGCTCAGCCCTCCA.....GT +AQP3nuc.SEQ GAGTGCCTGGGGACCCTCATCCTTGTGATGTTCGGCTGTGGTTCCGTGGCTCAA.GTGGT +AQP4nuc.SEQ GAGTTCCTGGCCATGCTCATCTTTGTTCTGCTCAGCGTGGGATCCACCATTAACTGGGGT +AQP5nuc.SEQ GAGTTCCTGGCCACCCTCATCTTCGTCTTCTTTGGCCTGGGCTCAGCACTCAA.....GT + + 181 240 +AQP1nuc.SEQ GA...AACCAGACGCTGGTCCA.GGACAATGTGAAGGTGTCACTGGCCTTTGGTCTGAGC +AQP2nuc.SEQ GGGCCAGCT....CCCCACCCTC...TGTGCTCCAGATCGCCGTGGCCTTTGGTCTGGGC +AQP3nuc.SEQ GCTCAGCCGAGGGACCCATG.GTGG.CTTCCTCACCATCAACTTGGCTTTTGGCTTCGCT +AQP4nuc.SEQ GGCTCAGAGAACCCCCTACCTGTGGACATGGTCCTCATCTCCCTCTGCTTTGGACTCAGC +AQP5nuc.SEQ GGCCCTCGG....CTCTGCCCAC...CATTCTGCAAATCTCAATTGCCTTTGGCCTGGCC + + 241 300 +AQP1nuc.SEQ ATCGCTACTCTGGCCCAAAGTGTGGGTCACATCAGTGGTGCTCACTCCAACCCAGCGGTC +AQP2nuc.SEQ ATCGGCATCCTGGTTCAGGCTCTGGGCCATGTCAGCGGGGCACACATCAACCCCGCCGTG +AQP3nuc.SEQ GTCACCCTTGCCATCTTGGTGGCTGGCCAAGTGTCTGGAGCCCACTTGAACCCTGCTGTG +AQP4nuc.SEQ ATTGCCACCATGGTTCAGTGCTTCGGCCACATCAGCGGTGGCCACATCAACCCAGCGGTG +AQP5nuc.SEQ ATAGGTACCTTAGCCCAAGCTCTGGGACCTGTGAGTGGTGGCCACATCAATCCAGCCATT + + 301 360 +AQP1nuc.SEQ ACACTGGGGCTTCTGCTCAGCTGTCAGATCAGCATCCTCCGGGCTGTCA.TGTATATCAT +AQP2nuc.SEQ ACTGTGGCATGCCTGGTGGGTTGCCATGTCTCCTTCCTTCGAGCTGCCT.TCTATGTGGC +AQP3nuc.SEQ ACCTTTGCAATG.TGCTTCCTGGCACGAGAGCCCTGGATCAAGCTGCCCATCTACACACT +AQP4nuc.SEQ ACAGTGGCCATGGTGTGCACACGAAAGATCAGCATCGCCAAGTCTGTCT.TCTACATCAC +AQP5nuc.SEQ ACTCTGGCCCTCTTAATAGGAAACCAGATCTCGCTGCTCCGAGCTGTCT.TCTACGTGGC + + 361 420 +AQP1nuc.SEQ CGCCCAGTGTGTGGGAGCCATCGTTGCCTCCGCCATCCTCTCCGGCATCACCTCCTCCCT +AQP2nuc.SEQ TGCCCAGCTGCTGGGCGCCGTGGCTGGGGCTGCCATCCTCCATGAGATTAC.TCCAGTAG +AQP3nuc.SEQ GGCACAGACCCTCGGGGCCTTCTTGGGTGCTGGGATTGTTTTTGGGCT..CTACTA..TG +AQP4nuc.SEQ TGCGCAGTGCCTGGGGGCCATCATCGGAGCTGGGATCCTCTACCTGGTCAC.ACCCCCCA +AQP5nuc.SEQ AGCCCAGCTGGTGGGCGCCATTGCTGGGGCAGGCATCCTGTACTGGCTGGC.GCCACTCA + + 421 480 +AQP1nuc.SEQ GCTCGAGAACTCACTTGGCCGA.AATGACCTGGCTCGAGGTGTGAACTCCGGCCAGGGCC +AQP2nuc.SEQ AAATCCGTGGGGACCTGGCTGTCAATGCTCTCCACAACAACGCCACAGCTGGCCAGGCTG +AQP3nuc.SEQ ATGCAATCTGGGCCTTTGCTGGCAATGAGCT.........TGTTGTCTCCGGCC.....C +AQP4nuc.SEQ GCGTGGTGGGAGGATTGGGAGTCACCACGGTTCATGGAAACCTCACTGCTGGCCATGGGC +AQP5nuc.SEQ ATGCCCGGGGTAACCTGGCCGTCAATGCGCTGAACAACAACACAACGCCTGGCAAGGCCA + + 481 540 +AQP1nuc.SEQ TGGGCATTGAGATCATTGGCACCCTGCAGCTGGTGCTGTGCGT.TCTGGCTACCACTGAC +AQP2nuc.SEQ TGACTGTAGAGCTCTTCCTGACCATGCAGCTGGTGCTGTGCAT.CTTTGCCTCCACCGAC +AQP3nuc.SEQ CAATGGCACAGCTGGTATC..TTTGCCACCTATCCCTCTGGACACTTGGATATGGTCAAT +AQP4nuc.SEQ TCCTGGTGGAGCTAATAATCACTTTCCAGCTGGTATTCACCAT.TTTTGCCAGCTGTGAT +AQP5nuc.SEQ TGGTGGTGGAGTTAATCTTGACTTTCCAGCTAGCCCTCTGCAT.CTTCTCCTCCACCGAC + + 541 600 +AQP1nuc.SEQ CGGAGGCGCCGAGACTTAGGTGGCTCAGCCCCACTTGCCATTGGCTTGTCTGTGGCTCTT +AQP2nuc.SEQ GAGCGCCGCGGTGACAACCTGGGTAGCCCTGCCCTCTCCATTGGTTTCTCTGTTACCCTG +AQP3nuc.SEQ GGCTTCTTTGATCAGTTCATAGGCACAGCAGCCCTTATTGTGTGTGTGCTGGCCATTGTT +AQP4nuc.SEQ TCCAAACGGACTGATGTTACTGGTTCCGTTGCTTTAGCAATTGGGTTTTCCGTTGCAATT +AQP5nuc.SEQ TCTCGCCGAACCAGCCCTGTGGGCTCCCCAGCCTTATCCATTGGCTTGTCTGTCACACTG + + 601 660 +AQP1nuc.SEQ GGACACCTGCTGGCCATTGACTACACTGGCTGTGGGATCAACCCTGCCCGGTCATT.TGG +AQP2nuc.SEQ GGCCACCTCCTTGGGATCTATTTCACCGGTTGCTCCATGAATCCAGCCCGCTCCCT.GGC +AQP3nuc.SEQ GACC..CTTATAACAACCCTGTGCCCCGGGGCCTGGAGGCCTTCACTGTGGGCCTTGTGG +AQP4nuc.SEQ GGACATTTGTTTGCAATCAATTATACCGGAGCCAGCATGAATCCAGCTCGATCCTT.TGG +AQP5nuc.SEQ GGCCATCTTGTGGGGATCTACTTCACCGGCTGTTCCATGAACCCAGCCCGATCTTT.CGG + + 661 720 +AQP1nuc.SEQ CTCTGCTGTGCTCACCCGCAACTTCTCAAAC...CACTGGATTTTCTGGGTGGGACCATT +AQP2nuc.SEQ TCCAGCAGTTGTCACTGGCAAGTTTGATGA...TCACTGGGTCTTCTGGATCGGACCCCT +AQP3nuc.SEQ TCCTG.....GTCATTGGGACCTCCATGGGCTTCAATTCTGGCTATGCCGTCAACCCAGC +AQP4nuc.SEQ CCCTGCAGTTATCATGGGAAACTGGGAAAAC...CACTGGATATATTGGGTTGGACCAAT +AQP5nuc.SEQ CCCTGCGGTGGTCATGAACCGGTTCAGCCCCTCTCACTGGGTCTTCTGGGTAGGGCCTAT + + 721 780 +AQP1nuc.SEQ CATTGGGAGTGCCCTGGCAGTGCTGATCTATGACTTCATC..CTGGCCCCACGC..AGC. +AQP2nuc.SEQ GGTGGGCGCCATCATCGGCTCCCTCCTCTACAACTAC..CTGCTGTTC..........CC +AQP3nuc.SEQ T.....CGTGACTTTGG..ACCTCGCCTTTTCACTGCCCTGGCTGGC......TGGGGTT +AQP4nuc.SEQ CATAGGCGCTGTGCTGGCAGGTGCACTTTACGAGTATGTCTTCTGTCCTGACGTGGAGCT +AQP5nuc.SEQ TGTGGGGGCCATGCTGGCGGCCATCCTCTATTTCTAC..CTGCTCTTC..........CC + + 781 840 +AQP1nuc.SEQ ..AGCG.........................ACTTTACAG.............ACCGCAT +AQP2nuc.SEQ C.....TCGGCAAAG...AGCCTGCAGGAGCGCTTGGCAGTGCTCAAGGG.......CCT +AQP3nuc.SEQ CAGAAGTC.TTTACGACTGGCC...AGAACTGGTGGTGGGTACCCATCGTCTCTCCACTC +AQP4nuc.SEQ CAAACGTCGCCTAAAGGAAGCCTTCAGCAAAGCTGCACAGCAGACGAAAGGGAGCTACAT +AQP5nuc.SEQ C.....TCCTCTCTG...AGCCTCCATGATCGCGTGGCTGTCGTCAAAGG.......CAC + + 841 900 +AQP1nuc.SEQ GAAGGTGTGGACCAGT...GGCCAAGTGGA.....GGAGTATGACCTGGATGC....... +AQP2nuc.SEQ GGAGCCCGACACCGACTGGGA.......GGAACGTGAAGTGCGG..CGGCGGCAGTCGGT +AQP3nuc.SEQ CTGGGTTC.CATTGGTGGTGTCTTCGTGT.ACCAGCT..CATGAT.TGGCTGCCACC..T +AQP4nuc.SEQ GGAGGTGGAGGACAACCGGAGCCAAGTGGAGACAGAAGACTTGATCCTGAAGCCCGGGGT +AQP5nuc.SEQ ATA...TGA.GCCGG..AGGA.......GGACTGGGAAGATCAT..CGAGAGGAGAGGAA + + 901 960 +AQP1nuc.SEQ ........TGAT.GATATCAACTCCAGGGTGGAGATGAAG.................... +AQP2nuc.SEQ GGAGC......TC..CACTCTCCTCAGAG...................CCTGCCTCGCG. +AQP3nuc.SEQ GGAGCA.GCCCCCGCCTTCCACT..GAGGCAGAGAATGTGAAGCTGG.CCCACATGAAGC +AQP4nuc.SEQ GGTGCATGTGATCGACATTGACCGTGGAGACGAGAAGAAGGGGAAGGACTCGTCTGGAGA +AQP5nuc.SEQ GAAG............ACCATC....GAG........................CTGACG. + + 961 979 +AQP1nuc.SEQ ..........CCCAAATAG +AQP2nuc.SEQ .GCAGCAAGGCCTG....A +AQP3nuc.SEQ ACAAGGA..GCAGATCTGA +AQP4nuc.SEQ GGTATTATCTTCTGTATGA +AQP5nuc.SEQ .GCA.CA....CTG....A + +%</AQPDNA> +% \end{macrocode} +% \begin{macrocode} +%<*AQPpro> +AQPpro.MSF MSF: 356 Type: P Freitag, 12. Februar 1999 Check: 2586 .. +Name: AQP1.PRO Len: 269 Check: 5367 Weight: 1.00 +Name: AQP2.PRO Len: 271 Check: 6176 Weight: 1.00 +Name: AQP3.PRO Len: 285 Check: 2893 Weight: 1.00 +Name: AQP4.PRO Len: 323 Check: 9737 Weight: 1.00 +Name: AQP5.PRO Len: 265 Check: 8413 Weight: 1.00 +// + 1 60 +AQP1.PRO MAS........................EIKKKLFWRAVVAEFLAMTLFVFISIGSALGFN +AQP2.PRO MW.........................ELRSIAFSRAVLAEFLATLLFVFFGLGSALQWA +AQP3.PRO M.........NRCG.....EMLHIRYR......LLRQALAECLGTLILVMFGCGSVAQVV +AQP4.PRO MSDGAAARRWGKCGPPCSRESIMVAFKGVWTQAFWKAVTAEFLAMLIFVLLSVGSTINWG +AQP5.PRO MK........................KEVCSLAFFKAVFAEFLATLIFVFFGLGSALKWP + + 61 120 +AQP1.PRO YPLERNQTLVQDNVKVSLAFGLSIATLAQSVGHISGAHSNPAVTLGLLLSCQISILRAVM +AQP2.PRO ...SS....PPSVLQIAVAFGLGIGILVQALGHVSGAHINPAVTVACLVGCHVSFLRAAF +AQP3.PRO LSRGTH....GGFLTINLAFGFAVTLAILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPI +AQP4.PRO ...GSENPLPVDMVLISLCFGLSIATMVQCFGHISGGHINPAVTVAMVCTRKISIAKSVF +AQP5.PRO ...SA....LPTILQISIAFGLAIGTLAQALGPVSGGHINPAITLALLIGNQISLLRAVF + + 121 180 +AQP1.PRO YIIAQCVGAIVASAILSGI..........TSSLLENSLGRNDLARGVNSGQ.....GLGI +AQP2.PRO YVAAQLLGAVAGAAILHEI..........TPVEIRGDLAVNALHNNATAGQ.....AVTV +AQP3.PRO YTLAQTLGAFLGAGIVFGLYYDAIWAFAGNELVVSGPNGTAGIFATYPSGHLDMVNGFFD +AQP4.PRO YITAQCLGAIIGAGILYLV..........TPPSVVGGLGVTTVHGNLTAGH.....GLLV +AQP5.PRO YVAAQLVGAIAGAGILYWL..........APLNARGNLAVNALNNNTTPGK.....AMVV + + 181 240 +AQP1.PRO EIIGTLQLVLCVLATTDR.RRRDLGGSAPLAIGLSVALGHLLAIDYTGCGINPARSFGSA +AQP2.PRO ELFLTMQLVLCIFASTDE.RRGDNLGSPALSIGFSVTLGHLLGIYFTGCSMNPARSLAPA +AQP3.PRO QFIGTAALIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPR +AQP4.PRO ELIITFQLVFTIFASCDS.KRTDVTGSVALAIGFSVAIGHLFAINYTGASMNPARSFGPA +AQP5.PRO ELILTFQLALCIFSSTDS.RRTSPVGSPALSIGLSVTLGHLVGIYFTGCSMNPARSFGPA + + 241 300 +AQP1.PRO VLTR..NFS.N......HWIFWVGPFIGSALAVL..IYDFILAPRSSDFTDRMK...... +AQP2.PRO VVTG..KFD.D......HWVFWIGPLVGAIIGSL..LYNYLLFPSAKSLQERL..AVLKG +AQP3.PRO LFTALAGWGSEVFTTGQNW..WWVPIVSPLLGSIGGVFVYQL.................. +AQP4.PRO VIMG..NWE.N......HWIYWVGPIIGAVLAGA..LYEYV.FCPDVELKRRLKEAFSKA +AQP5.PRO VVMN..RFSPS......HWVFWVGPIVGAMLAAI..LYFYLLFPSSLSLHDRV..AVVKG + + 301 354 +AQP1.PRO ......VWTS.....GQVEEYDLDAD.......DINSRVEMKPK.......... +AQP2.PRO .LEPDTDWEEREVRRRQ..SVELHSPQSLPRG...................SKA +AQP3.PRO .................MIGCHLEQPPPSTEAENV.KLAHMKHKE.......QI +AQP4.PRO AQQTKGSYMEVEDNRSQVETEDLILKPGVVHVIDIDRGDEKKGKDSSGEVLSSV +AQP5.PRO TYEPEEDWEDHREERKK..TIELTAH............................ + +%</AQPpro> +% \end{macrocode} +% \begin{macrocode} +%<*AQP2spec> +AQP2bt SIAFSRAVLAEFLATLLFVFFGLGSALNWPQALPSVLQIAMAFGLAIGTLVQALGHVSGA +AQP2cf SVAFSRAVFAEFLATLLFVFFGLGSALNWPQALPSVLQIAMAFGLGIGTLVQALGHVSGA +AQP2dd SIAFSRAVFSEFLATLLFVFFGLGSALNWPQALPSVLQIAMAFGLAIGTLVQALGHISGA +AQP2ec SIAFSRAVLAEFLATLLFVFFGLGSALNWPQAMPSVLQIAMAFGLAIGTLVQALGHVSGA +AQP2em SIAFSRAVFSEFLATLLFVFFGLGSALNWPQALPSVLQIAMAFGLAIGTLVQTLGHISGA + + +AQP2bt HINPAVTVACLVGCHVSFLRAVFYVAAQLLGAVAGAALLHEITPPAIRG +AQP2cf HINPAVTVACLVGCHVSFLRAAFYVAAQLLGAVAGAALLHEITPPHVRG +AQP2dd HINPAVTVACLVGCHVSFLRATFYLAAQLLGAVAGAAILHEITPPDIRG +AQP2ec HINPAVTVACLVGCHVSFLRAAFYVAAQLLGAVAGAALLHEITPPDIRR +AQP2em HINPAVTVACLVGCHVSFLRATFYLAAQLLGAVAGAALLHELTPPDIRG + +%</AQP2spec> +% \end{macrocode} +% \begin{macrocode} +%<*AQP1topo> +\feature{bottom}{1}{1..14}{'-'}{int.\ A} +\feature{top}{1}{15..32}{box[LightGray]:TM1}{} +\feature{top}{1}{33..49}{,-,}{ext.\ B} +\feature{top}{1}{50..68}{box[LightGray]:TM2}{} +\feature{bottom}{1}{69..81}{'-'}{int.\ C} +\feature{top}{1}{82..106}{box[LightGray]:TM3}{} +\feature{top}{1}{107..136}{,-,}{ext.\ D} +\feature{top}{1}{137..154}{box[LightGray]:TM4}{} +\feature{bottom}{1}{155..168}{'-'}{int.\ E} +\feature{top}{1}{169..186}{box[LightGray]:TM5}{} +\feature{top}{1}{187..211}{,-,}{ext.\ F} +\feature{top}{1}{212..230}{box[LightGray]:TM6}{} +\feature{bottom}{1}{231..269}{'-'}{int.\ G} +%</AQP1topo> +% \end{macrocode} +% \begin{macrocode} +%<*AQP1PHD> + +From phd@EMBL-Heidelberg.de Wed Nov 25 10:24:25 1998 +Date: Tue, 24 Nov 1998 17:45:25 +0100 +From: Protein Prediction <phd@EMBL-Heidelberg.de> +To: eric.beitz@uni-tuebingen.de +Subject: PredictProtein + + + + +The following information has been received by the server: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +________________________________________________________________________________ + +reference predict_h25873 (Tue Nov 24 17:43:21 MET 1998) +from eric.beitz@uni-tuebingen.de +password(###) +resp MAIL +orig HTML +prediction of: -secondary structure (PHDsec)-solvent accessibility (PHDacc)- +return msf format +# no description +MASEIKKKLFWRAVVAEFLAMTLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSIATLAQSVGHISGAHSNPAVT +LGLLLSCQISILRAVMYIIAQCVGAIVASAILSGITSSLLENSLGRNDLARGVNSGQGLGIEIIGTLQLVLCVLATTDRR +RRDLGGSAPLAIGLSVALGHLLAIDYTGCGINPARSFGSAVLTRNFSNHWIFWVGPFIGSALAVLIYDFILAPRSSDFTD +RMKVWTSGQVEEYDLDADDINSRVEMKPK + +________________________________________________________________________________ + + + + + +Result of PROSITE search (Amos Bairoch): +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +please quote: A Bairoch, P Bucher & K Hofmann: The PROSITE database, +its status in 1997. Nucl. Acids Res., 1997, 25, 217-221. + +________________________________________________________________________________ + + +-------------------------------------------------------- + +-------------------------------------------------------- + +Pattern-ID: ASN_GLYCOSYLATION PS00001 PDOC00001 +Pattern-DE: N-glycosylation site +Pattern: N[^P][ST][^P] + 42 NQTL + 250 NFSN + +Pattern-ID: GLYCOSAMINOGLYCAN PS00002 PDOC00002 +Pattern-DE: Glycosaminoglycan attachment site +Pattern: SG.G + 135 SGQG + +Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005 +Pattern-DE: Protein kinase C phosphorylation site +Pattern: [ST].[RK] + 157 TDR + 398 TDR + +Pattern-ID: CK2_PHOSPHO_SITE PS00006 PDOC00006 +Pattern-DE: Casein kinase II phosphorylation site +Pattern: [ST].{2}[DE] + 118 SLLE + 383 SRVE + +Pattern-ID: MYRISTYL PS00008 PDOC00008 +Pattern-DE: N-myristoylation site +Pattern: G[^EDRKHPFYW].{2}[STAGCN][^P] + 30 GSALGF + 92 GLSIAT + 179 GLLLSC + 288 GAIVAS + 407 GITSSL + 544 GVNSGQ + 722 GLSVAL + 917 GINPAR + 1141 GSALAV + +Pattern-ID: PROKAR_LIPOPROTEIN PS00013 PDOC00013 +Pattern-DE: Prokaryotic membrane lipoprotein lipid attachment site +Pattern: [^DERK]{6}[LIVMFWSTAG]{2}[LIVMFYSTAGCQ][AGS]C + 77 PAVTLGLLLSC + +Pattern-ID: MIP PS00221 PDOC00193 +Pattern-DE: MIP family signature +Pattern: [HNQA].NP[STA][LIVMF][ST][LIVMF][GSTAFY] + 74 HSNPAVTLG + + + + +________________________________________________________________________________ + + + + + +Result of ProDom domain search (Corpet, Gouzy, Kahn): +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- please quote: ELL Sonnhammer & D Kahn, Prot. Sci., 1994, 3, 482-492 + +________________________________________________________________________________ + + +--- ------------------------------------------------------------ +--- Results from running BLAST against PRODOM domains +--- +--- PLEASE quote: +--- F Corpet, J Gouzy, D Kahn (1998). The ProDom database +--- of protein domain families. Nucleic Ac Res 26:323-326. +--- +--- BEGIN of BLASTP output +BLASTP 1.4.7 [16-Oct-94] [Build 17:06:52 Oct 31 1994] + +Reference: Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, +and David J. Lipman (1990). Basic local alignment search tool. J. Mol. Biol. +215:403-10. + +Query= prot (#) ppOld, no description /home/phd/server/work/predict_h25873 + (269 letters) + +Database: /home/phd/ut/prodom/prodom_34_2 + 53,597 sequences; 6,740,067 total letters. +Searching..................................................done + + Smallest + Sum + High Probability +Sequences producing High-scoring Segment Pairs: Score P(N) N + + 390 p34.2 (45) MIP(6) AQP1(4) GLPF(4) // PROTEIN INTRIN... 270 2.0e-32 1 + 45663 p34.2 (1) AQPZ_ECOLI // AQUAPORIN Z. 90 3.2e-13 2 + 45611 p34.2 (1) AQP2_HUMAN // AQUAPORIN-CD (AQP-CD) (WAT... 136 6.0e-13 1 + 304 p34.2 (61) AQP2(10) GLPF(6) MIP(5) // PROTEIN CHANN... 121 9.2e-11 1 + 45607 p34.2 (1) PMIP_NICAL // POLLEN-SPECIFIC MEMBRANE I... 80 1.2e-07 2 + 45606 p34.2 (1) BIB_DROME // NEUROGENIC PROTEIN BIG BRAIN. 80 1.2e-05 2 + 2027 p34.2 (15) GLPF(9) AQP3(2) // PROTEIN FACILITATOR ... 60 3.4e-05 2 + 45615 p34.2 (1) GLPF_STRPN // GLYCEROL UPTAKE FACILITATO... 63 0.024 1 + 45638 p34.2 (1) AQP5_HUMAN // AQUAPORIN 5. 61 0.044 1 + + + +>390 p34.2 (45) MIP(6) AQP1(4) GLPF(4) // PROTEIN INTRINSIC CHANNEL WATER + AQUAPORIN TONOPLAST MEMBRANE FOR PLASMA LENS + Length = 88 + + Score = 270 (125.3 bits), Expect = 2.0e-32, P = 2.0e-32 + Identities = 47/67 (70%), Positives = 56/67 (83%) + +Query: 156 TTDRRRRDLGGSAPLAIGLSVALGHLLAIDYTGCGINPARSFGSAVLTRNFSNHWIFWVG 215 + T D+RR +GGSAPL IG SVALGHL+ I YTGCG+NPARSFG AV+T NF+NHW++WVG +Sbjct: 22 TDDKRRGSVGGSAPLPIGFSVALGHLIGIPYTGCGMNPARSFGPAVVTGNFTNHWVYWVG 81 + +Query: 216 PFIGSAL 222 + P IG+ L +Sbjct: 82 PIIGAVL 88 + + Score = 95 (44.1 bits), Expect = 2.3e-06, P = 2.3e-06 + Identities = 20/33 (60%), Positives = 23/33 (69%) + +Query: 136 GQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSA 168 + GQ L +EIIGT QLV CV ATTD +RR G + +Sbjct: 1 GQNLVVEIIGTFQLVYCVFATTDDKRRGSVGGS 33 + + +>45663 p34.2 (1) AQPZ_ECOLI // AQUAPORIN Z. + Length = 96 + + Score = 90 (41.8 bits), Expect = 3.2e-13, Sum P(2) = 3.2e-13 + Identities = 18/36 (50%), Positives = 25/36 (69%) + +Query: 166 GSAPLAIGLSVALGHLLAIDYTGCGINPARSFGSAV 201 + G AP+AIGL++ L HL++I T +NPARS A+ +Sbjct: 25 GFAPIAIGLALTLIHLISIPVTNTSVNPARSTAVAI 60 + + Score = 63 (29.2 bits), Expect = 3.2e-13, Sum P(2) = 3.2e-13 + Identities = 11/25 (44%), Positives = 14/25 (56%) + +Query: 210 WIFWVGPFIGSALAVLIYDFILAPR 234 + W FWV P +G + LIY +L R +Sbjct: 71 WFFWVVPIVGGIIGGLIYRTLLEKR 95 + + +>45611 p34.2 (1) AQP2_HUMAN // AQUAPORIN-CD (AQP-CD) (WATER CHANNEL PROTEIN FOR + RENAL COLLECTING DUCT) (ADH WATER CHANNEL) (AQUAPORIN 2) (COLLECTING DUCT + WATER CHANNEL PROTEIN) (WCH-CD). + Length = 49 + + Score = 136 (63.1 bits), Expect = 6.0e-13, P = 6.0e-13 + Identities = 23/42 (54%), Positives = 34/42 (80%) + +Query: 50 VKVSLAFGLSIATLAQSVGHISGAHSNPAVTLGLLLSCQISI 91 + +++++AFGL I TL Q++GHISGAH NPAVT+ L+ C +S+ +Sbjct: 8 LQIAMAFGLGIGTLVQALGHISGAHINPAVTVACLVGCHVSV 49 + + +>304 p34.2 (61) AQP2(10) GLPF(6) MIP(5) // PROTEIN CHANNEL WATER AQUAPORIN + INTRINSIC DUCT COLLECTING FOR TONOPLAST WCH-CD + Length = 43 + + Score = 121 (56.1 bits), Expect = 9.2e-11, P = 9.2e-11 + Identities = 24/43 (55%), Positives = 31/43 (72%) + +Query: 70 ISGAHSNPAVTLGLLLSCQISILRAVMYIIAQCVGAIVASAIL 112 + ISG H NPAVT+GLL+ + LRAV YI AQ +GA+ +A+L +Sbjct: 1 ISGGHINPAVTIGLLIGGRFPFLRAVFYIAAQLLGAVAGAALL 43 + + +>45607 p34.2 (1) PMIP_NICAL // POLLEN-SPECIFIC MEMBRANE INTEGRAL PROTEIN. + Length = 69 + + Score = 80 (37.1 bits), Expect = 1.2e-07, Sum P(2) = 1.2e-07 + Identities = 17/54 (31%), Positives = 32/54 (59%) + +Query: 149 LVLCVLATTDRRRRDLGGSAPLAIGLSVALGHLLAIDYTGCGINPARSFGSAVL 202 + L++ V++ R +G A +A+G+++ L +A +G +NPARS G A++ +Sbjct: 13 LLMFVISGVATDDRAIGQVAGIAVGMTITLNVFVAGPISGASMNPARSIGPAIV 66 + + Score = 34 (15.8 bits), Expect = 1.2e-07, Sum P(2) = 1.2e-07 + Identities = 8/18 (44%), Positives = 11/18 (61%) + +Query: 136 GQGLGIEIIGTLQLVLCV 153 + GQ L IEII + L+ + +Sbjct: 1 GQSLAIEIIISFLLMFVI 18 + + +>45606 p34.2 (1) BIB_DROME // NEUROGENIC PROTEIN BIG BRAIN. + Length = 119 + + Score = 80 (37.1 bits), Expect = 1.2e-05, Sum P(2) = 1.2e-05 + Identities = 15/34 (44%), Positives = 24/34 (70%) + +Query: 1 MASEIKKKLFWRAVVAEFLAMTLFVFISIGSALG 34 + M +EI+ FWR++++E LA ++VFI G+A G +Sbjct: 55 MQAEIRTLEFWRSIISECLASFMYVFIVCGAAAG 88 + + Score = 39 (18.1 bits), Expect = 1.2e-05, Sum P(2) = 1.2e-05 + Identities = 9/17 (52%), Positives = 12/17 (70%) + +Query: 53 SLAFGLSIATLAQSVGH 69 + +LA GL++ATL Q H +Sbjct: 103 ALASGLAMATLTQCFLH 119 + + +>2027 p34.2 (15) GLPF(9) AQP3(2) // PROTEIN FACILITATOR GLYCEROL UPTAKE + AQUAPORIN DIFFUSION UPTAKE/EFFLUX PEPX 5'REGION ORF1 + Length = 55 + + Score = 60 (27.8 bits), Expect = 3.4e-05, Sum P(2) = 3.4e-05 + Identities = 17/46 (36%), Positives = 20/46 (43%) + +Query: 156 TTDRRRRDLGGSAPLAIGLSVALGHLLAIDYTGCGINPARSFGSAV 201 + T D GG PL +G V + TG INPAR FG + +Sbjct: 10 TDDGNNVPSGGLHPLMVGFLVMGIGMSLGGTTGYAINPARDFGPRI 55 + + Score = 37 (17.2 bits), Expect = 3.4e-05, Sum P(2) = 3.4e-05 + Identities = 7/10 (70%), Positives = 8/10 (80%) + +Query: 149 LVLCVLATTD 158 + L+ CVLA TD +Sbjct: 2 LIACVLALTD 11 + + +>45615 p34.2 (1) GLPF_STRPN // GLYCEROL UPTAKE FACILITATOR PROTEIN. + Length = 26 + + Score = 63 (29.2 bits), Expect = 0.025, P = 0.024 + Identities = 13/23 (56%), Positives = 18/23 (78%) + +Query: 205 NFSNHWIFWVGPFIGSALAVLIY 227 + ++S WI VGP IG+ALAVL++ +Sbjct: 1 DWSYAWIPVVGPVIGAALAVLVF 23 + + +>45638 p34.2 (1) AQP5_HUMAN // AQUAPORIN 5. + Length = 27 + + Score = 61 (28.3 bits), Expect = 0.045, P = 0.044 + Identities = 11/19 (57%), Positives = 18/19 (94%) + +Query: 50 VKVSLAFGLSIATLAQSVG 68 + ++++LAFGL+I TLAQ++G +Sbjct: 8 LQIALAFGLAIGTLAQALG 26 + + +Parameters: + E=0.1 + B=500 + + V=500 + -ctxfactor=1.00 + + Query ----- As Used ----- ----- Computed ---- + Frame MatID Matrix name Lambda K H Lambda K H + +0 0 BLOSUM62 0.322 0.138 0.394 same same same + + Query + Frame MatID Length Eff.Length E S W T X E2 S2 + +0 0 269 269 0.10 69 3 11 22 0.22 33 + + +Statistics: + Query Expected Observed HSPs HSPs + Frame MatID High Score High Score Reportable Reported + +0 0 59 (27.4 bits) 270 (125.3 bits) 14 14 + + Query Neighborhd Word Excluded Failed Successful Overlaps + Frame MatID Words Hits Hits Extensions Extensions Excluded + +0 0 5349 3124825 609708 2510548 4569 2 + + Database: /home/phd/ut/prodom/prodom_34_2 + Release date: unknown + Posted date: 12:24 PM MET DST May 06, 1998 + # of letters in database: 6,740,067 + # of sequences in database: 53,597 + # of database sequences satisfying E: 9 + No. of states in DFA: 564 (111 KB) + Total size of DFA: 226 KB (256 KB) + Time to generate neighborhood: 0.03u 0.00s 0.03t Real: 00:00:00 + Time to search database: 9.80u 0.03s 9.83t Real: 00:00:10 + Total cpu time: 9.90u 0.06s 9.96t Real: 00:00:10 +--- END of BLASTP output +--- ------------------------------------------------------------ +--- +--- Again: these results were obtained based on the domain data- +--- base collected by Daniel Kahn and his coworkers in Toulouse. +--- +--- PLEASE quote: +--- F Corpet, J Gouzy, D Kahn (1998). The ProDom database +--- of protein domain families. Nucleic Ac Res 26:323-326. +--- +--- The general WWW page is on: +---- --------------------------------------- +--- http://www.toulouse.inra.fr/prodom.html +---- --------------------------------------- +--- +--- For WWW graphic interfaces to PRODOM, in particular for your +--- protein family, follow the following links (each line is ONE +--- single link for your protein!!): +--- +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=390 ==> multiple alignment, consensus, PDB and PROSITE links of domain 390 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=390 ==> graphical output of all proteins having domain 390 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=45663 ==> multiple alignment, consensus, PDB and PROSITE links of domain 45663 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=45663 ==> graphical output of all proteins having domain 45663 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=45611 ==> multiple alignment, consensus, PDB and PROSITE links of domain 45611 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=45611 ==> graphical output of all proteins having domain 45611 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=304 ==> multiple alignment, consensus, PDB and PROSITE links of domain 304 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=304 ==> graphical output of all proteins having domain 304 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=45607 ==> multiple alignment, consensus, PDB and PROSITE links of domain 45607 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=45607 ==> graphical output of all proteins having domain 45607 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=45606 ==> multiple alignment, consensus, PDB and PROSITE links of domain 45606 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=45606 ==> graphical output of all proteins having domain 45606 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=2027 ==> multiple alignment, consensus, PDB and PROSITE links of domain 2027 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=2027 ==> graphical output of all proteins having domain 2027 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=45615 ==> multiple alignment, consensus, PDB and PROSITE links of domain 45615 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=45615 ==> graphical output of all proteins having domain 45615 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom1=45638 ==> multiple alignment, consensus, PDB and PROSITE links of domain 45638 +http://www.toulouse.inra.fr/prodom/cgi-bin/ReqProdomII.pl?id_dom2=45638 ==> graphical output of all proteins having domain 45638 +--- +--- NOTE: if you want to use the link, make sure the entire line +--- is pasted as URL into your browser! +--- +--- END of PRODOM +--- ------------------------------------------------------------ + +________________________________________________________________________________ + + +--- Database used for sequence comparison: +--- SEQBASE RELEASE 34.0 OF EMBL/SWISS-PROT WITH 59021 SEQUENCES + + + + +The alignment that has been used as input to the network is: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +________________________________________________________________________________ + +--- ------------------------------------------------------------ +--- MAXHOM multiple sequence alignment +--- ------------------------------------------------------------ +--- +--- MAXHOM ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY +--- ID : identifier of aligned (homologous) protein +--- STRID : PDB identifier (only for known structures) +--- PIDE : percentage of pairwise sequence identity +--- WSIM : percentage of weighted similarity +--- LALI : number of residues aligned +--- NGAP : number of insertions and deletions (indels) +--- LGAP : number of residues in all indels +--- LSEQ2 : length of aligned sequence +--- ACCNUM : SwissProt accession number +--- NAME : one-line description of aligned protein +--- +--- MAXHOM ALIGNMENT HEADER: SUMMARY +ID STRID IDE WSIM LALI NGAP LGAP LEN2 ACCNUM NAME +aqp1_rat 100 100 269 0 0 269 P29975 PROXIMAL TUBULE) (AQUAPOR +aqp1_mouse 98 99 269 0 0 269 Q02013 PROXIMAL TUBULE) (AQUAPOR +aqp1_human 93 97 269 0 0 269 P29972 PROXIMAL TUBULE) (AQUAPOR +aqp1_bovin 90 95 269 1 2 271 P47865 PROXIMAL TUBULE) (AQUAPOR +aqp1_sheep 90 94 269 2 3 272 P56401 PROXIMAL TUBULE) (AQUAPOR +aqpa_ranes 78 89 268 2 5 272 P50501 AQUAPORIN FA-CHIP. +aqp2_dasno 49 73 109 1 7 109 P79164 PROTEIN) (WCH-CD) (FRAGME +aqp2_bovin 49 73 109 1 7 109 P79099 PROTEIN) (WCH-CD) (FRAGME +aqp2_canfa 48 72 109 1 7 109 P79144 PROTEIN) (WCH-CD) (FRAGME +aqp2_rabit 48 73 109 1 7 109 P79213 PROTEIN) (WCH-CD) (FRAGME +aqp2_elema 47 72 109 1 7 109 P79168 PROTEIN) (WCH-CD) (FRAGME +aqp2_horse 47 72 109 1 7 109 P79165 PROTEIN) (WCH-CD) (FRAGME +aqp2_proha 47 73 109 1 7 109 P79229 PROTEIN) (WCH-CD) (FRAGME +mip_rat 46 73 259 1 7 261 P09011 LENS FIBER MAJOR INTRINSI +aqp2_oryaf 46 72 109 1 7 109 P79200 PROTEIN) (WCH-CD) (FRAGME +mip_mouse 46 73 261 1 7 263 P51180 LENS FIBER MAJOR INTRINSI +mip_ranpi 45 73 261 1 7 263 Q06019 LENS FIBER MAJOR INTRINSI +mip_bovin 45 73 261 1 7 263 P06624 LENS FIBER MAJOR INTRINSI +mip_human 45 73 261 1 7 263 P30301 LENS FIBER MAJOR INTRINSI +mip_chick 45 72 110 1 1 112 P28238 LENS FIBER MAJOR INTRINSI +aqp5_rat 44 71 262 2 8 265 P47864 AQUAPORIN 5. +aqp5_human 44 71 262 2 8 265 P55064 AQUAPORIN 5. +aqp2_human 44 72 261 2 8 271 P41181 PROTEIN) (WCH-CD). +aqp4_human 43 70 266 2 5 323 P55087 AQUAPORIN 4 (WCH4) (MERCU +aqp4_rat 43 70 266 2 5 323 P47863 AQUAPORIN 4 (WCH4) (MERCU +aqp4_mouse 43 69 265 3 6 322 P55088 AQUAPORIN 4 (WCH4) (MERCU +aqp2_rat 42 71 261 2 8 271 P34080 PROTEIN) (WCH-CD). +aqp2_mouse 42 71 261 2 8 271 P56402 PROTEIN) (WCH-CD). +wc2a_arath 42 67 248 4 12 287 P43286 PLASMA MEMBRANE INTRINSIC +aqp6_human 42 68 260 2 9 282 Q13520 AQUAPORIN 6 (AQUAPORIN-2 +wc2c_arath 41 66 248 4 12 285 P30302 INTRINSIC PROTEIN) (WSI-T +wc2b_arath 41 66 248 4 12 285 P43287 PLASMA MEMBRANE INTRINSIC +wc1c_arath 41 65 238 4 10 286 Q08733 (TMP-B). +wc1b_arath 41 65 238 4 10 286 Q06611 (TMP-A). +tipw_lyces 40 65 237 4 10 286 Q08451 (RIPENING-ASSOCIATED MEMB +wc1a_arath 40 64 238 4 10 286 P43285 PLASMA MEMBRANE INTRINSIC +tipw_pea 40 64 237 4 11 289 P25794 RESPONSIVE PROTEIN 7A). +tipa_arath 38 64 250 3 9 268 P26587 TONOPLAST INTRINSIC PROTE +aqua_atrca 38 64 246 4 10 282 P42767 AQUAPORIN. +dip_antma 38 65 242 2 4 250 P33560 PROBABLE TONOPLAST INTRIN +aqpz_ecoli 37 59 220 4 17 231 P48838 AQUAPORIN Z (BACTERIAL NO +tip2_tobac 37 64 242 2 4 250 P24422 TONOPLAST INTRINSIC PROTE +tip1_tobac 37 64 242 2 4 250 P21653 TONOPLAST INTRINSIC PROTE +tipg_arath 33 62 241 2 4 251 P25818 TONOPLAST INTRINSIC PROTE +bib_drome 33 60 260 4 10 700 P23645 NEUROGENIC PROTEIN BIG BR +tipr_arath 33 62 243 2 4 253 P21652 TONOPLAST INTRINSIC PROTE +tipa_phavu 33 62 246 2 4 256 P23958 TONOPLAST INTRINSIC PROTE +tipg_orysa 32 62 240 2 5 250 P50156 TONOPLAST INTRINSIC PROTE +--- +--- MAXHOM ALIGNMENT: IN MSF FORMAT +MSF of: /home/phd/server/work/predict_h25873-22040.hssp from: 1 to: 269 + /home/phd/server/work/predict_h25873-22040.msfRet MSF: 269 Type: P 24-Nov-98 17:44:5 Check: 3448 .. + + + Name: predict_h258 Len: 269 Check: 8331 Weight: 1.00 + Name: aqp1_rat Len: 269 Check: 8331 Weight: 1.00 + Name: aqp1_mouse Len: 269 Check: 7552 Weight: 1.00 + Name: aqp1_human Len: 269 Check: 6501 Weight: 1.00 + Name: aqp1_bovin Len: 269 Check: 7067 Weight: 1.00 + Name: aqp1_sheep Len: 269 Check: 7582 Weight: 1.00 + Name: aqpa_ranes Len: 269 Check: 4844 Weight: 1.00 + Name: aqp2_dasno Len: 269 Check: 8933 Weight: 1.00 + Name: aqp2_bovin Len: 269 Check: 9649 Weight: 1.00 + Name: aqp2_canfa Len: 269 Check: 8990 Weight: 1.00 + Name: aqp2_rabit Len: 269 Check: 8787 Weight: 1.00 + Name: aqp2_elema Len: 269 Check: 9381 Weight: 1.00 + Name: aqp2_horse Len: 269 Check: 8993 Weight: 1.00 + Name: aqp2_proha Len: 269 Check: 8855 Weight: 1.00 + Name: mip_rat Len: 269 Check: 9773 Weight: 1.00 + Name: aqp2_oryaf Len: 269 Check: 8554 Weight: 1.00 + Name: mip_mouse Len: 269 Check: 9723 Weight: 1.00 + Name: mip_ranpi Len: 269 Check: 5937 Weight: 1.00 + Name: mip_bovin Len: 269 Check: 1430 Weight: 1.00 + Name: mip_human Len: 269 Check: 372 Weight: 1.00 + Name: mip_chick Len: 269 Check: 4658 Weight: 1.00 + Name: aqp5_rat Len: 269 Check: 9033 Weight: 1.00 + Name: aqp5_human Len: 269 Check: 6547 Weight: 1.00 + Name: aqp2_human Len: 269 Check: 6209 Weight: 1.00 + Name: aqp4_human Len: 269 Check: 2589 Weight: 1.00 + Name: aqp4_rat Len: 269 Check: 4412 Weight: 1.00 + Name: aqp4_mouse Len: 269 Check: 2845 Weight: 1.00 + Name: aqp2_rat Len: 269 Check: 5748 Weight: 1.00 + Name: aqp2_mouse Len: 269 Check: 6526 Weight: 1.00 + Name: wc2a_arath Len: 269 Check: 4866 Weight: 1.00 + Name: aqp6_human Len: 269 Check: 9404 Weight: 1.00 + Name: wc2c_arath Len: 269 Check: 6187 Weight: 1.00 + Name: wc2b_arath Len: 269 Check: 7328 Weight: 1.00 + Name: wc1c_arath Len: 269 Check: 8575 Weight: 1.00 + Name: wc1b_arath Len: 269 Check: 9544 Weight: 1.00 + Name: tipw_lyces Len: 269 Check: 9283 Weight: 1.00 + Name: wc1a_arath Len: 269 Check: 598 Weight: 1.00 + Name: tipw_pea Len: 269 Check: 9253 Weight: 1.00 + Name: tipa_arath Len: 269 Check: 6544 Weight: 1.00 + Name: aqua_atrca Len: 269 Check: 2848 Weight: 1.00 + Name: dip_antma Len: 269 Check: 9619 Weight: 1.00 + Name: aqpz_ecoli Len: 269 Check: 5641 Weight: 1.00 + Name: tip2_tobac Len: 269 Check: 490 Weight: 1.00 + Name: tip1_tobac Len: 269 Check: 622 Weight: 1.00 + Name: tipg_arath Len: 269 Check: 3231 Weight: 1.00 + Name: bib_drome Len: 269 Check: 7687 Weight: 1.00 + Name: tipr_arath Len: 269 Check: 4476 Weight: 1.00 + Name: tipa_phavu Len: 269 Check: 5563 Weight: 1.00 + Name: tipg_orysa Len: 269 Check: 3537 Weight: 1.00 + +// + + + 1 50 +predict_h258 MASEIKKKLF WRAVVAEFLA MTLFVFISIG SALGFNYPLE RNQTLVQDNV +aqp1_rat MASEIKKKLF WRAVVAEFLA MTLFVFISIG SALGFNYPLE RNQTLVQDNV +aqp1_mouse MASEIKKKLF WRAVVAEFLA MTLFVFISIG SALGFNYPLE RNQTLVQDNV +aqp1_human MASEFKKKLF WRAVVAEFLA TTLFVFISIG SALGFKYPVG NNQTAVQDNV +aqp1_bovin MASEFKKKLF WRAVVAEFLA MILFIFISIG SALGFHYPIK SNQTtvQDNV +aqp1_sheep MASEFKKKLF WRAVVAEFLA MILFIFISIG SALGFHYPIK SNQTtvQDNV +aqpa_ranes MASEFKKKAF WRAVIAEFLA MILFVFISIG AALGFNFPIE EKANQtqDIV +aqp2_dasno ......SVAF SRAVLAEFLA TLIFVFFGLG SALSWPQALP S.......VL +aqp2_bovin ......SIAF SRAVLAEFLA TLLFVFFGLG SALNWPQALP S.......VL +aqp2_canfa ......SVAF SRAVFAEFLA TLLFVFFGLG SALNWPQALP S.......VL +aqp2_rabit ......SIAF SRAVFAEFLA TLLFVFFGLG SALNWPSALP S.......TL +aqp2_elema ......SIAF SRAVFSEFLA TLLFVFFGLG SALNWPQALP S.......VL +aqp2_horse ......SIAF SRAVLAEFLA TLLFVFFGLG SALNWPQAMP S.......VL +aqp2_proha ......SIAF SRAVLSEFLA TLLFVFFGLG SALNWPQALP S.......VL +mip_rat ...ELRSASF WRAIFAEFFA TLFYVFFGLG SSLRWA.... ...PGPLHVL +aqp2_oryaf ......SIAF SKAVFSEFLA TLLFVFFGLG SALNWPQALP S.......GL +mip_mouse .MWELRSASF WRAIFAEFFA TLFYVFFGLG ASLRWA.... ...PGPLHVL +mip_ranpi .MWEFRSFSF WRAVFAEFFG TMFYVFFGLG ASLKWAAGPA .......NVL +mip_bovin .MWELRSASF WRAICAEFFA SLFYVFFGLG ASLRWA.... ...PGPLHVL +mip_human .MWELRSASF WRAIFAEFFA TLFYVFFGLG SSLRWA.... ...PGPLHVL +mip_chick .......... .......... .......... .......... .......... +aqp5_rat MKKEVCSLAF FKAVFAEFLA TLIFVFFGLG SALKWPSALP T.......IL +aqp5_human MKKEVCSVAF LKAVFAEFLA TLIFVFFGLG SALKWPSALP T.......IL +aqp2_human .MWELRSIAF SRAVFAEFLA TLLFVFFGLG SALNWPQALP S.......VL +aqp4_human AFKGVWTQAF WKAVTAEFLA MLIFVLLSLG STINWG...G TEKPLPVDMV +aqp4_rat AFKGVWTQAF WKAVTAEFLA MLIFVLLSVG STINWG...G SENPLPVDMV +aqp4_mouse AFKGVWTQAF WKAVSAEFLA TLIFVL.GVG STINWG...G SENPLPVDMV +aqp2_rat .MWELRSIAF SRAVLAEFLA TLLFVFFGLG SALQWASSPP S.......VL +aqp2_mouse .MWELRSIAY CRAVLAEFLA TLLFVFFGLG SALQWASSPP S.......VL +wc2a_arath DGAELKKWSF YRAVIAEFVA TLLFLYITVL TVIGYKIQSD TDAGGVdgIL +aqp6_human MLACRLWKAI SRALFAEFLA TGLYVFFGVG SVMRWPTALP S.......VL +wc2c_arath DAEELTKWSL YRAVIAEFVA TLLFLYVTVL TVIGYKIQSD TKAGGVdgIL +wc2b_arath DADELTKWSL YRAVIAEFVA TLLFLYITVL TVIGYKIQSD TKAGGVdgIL +wc1c_arath EPGELSSWSF YRAGIAEFIA TFLFLYITVL TVMGVKRA.. PNMCASVGIQ +wc1b_arath EPGELASWSF WRAGIAEFIA TFLFLYITVL TVMGVKR..S PNMCASVGIQ +tipw_lyces EPGELSSWSF YRAGIAEFMA TFLFLYITIL TVMGLKRSDS LCSSV..GIQ +wc1a_arath EPGELSSWSF WRAGIAEFIA TFLFLYITVL TVMGVKR..S PNMCASVGIQ +tipw_pea EPSELTSWSF YRAGIAEFIA TFLFLYITVL TVMGVVRESS KCKTV..GIQ +tipa_arath RADEATHPDS IRATLAEFLS TFVFVFAAEG SILSLDKLYW EHAAHAGTni +aqua_atrca DMGELKLWSF WRAAIAEFIA TLLFLYITVA TVIGYKKETD PCASVGL..L +dip_antma SIGDSFSVAS IKAYVAEFIA TLLFVFAGVG SAIAYNKLTS DAALDPAGLV +aqpz_ecoli .........M FRKLAAECFG TFWLVFGGCG SAVLAAGFPE ....LGIGFA +tip2_tobac SIGDSFSVGS LKAYVAEFIA TLLFVFAGVG SAIAYNKLTA DAALDPAGLV +tip1_tobac SIGDSFSVGS LKAYVAEFIA TLLFVFAGVG SAIAYNKLTA DAALDPAGLV +tipg_arath RPDEATRPDA LKAALAEFIS TLIFVVAGSG SGMAFNKLTE NGATTPSGLV +bib_drome MQAEIRTLEF WRSIISECLA SFMYVFIVCG AAAGVGVGAS VSSVL....L +tipr_arath RPDEATRPDA LKAALAEFIS TLIFVVAGSG SGMAFNKLTE NGATTPSGLV +tipa_phavu RTDEATHPDS MRASLAEFAS TFIFVFAGEG SGLALVKIYQ DSAFSAGELL +tipg_orysa SHQEVYHPGA LKAALAEFIS TLIFVFAGQG SGMAFSKLTG GGATTPAGLI + + 51 100 +predict_h258 KVSLAFGLSI ATLAQSVGHI SGAHSNPAVT LGLLLSCQIS ILRAVMYIIA +aqp1_rat KVSLAFGLSI ATLAQSVGHI SGAHSNPAVT LGLLLSCQIS ILRAVMYIIA +aqp1_mouse KVSLAFGLSI ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS ILRAVMYIIA +aqp1_human KVSLAFGLSI ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS IFRALMYIIA +aqp1_bovin KVSLAFGLSI ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS VLRAIMYIIA +aqp1_sheep KVSLAFGLSI ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS ILRAIMYIIA +aqpa_ranes KVSLAFGISI ATMAQSVGHV SGAHLNPAVT LGCLLSCQIS ILKAVMYIIA +aqp2_dasno QIALAFGLAI GTLVQALGHV SGAHINPAVT VACLVGCHVS FLRAAFYVAA +aqp2_bovin QIAMAFGLAI GTLVQALGHV SGAHINPAVT VACLVGCHVS FLRAVFYVAA +aqp2_canfa QIAMAFGLGI GTLVQALGHV SGAHINPAVT VACLVGCHVS FLRAAFYVAA +aqp2_rabit QIAMAFGLGI GTLVQALGHV SGAHINPAVT VACLVGCHVS FLRAAFYVAA +aqp2_elema QIAMAFGLAI GTLVQTLGHI SGAHINPAVT VACLVGCHVS FLRATFYLAA +aqp2_horse QIAMAFGLAI GTLVQALGHV SGAHINPAVT VACLVGCHVS FLRAAFYVAA +aqp2_proha QIAMAFGLAI GTLVQTLGHI SGAHINPAVT IACLVGCHVS FLRALFYLAA +mip_rat QVALAFGLAL ATLVQTVGHI SGAHVNPAVT FAFLVGSQMS LLRAFCYIAA +aqp2_oryaf QIAMAFGLAI GTLVQTLGHI SGAHINPAVT VACLVGCHVS FLRAIFYVAA +mip_mouse QVALAFGLAL ATLVQTVGHI SGAHVNPAVT FAFLVGSQMS LLRAFCYIAA +mip_ranpi VIALAFGLVL ATMVQSIGHV SGAHINPAVT FAFLIGSQMS LFRAIFYIAA +mip_bovin QVALAFGLAL ATLVQAVGHI SGAHVNPAVT FAFLVGSQMS LLRAICYMVA +mip_human QVAMAFGLAL ATLVQSVGHI SGAHVNPAVT FAFLVGSQMS LLRAFCYMAA +mip_chick .......... .......... .......... .......... .......... +aqp5_rat QISIAFGLAI GTLAQALGPV SGGHINPAIT LALLIGNQIS LLRAVFYVAA +aqp5_human QIALAFGLAI GTLAQALGPV SGGHINPAIT LALLVGNQIS LLRAFFYVAA +aqp2_human QIAMAFGLGI GTLVQALGHI SGAHINPAVT VACLVGCHVS VLRAAFYVAA +aqp4_human LISLCFGLSI ATMVQCFGHI SGGHINPAVT VAMVCTRKIS IAKSVFYIAA +aqp4_rat LISLCFGLSI ATMVQCFGHI SGGHINPAVT VAMVCTRKIS IAKSVFYITA +aqp4_mouse LISLCFGLSI ATMVQCLGHI SGGHINPAVT VAMVCTRKIS IAKSVFYIIA +aqp2_rat QIAVAFGLGI GILVQALGHV SGAHINPAVT VACLVGCHVS FLRAAFYVAA +aqp2_mouse QIAVAFGLGI GTLVQALGHV SGAHINPAVT VACLVGCHVS FLRAAFYVAA +wc2a_arath GIAWAFGGMI FILVYCTAGI SGGHINPAVT FGLFLARKVS LPRALLYIIA +aqp6_human QIAITFNLVT AMAVQVTWKT SGAHANPAVT LAFLVGSHIS LPRAVAYVAA +wc2c_arath GIAWAFGGMI FILVYCTAGI SGGHINPAVT FGLFLARKVS LIRAVLYMVA +wc2b_arath GIAWAFGGMI FILVYCTAGI SGGHINPAVT FGLFLARKVS LIRAVLYMVA +wc1c_arath GIAWAFGGMI FALVYCTAGI SGGHINPAVT FGLFLARKLS LTRAVFYIVM +wc1b_arath GIAWAFGGMI FALVYCTAGI SGGHINPAVT FGLFLARKLS LTRAVYYIVM +tipw_lyces GVAWAFGGMI FALVYCTAGI SGGHINPAVT FGLFLARKLS LTRAVFYMVM +wc1a_arath GIAWAFGGMI FALVYCTAGI SGGHINPAVT FGLFLARKLS LTRALYYIVM +tipw_pea GIAWAFGGMI FALVYCTAGI SGGHINPAVT FGLFLARKLS LTRAIFYMVM +tipa_arath LVALAHAFAL FAAVSAAINV SGGHVNPAVT FGALVGGRVT AIRAIYYWIA +aqua_atrca GIAWSFGGMI FVLVYCTAGI SGGHINPAVT FGLFLARKVS LLRALVYMIA +dip_antma AVAVAHAFAL FVGVSMAANV SGGHLNPAVT LGLAVGGNIT ILTGLFYWIA +aqpz_ecoli GVALAFGLTV LTMAFAVGHI SGGHFNPAVT IGLWAGGRFP AKEVVGYVIA +tip2_tobac AVAVAHAFAL FVGVSIAANI SGGHLNPAVT LGLAVGGNIT ILTGFFYWIA +tip1_tobac AVAVAHAFAL FVGVSIAANI SGGHLNPAVT LGLAVGGNIT ILTGFFYWIA +tipg_arath AAAVAHAFGL FVAVSVGANI SGGHVNPAVT FGAFIGGNIT LLRGILYWIA +bib_drome ATALASGLAM ATLTQCFLHI SGAHINPAVT LALCVVRSIS PIRAAMYITA +tipr_arath AAAVAHAFGL FVAVSVGANI SGGHVNPAVT FGAFIGGNIT LLRGILYWIA +tipa_phavu ALALAHAFAL FAAVSASMHV SGGHVNPAVS FGALIGGRIS VIRAVYYWIA +tipg_orysa AAAVAHAFAL FVAVSVGANI SGGHVNPAVT FGAFVGGNIT LFRGLLYWIA + + 101 150 +predict_h258 QCVGAIVASA ILSGITSSLL ENSLGRNDLA RGVNSGQGLG IEIIGTLQLV +aqp1_rat QCVGAIVASA ILSGITSSLL ENSLGRNDLA RGVNSGQGLG IEIIGTLQLV +aqp1_mouse QCVGAIVATA ILSGITSSLV DNSLGRNDLA HGVNSGQGLG IEIIGTLQLV +aqp1_human QCVGAIVATA ILSGITSSLT GNSLGRNDLA DGVNSGQGLG IEIIGTLQLV +aqp1_bovin QCVGAIVATA ILSGITSSLP DNSLGLNALA PGVNSGQGLG IEIIGTLQLV +aqp1_sheep QCVGAIVATV ILSGITSSLP DNSLGLNALA PGVNSGQGLG IEIIGTLQLV +aqpa_ranes QCLGAVVATA ILSGITSGLE NNSLGLNGLS PGVSAGQGLG VEILVTFQLV +aqp2_dasno QLLGAVAGAA ILHEITPPDV RG........ .......... .......... +aqp2_bovin QLLGAVAGAA LLHEITPPAI RG........ .......... .......... +aqp2_canfa QLLGAVAGAA LLHEITPPHV RG........ .......... .......... +aqp2_rabit QLLGAVAGAA LLHEITPAEV RG........ .......... .......... +aqp2_elema QLLGAVAGAA LLHELTPPDI RG........ .......... .......... +aqp2_horse QLLGAVAGAA LLHEITPPDI RR........ .......... .......... +aqp2_proha QLLGAVAGAA LLHELTPPDI RG........ .......... .......... +mip_rat QLLGAVAGAA VLYSVTPPAV RGNLALNTLH AGVSVGQATT VEIFLTLQFV +aqp2_oryaf QLLGAVAGAA LLHELTPPDI RG........ .......... .......... +mip_mouse QLLGAVAGAA VLYSVTPPAV RGNLALNTLH TGVSVGQATT VEIFLTLQFV +mip_ranpi QLLGAVAGAA VLYGVTPAAI RGNLALNTLH PGVSLGQATT VEIFLTLQFV +mip_bovin QLLGAVAGAA VLYSVTPPAV RGNLALNTLH PGVSVGQATI VEIFLTLQFV +mip_human QLLGAVAGAA VLYSVTPPAV RGNLALNTLH PAVSVGQATT VEIFLTLQFV +mip_chick .......... .......... .......... .......... .......... +aqp5_rat QLVGAIAGAG ILYWLAPLNA RGNLAVNALN NNTTPGKAMV VELILTFQLA +aqp5_human QLVGAIAGAG ILYGVAPLNA RGNLAVNALN NNTTQGQAMV VELILTFQLA +aqp2_human QLLGAVAGAA LLHEITPADI RGDLAVNALS NSTTAGQAVT VELFLTLQLV +aqp4_human QCLGAIIGAG ILYLVTPPSV VGGLGVTMVH GNLTAGHGLL VELIITFQLV +aqp4_rat QCLGAIIGAG ILYLVTPPSV VGGLGVTTVH GNLTAGHGLL VELIITFQLV +aqp4_mouse QCLGAIIGAG ILYLVTPPSV VGGLGVTTVH GNLTAGHGLL VELIITFQLV +aqp2_rat QLLGAVAGAA ILHEITPVEI RGDLAVNALH NNATAGQAVT VELFLTMQLV +aqp2_mouse QLLGAVAGAA ILHEITPVEI RGDLAVNALH NNATAGQAVT VELFLTMQLV +wc2a_arath QCLGAICGVG FVKAFQSSYY TRYGGgnSLA DGYSTGTGLA AEIIGTFVLV +aqp6_human QLVGATVGAA LLYGVMPGDI RETLGINVVR NSVSTGQAVA VELLLTLQLV +wc2c_arath QCLGAICGVG FVKAFQSSHY VNYGGgnFLA DGYNTGTGLA AEIIGTFVLV +wc2b_arath QCLGAICGVG FRQSFQSSYY DRYGGgnSLA DGYNTGTGLA AEIIGTFVLV +wc1c_arath QCLGAICGAG VVKGFQPNPY QtgGGANTVA HGYTKGSGLG AEIIGTFVLV +wc1b_arath QCLGAICGAG VVKGFQPKQY QagGGANTIA HGYTKGSGLG AEIIGTFVLV +tipw_lyces QCLGAICGAG VVKGFMVGPY QrgGGANVVN PGYTKGDGLG AEIIGTFVLV +wc1a_arath QCLGAICGAG VVKGFQPKQY QagGGANTVA HGYTKGSGLG AEIIGTFVLV +tipw_pea QVLGAICGAG VVKGFEGKQR FGDLNgnFVA PGYTKGDGLG AEIVGTFILV +tipa_arath QLLGAILACL LLRLTTNGMR PVGFR...LA SGVGAVNGLV LEIILTFGLV +aqua_atrca QCAGAICGVG LVKAFMKGPY NqgGGANSVA LGYNKGTAFG AELIGTFVLV +dip_antma QCLGSTVACL LLKFVTNGL. ..SVPTHGVA AGMDAIQGVV MEIIITFALV +aqpz_ecoli QVVGGIVAAA LLYLIASGKT GFDAAASGFA sgYSMLSALV VELVLSAGFL +tip2_tobac QLLGSTVACL LLKYVTNGL. ..AVPTHGVA AGLNGFQGVV MEIIITFALV +tip1_tobac QLLGSTVACL LLKYVTNGL. ..AVPTHGVA AGLNGLQGVV MEIIITFALV +tipg_arath QLLGSVVACL ILKFATGGLA VPAFG...LS AGVGVLNAFV FEIVMTFGLV +bib_drome QCGGGIAGAA LLYGVTVPGY QGNLQAasHS AALAAWERFG VEFILTSLVV +tipr_arath QLLGSVVACL ILKFATGGLA VPPFG...LS AGVGVLNAFV FEIVMTFGLV +tipa_phavu QLLGSIVAAL VLRLVTNNMR PSGF...HVS PGVGVGHMFI LEVVMTFGLM +tipg_orysa QLLGSTVACF LLRFSTGGLA TGTFGL.... TGVSVWEALV LEIVMTFGLV + + 151 200 +predict_h258 LCVLATTDRR RRDLGGSAPL AIGLSVALGH LLAIDYTGCG INPARSFGSA +aqp1_rat LCVLATTDRR RRDLGGSAPL AIGLSVALGH LLAIDYTGCG INPARSFGSA +aqp1_mouse LCVLATTDRR RRDLGGSAPL AIGLSVALGH LLAIDYTGCG INPARSFGSA +aqp1_human LCVLATTDRR RRDLGGSAPL AIGLSVALGH LLAIDYTGCG INPARSFGSA +aqp1_bovin LCVLATTDRR RRDLGGSGPL AIGFSVALGH LLAIDYTGCG INPARSFGSS +aqp1_sheep LCVLATTDRR RrdLGDSGPL AIGFSVALGH LLAIDYTGCG INPARSFGSS +aqpa_ranes LCVVAVTDRR RHDVSGSVPL AIGLSVALGH LIAIDYTGCG MNPARSFGSA +aqp2_dasno .......... .......... .......... .......... .......... +aqp2_bovin .......... .......... .......... .......... .......... +aqp2_canfa .......... .......... .......... .......... .......... +aqp2_rabit .......... .......... .......... .......... .......... +aqp2_elema .......... .......... .......... .......... .......... +aqp2_horse .......... .......... .......... .......... .......... +aqp2_proha .......... .......... .......... .......... .......... +mip_rat LCIFATYDER RNGRMGSVAL AVGFSLTLGH LFGMYYTGAG MNPARSFAPA +aqp2_oryaf .......... .......... .......... .......... .......... +mip_mouse LCIFATYDER RNGRMGSVAL AVGFSLTLGH LFGMYYTGAG MNPARSFAPA +mip_ranpi LCIFATYDER RNGRLGSVSL AIGFSLTLGH LFGLYYTGAS MNPARSFAPA +mip_bovin LCIFATYDER RNGRLGSVAL AVGFSLTLGH LFGMYYTGAG MNPARSFAPA +mip_human LCIFATYDER RNGQLGSVAL AVGFSLALGH LFGMYYTGAG MNPARSFAPA +mip_chick ........DR HDGRPGSAAL PVGFSLALGH LFGIPFTGAG MNPARSFAPA +aqp5_rat LCIFSSTDSR RTSPVGSPAL SIGLSVTLGH LVGIYFTGCS MNPARSFGPA +aqp5_human LCIFASTDSR RTSPVGSPAL SIGLSVTLGH LVGIYFTGCS MNPARSFGPA +aqp2_human LCIFASTDER RGENPGTPAL SIGFSVALGH LLGIHYTGCS MNPARSLAPA +aqp4_human FTIFASCDSK RTDVTGSIAL AIGFSVAIGH LFAINYTGAS MNPARSFGPA +aqp4_rat FTIFASCDSK RTDVTGSVAL AIGFSVAIGH LFAINYTGAS MNPARSFGPA +aqp4_mouse FTVFASCDSK RTDVTGSIAL AIGFSVAIGH LFAINYTGAS MNPARSFGPA +aqp2_rat LCIFASTDER RGDNLGSPAL SIGFSVTLGH LLGIYFTGCS MNPARSLAPA +aqp2_mouse LCIFASTDER RSDNLGSPAL SIGFSVTLGH LLGIYFTGCS MNPARSLAPA +wc2a_arath YTVFSATDPK RSavPVLAPL PIGFAVFMVH LATIPITGTG INPARSFGAA +aqp6_human LCVFASTDSR QTS..GSPAT MIGISWALGH LIGILFTGCS MNPARSFGPA +wc2c_arath YTVFSATDPK RNavPVLAPL PIGFAVFMVH LATIPITGTG INPARSFGAA +wc2b_arath YTVFSATDPK RNavPVLAPL PIGFAVFMVH LATIPITGTG INPARSFGAS +wc1c_arath YTVFSATDAK RSavPILAPL PIGFAVFLVH LATIPITGTG INPARSLGAA +wc1b_arath YTVFSATDAK RNavPILAPL PIGFAVFLVH LATIPITGTG INPARSLGAA +tipw_lyces YTVFSATDAK RNavPILAPL PIGFAVFLVH LATIPITGTG INPARSLGAA +wc1a_arath YTVFSATDAK RNavPILAPL PIGFAVFLVH LATIPITATG INPARSLGAA +tipw_pea YTVFSATDAK RSavPILAPL PIGFAVFLVH LATIPITGTG INPARSLGAA +tipa_arath YVVYStiDPK RGSLGIIAPL AIGLIVGANI LVGGPFSGAS MNPARAFGPA +aqua_atrca YTVFSATDPK RSavPILAPL PIGFAVFMVH LATIPITGTG INPARSFGAA +dip_antma YTVYAtaDPK KGSLGVIAPI AIGFIVGANI LAAGPFSGGS MNPARSFGPA +aqpz_ecoli LVIHGATDKF APA..GFAPI AIGLALTLIH LISIPVTNTS VNPARSTAVA +tip2_tobac YTVYAtaDPK KGSLGTIAPI AIGFIVGANI LAAGPFSGGS MNPARSFGPA +tip1_tobac YTVYAtaDPK KGSLGTIAPI AIGFIVGANI LAAGPFSGGS MNPARSFGPA +tipg_arath YTVYAtiDPK NGSLGTIAPI AIGFIVGANI LAGGAFSGAS MNPAVAFGPA +bib_drome LCYFVSTDPM KKFMGNS.AA SIGCAYSACC FVSMPYLN.. ..PARSLGPS +tipr_arath YTVYAtiDPK NGSLGTIAPI AIGFIVGANI LAGGAFSGAS MNPAVAFGPA +tipa_phavu YTVYGtiDPK RGAVSYIAPL AIGLIVGANI LVGGPFDGAC MNPALAFGPS +tipg_orysa YTVYAtvDPK KGSLGTIAPI AIGFIVGANI LVGGAFDGAS MNPAVSFGPA + + 201 250 +predict_h258 VLTRNFSNHW IFWVGPFIGS ALAVLIYDFI LAPRSSDFTD RMKVWTSGQV +aqp1_rat VLTRNFSNHW IFWVGPFIGS ALAVLIYDFI LAPRSSDFTD RMKVWTSGQV +aqp1_mouse VLTRNFSNHW IFWVGPFIGG ALAVLIYDFI LAPRSSDFTD RMKVWTSGQV +aqp1_human VITHNFSNHW IFWVGPFIGG ALAVLIYDFI LAPRSSDLTD RVKVWTSGQV +aqp1_bovin VITHNFQDHW IFWVGPFIGA ALAVLIYDFI LAPRSSDLTD RVKVWTSGQV +aqp1_sheep VITHNFQDHW IFWVGPFIGA ALAVLIYDFI LAPRSSDLTD RVKVWTSGQV +aqpa_ranes VLTKNFTYHW IFWVGPMIGG AAAAIIYDFI LAPRTSDLTD RMKVWTNGQV +aqp2_dasno .......... .......... .......... .......... .......... +aqp2_bovin .......... .......... .......... .......... .......... +aqp2_canfa .......... .......... .......... .......... .......... +aqp2_rabit .......... .......... .......... .......... .......... +aqp2_elema .......... .......... .......... .......... .......... +aqp2_horse .......... .......... .......... .......... .......... +aqp2_proha .......... .......... .......... .......... .......... +mip_rat ILTRNFSNHW VYWVGPIIGG GLGSLLYDFL LFPRLKSVSE RLSILKGARP +aqp2_oryaf .......... .......... .......... .......... .......... +mip_mouse ILTRNFSNHW VYWVGPIIGG GLGSLLYDFL LFPRLKSVSE RLSILKGARP +mip_ranpi VLTRNFTNHW VYWVGPIIGG ALGGLVYDFI LFPRMRGLSE RLSILKGARP +mip_bovin ILTRNFTNHW VYWVGPVIGA GLGSLLYDFL LFPRLKSVSE RLSILKGSRP +mip_human ILTGNFTNHW VYWVGPIIGG GLGSLLYDFL LFPRLKSISE RLSVLKGAKP +mip_chick VITRNFTNHW VFWAGPLLGA ALAALLYELA LCPRARSMAE RLAV.LRGEP +aqp5_rat VVMNRFssHW VFWVGPIVGA MLAAILYFYL LFPSSLSLHD RVAVVKGTYE +aqp5_human VVMNRFsaHW VFWVGPIVGA VLAAILYFYL LFPNSLSLSE RVAIIKGTYE +aqp2_human VVTGKFDDHW VFWIGPLVGA ILGSLLYNYV LFPPAKSLSE RLAVLKGLEp +aqp4_human VIMGNWENHW IYWVGPIIGA VLAGGLYEYV FCPDVEFKRR FKEAFSKaqT +aqp4_rat VIMGNWENHW IYWVGPIIGA VLAGALYEYV FCPDVELKRR LKEAFSKaqT +aqp4_mouse VIMGNWANHW IYWVGPIMGA VLAGALYEYV FCPDVELKRR LKEAFSKaqT +aqp2_rat VVTGKFDDHW VFWIGPLVGA IIGSLLYNYL LFPSAKSLQE RLAVLKGLEp +aqp2_mouse VVTGKFDDHW VFWIGPLVGA IIGSLLYNYL LFPSTKSLQE RLAVLKGLEp +wc2a_arath VIYnpWDDHW IFWVGPFIGA AIAAFYHQFV LRASGSKSLG SFRSAANV.. +aqp6_human IIIGKFTVHW VFWVGPLMGA LLASLIYNFV LFPDTKTLAQ RLAILTGTVE +wc2c_arath VIFnpWDDHW IFWVGPFIGA TIAAFYHQFV LRASGSKSLG SFRSAANV.. +wc2b_arath VIYnpWDDHW IFWVGPFIGA AIAAFYHQFV LRASGSKSLG SFRSAANV.. +wc1c_arath IIYnaWDDHW IFWVGPFIGA ALAALYHQLV IRAIPFKSRS .......... +wc1b_arath IIFnaWDDHW VFWVGPFIGA ALAALYHVIV IRAIPFKSRS .......... +tipw_lyces IIYnaWNDHW IFWVGPMIGA ALAAIYHQII IRAMPFHRS. .......... +wc1a_arath IIYnsWDDHW VFWVGPFIGA ALAALYHVVV IRAIPFKSRS .......... +tipw_pea IVFngWNDHW IFWVGPFIGA ALAALYHQVV IRAIPFKSK. .......... +tipa_arath LVGWRWHDHW IYWVGPFIGS ALAALIYEYM VIPTEPPTHH AHGVHQPLAP +aqua_atrca VIyrVWDDHW IFWVGPFVGA LAAAAYHQYV LRAAAIKALG SFRSNPTN.. +dip_antma VASGDFSQNW IYWAGPLIGG ALAGFIYGDV FITAHAPLPT SEDYA..... +aqpz_ecoli IFQgaLEQLW FFWVVPIVGG IIGGLIYRTL LEKRD..... .......... +tip2_tobac VVAGDFSQNW IYWAGPLIGG GLAGFIYGDV FIGCHTPLPT SEDYA..... +tip1_tobac VVAGDFSQNW IYWAGPLIGG GLAGFIYGDV FIGCHTPLPT SEDYA..... +tipg_arath VVSWTWTNHW VYWAGPLVGG GIAGLIYEVF FINTTHEQLP TTDY...... +bib_drome FVLNKWDSHW VYWFGPLVGG MASGLVYEYI FNSRNRNLRH NKGSIDNDSS +tipr_arath VVSWTWTNHW VYWAGPLVGG GIAGLIYEVF FINTTHTSSS NHRLLN.... +tipa_phavu LVGWQWHQHW IFWVGPLLGA ALAALVYEYA VIPIEPPPHH HQPLATEDY. +tipg_orysa LVSWSWESQW VYWVGPLIGG GLAGVIYEVL FISHTHEQLP TTDY...... + + 251 269 +predict_h258 EEYDLDADDI NSRVEMKPK +aqp1_rat EEYDLDADDI NSRVEMKPK +aqp1_mouse EEYDLDADDI NSRVEMKPK +aqp1_human EEYDLDADDI NSRVEMKPK +aqp1_bovin EEYDLDADDI NSRVEMKPK +aqp1_sheep EEYDLDADDI NSRVEMKPK +aqpa_ranes EEYELDGDD. NTRVEMKPK +aqp2_dasno .......... ......... +aqp2_bovin .......... ......... +aqp2_canfa .......... ......... +aqp2_rabit .......... ......... +aqp2_elema .......... ......... +aqp2_horse .......... ......... +aqp2_proha .......... ......... +mip_rat SDSNGQPEGT GEPVELKTQ +aqp2_oryaf .......... ......... +mip_mouse SDSNGQPEGT GEPVELKTQ +mip_ranpi AEPEGQQEAT GEPIELKTQ +mip_bovin SESNGQPEVT GEPVELKTQ +mip_human DVSNGQPEVT GEPVELNTQ +mip_chick PAAAPPPEPP AEPLELKTQ +aqp5_rat PEEDWEDHRE ERKKTIELT +aqp5_human PDEDWEEQRE ERKKTMELT +aqp2_human tDWEEREVRR RQSVELHSP +aqp4_human KGSYMEVEDN RSQVETDDL +aqp4_rat KGSYMEVEDN RSQVETEDL +aqp4_mouse KGSYMEVEDN RSQVETEDL +aqp2_rat tDWEEREVRR RQSVELHSP +aqp2_mouse tDWEEREVRR RQSVELHSP +wc2a_arath .......... ......... +aqp6_human VGTGARAGAE PLKKESQPG +wc2c_arath .......... ......... +wc2b_arath .......... ......... +wc1c_arath .......... ......... +wc1b_arath .......... ......... +tipw_lyces .......... ......... +wc1a_arath .......... ......... +tipw_pea .......... ......... +tipa_arath EDY....... ......... +aqua_atrca .......... ......... +dip_antma .......... ......... +aqpz_ecoli .......... ......... +tip2_tobac .......... ......... +tip1_tobac .......... ......... +tipg_arath .......... ......... +bib_drome SIHSEDELNY DMDMEKPNK +tipr_arath .......... ......... +tipa_phavu .......... ......... +tipg_orysa .......... ......... + + +________________________________________________________________________________ + + + + + Prediction of: + + - secondary structure, by PHDsec + - solvent accessibility, by PHDacc + - and helical transmembrane regions, by PHDhtm + + PHD: Profile fed neural network systems from HeiDelberg + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + Author: Burkhard Rost + EMBL, Heidelberg, FRG + Meyerhofstrasse 1, 69 117 Heidelberg + Internet: Predict-Help@EMBL-Heidelberg.DE + + All rights reserved. + + + + + + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Secondary structure prediction by PHDsec: + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + Author: Burkhard Rost + EMBL, Heidelberg, FRG + Meyerhofstrasse 1, 69 117 Heidelberg + Internet: Rost@EMBL-Heidelberg.DE + + All rights reserved. + + + + +About the network method +~~~~~~~~~~~~~~~~~~~~~~~ + +The network procedure is described in detail in: +1) Rost, Burkhard; Sander, Chris: + Prediction of protein structure at better than 70% accuracy. + J. Mol. Biol., 1993, 232, 584-599. + +A brief description is given in: + Rost, Burkhard; Sander, Chris: + Improved prediction of protein secondary structure by use of se- + quence profiles and neural networks. + Proc. Natl. Acad. Sci. U.S.A., 1993, 90, 7558-7562. + +The PHD mail server is described in: +2) Rost, Burkhard; Sander, Chris; Schneider, Reinhard: + PHD - an automatic mail server for protein secondary structure + prediction. + CABIOS, 1994, 10, 53-60. + +The latest improvement steps (up to 72%) are explained in: +3) Rost, Burkhard; Sander, Chris: + Combining evolutionary information and neural networks to predict + protein secondary structure. + Proteins, 1994, 19, 55-72. + +To be quoted for publications of PHD output: + Papers 1-3 for the prediction of secondary structure and the pre- + diction server. + + + +About the input to the network +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The prediction is performed by a system of neural networks. +The input is a multiple sequence alignment. It is taken from an HSSP +file (produced by the program MaxHom: + Sander, Chris & Schneider, Reinhard: Database of Homology-Derived + Structures and the Structural Meaning of Sequence Alignment. + Proteins, 1991, 9, 56-68. + +For optimal results the alignment should contain sequences with varying +degrees of sequence similarity relative to the input protein. +The following is an ideal situation: + ++-----------------+----------------------+ +| sequence: | sequence identity | ++-----------------+----------------------+ +| target sequence | 100 % | +| aligned seq. 1 | 90 % | +| aligned seq. 2 | 80 % | +| ... | ... | +| aligned seq. 7 | 30 % | ++-----------------+----------------------+ + + + +Estimated Accuracy of Prediction +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +A careful cross validation test on some 250 protein chains (in total +about 55,000 residues) with less than 25% pairwise sequence identity +gave the following results: + +++================++-----------------------------------------+ +|| Qtotal = 72.1% || ("overall three state accuracy") | +++================++-----------------------------------------+ + ++----------------------------+-----------------------------+ +| Qhelix (% of observed)=70% | Qhelix (% of predicted)=77% | +| Qstrand(% of observed)=62% | Qstrand(% of predicted)=64% | +| Qloop (% of observed)=79% | Qloop (% of predicted)=72% | ++----------------------------+-----------------------------+ +.......................................................................... + +These percentages are defined by: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +| number of correctly predicted residues +|Qtotal = --------------------------------------- (*100) +| number of all residues +| +| no of res correctly predicted to be in helix +|Qhelix (% of obs) = -------------------------------------------- (*100) +| no of all res observed to be in helix +| +| +| no of res correctly predicted to be in helix +|Qhelix (% of pred)= -------------------------------------------- (*100) +| no of all residues predicted to be in helix + +.......................................................................... + +Averaging over single chains +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The most reasonable way to compute the overall accuracies is the above +quoted percentage of correctly predicted residues. However, since the +user is mainly interested in the expected performance of the prediction +for a particular protein, the mean value when averaging over protein +chains might be of help as well. Computing first the three state +accuracy for each protein chain, and then averaging over 250 chains +yields the following average: + ++-------------------------------====--+ +| Qtotal/averaged over chains = 72.2% | ++-------------------------------====--+ +| standard deviation = 9.3% | ++-------------------------------------+ + +.......................................................................... + +Further measures of performance +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Matthews correlation coefficient: + ++---------------------------------------------+ +| Chelix = 0.63, Cstrand = 0.53, Cloop = 0.52 | ++---------------------------------------------+ +.......................................................................... + +Average length of predicted secondary structure segments: + +. +------------+----------+ +. | predicted | observed | ++-----------+------------+----------+ +| Lhelix = | 10.3 | 9.3 | +| Lstrand = | 5.0 | 5.3 | +| Lloop = | 7.2 | 5.9 | ++-----------+------------+----------+ +.......................................................................... + +The accuracy matrix in detail: + ++---------------------------------------+ +| number of residues with H, E, L | ++---------+------+------+------+--------+ +| |net H |net E |net L |sum obs | ++---------+------+------+------+--------+ +| obs H |12447 | 1255 | 3990 | 17692 | +| obs E | 949 | 7493 | 3750 | 12192 | +| obs L | 2604 | 2875 |19962 | 25441 | ++---------+------+------+------+--------+ +| sum Net |16000 |11623 |27702 | 55325 | ++---------+------+------+------+--------+ + +Note: This table is to be read in the following manner: + 12447 of all residues predicted to be in helix, were observed to + be in helix, 949 however belong to observed strands, 2604 to + observed loop regions. The term "observed" refers to the DSSP + assignment of secondary structure calculated from 3D coordinates + of experimentally determined structures (Dictionary of Secondary + Structure of Proteins: Kabsch & Sander (1983) Biopolymers, 22, + 2577-2637). + + + +Position-specific reliability index +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The network predicts the three secondary structure types using real +numbers from the output units. The prediction is assigned by choosing +the maximal unit ("winner takes all"). However, the real numbers +contain additional information. +E.g. the difference between the maximal and the second largest output +unit can be used to derive a "reliability index". This index is given +for each residue along with the prediction. The index is scaled to +have values between 0 (lowest reliability), and 9 (highest). +The accuracies (Qtot) to be expected for residues with values above a +particular value of the index are given below as well as the fraction +of such residues (%res).: + ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ +| index| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | +| %res |100.0| 99.2| 90.4| 80.9| 71.6| 62.5| 52.8| 42.3| 29.8| 14.1| ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ +| | | | | | | | | | | | +| Qtot | 72.1| 72.3| 74.8| 77.7| 80.3| 82.9| 85.7| 88.5| 91.1| 94.2| +| | | | | | | | | | | | ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ +| H%obs| 70.4| 70.6| 73.7| 77.1| 80.1| 83.1| 86.0| 89.3| 92.5| 96.4| +| E%obs| 61.5| 61.7| 63.7| 66.6| 69.1| 71.7| 74.6| 77.0| 77.8| 68.1| +| | | | | | | | | | | | +| H%prd| 77.8| 78.0| 80.0| 82.6| 84.7| 86.9| 89.2| 91.3| 93.1| 95.4| +| E%prd| 64.5| 64.7| 67.8| 71.0| 74.2| 77.6| 81.4| 85.1| 89.8| 93.5| ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ + +The above table gives the cumulative results, e.g. 62.5% of all +residues have a reliability of at least 5. The overall three-state +accuracy for this subset of almost two thirds of all residues is 82.9%. +For this subset, e.g., 83.1% of the observed helices are correctly +predicted, and 86.9% of all residues predicted to be in helix are +correct. + +.......................................................................... + +The following table gives the non-cumulative quantities, i.e. the +values per reliability index range. These numbers answer the question: +how reliable is the prediction for all residues labeled with the +particular index i. + ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ +| index| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | +| %res | 8.8| 9.5| 9.3| 9.1| 9.7| 10.5| 12.5| 15.7| 14.1| ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ +| | | | | | | | | | | +| Qtot | 46.6| 50.6| 57.7| 62.6| 67.9| 74.2| 82.2| 88.3| 94.2| +| | | | | | | | | | | ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ +| H%obs| 36.8| 42.3| 49.5| 55.2| 61.7| 69.9| 78.8| 87.4| 96.4| +| E%obs| 44.7| 44.5| 52.1| 55.4| 60.9| 68.0| 75.9| 81.0| 68.1| +| | | | | | | | | | | +| H%prd| 49.9| 52.5| 60.3| 64.2| 69.2| 77.5| 85.4| 89.9| 95.4| +| E%prd| 41.7| 47.1| 53.6| 57.0| 64.0| 71.6| 78.8| 88.8| 93.5| ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+ + +For example, for residues with Relindex = 5 64% of all predicted betha- +strand residues are correctly identified. + + + + + + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Solvent accessibility prediction by PHDacc: + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + Author: Burkhard Rost + EMBL, Heidelberg, FRG + Meyerhofstrasse 1, 69 117 Heidelberg + Internet: Rost@EMBL-Heidelberg.DE + + All rights reserved. + + + + +About the network method +~~~~~~~~~~~~~~~~~~~~~~~ + +The network for prediction of secondary structure is described in +detail in: + Rost, Burkhard; Sander, Chris: + Prediction of protein structure at better than 70% accuracy. + J. Mol. Biol., 1993, 232, 584-599. + +The analysis of the prediction of solvent exposure is given in: + Rost, Burkhard; Sander, Chris: + Conservation and prediction of solvent accessibility in protein + families. Proteins, 1994, 20, 216-226. + +To be quoted for publications of PHD exposure prediction: + Both papers quoted above. + + + +Definition of accessibility +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +For training the residue solvent accessibility the DSSP (Dictionary of +Secondary Structure of Proteins; Kabsch & Sander (1983) Biopolymers, 22, +2577-2637) values of accessible surface area have been used. The +prediction provides values for the relative solvent accessibility. The +normalisation is the following: + +| ACCESSIBILITY (from DSSP in Angstrom) +|RELATIVE_ACCESSIBILITY = ------------------------------------- * 100 +| MAXIMAL_ACC (amino acid type i) + +where MAXIMAL_ACC (i) is the maximal accessibility of amino acid type i. +The maximal values are: + ++----+----+----+----+----+----+----+----+----+----+----+----+ +| A | B | C | D | E | F | G | H | I | K | L | M | +| 106| 160| 135| 163| 194| 197| 84| 184| 169| 205| 164| 188| ++----+----+----+----+----+----+----+----+----+----+----+----+ +| N | P | Q | R | S | T | V | W | X | Y | Z | +| 157| 136| 198| 248| 130| 142| 142| 227| 180| 222| 196| ++----+----+----+----+----+----+----+----+----+----+----+ + +Notation: one letter code for amino acid, B stands for D or N; Z stands + for E or Q; and X stands for undetermined. + +The relative solvent accessibility can be used to estimate the number +of water molecules (W) in contact with the residue: + +W = ACCESSIBILITY /10 + +The prediction is given in 10 states for relative accessibility, with + +RELATIVE_ACCESSIBILITY = (PREDICTED_ACC * PREDICTED_ACC) + +where PREDICTED_ACC = 0 - 9. + + + +Estimated Accuracy of Prediction +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +A careful cross validation test on some 238 protein chains (in total +about 62,000 residues) with less than 25% pairwise sequence identity +gave the following results: + + +Correlation +........... + +The correlation between observed and predicted solvent accessibility +is: + +----------- +corr = 0.53 +----------- + +This value ought to be compared to the worst and best case prediction +scenario: random prediction (corr = 0.0) and homology modelling +(corr = 0.66). (Note: homology modelling yields a relative accurate +prediction in 3D if, and only if, a significantly identical sequence +has a known 3D structure.) + + +3-state accuracy +................ + +Often the relative accessibility is projected onto, e.g., 3 states: + b = buried (here defined as < 9% relative accessibility), + i = intermediate ( 9% <= rel. acc. < 36% ), + e = exposed ( rel. acc. >= 36% ). + +A projection onto 3 states or 2 states (buried/exposed) enables the +compilation of a 3- and 2-state prediction accuracy. PHD reaches an +overall 3-state accuracy of: + Q3 = 57.5% +(compared to 35% for random prediction and 70% for homology modelling). + +In detail: + ++-----------------------------------+-------------------------+ +| Qburied (% of observed)=77% | Qb (% of predicted)=60% | +| Qintermediate (% of observed)= 9% | Qi (% of predicted)=44% | +| Qexposed (% of observed)=78% | Qe (% of predicted)=56% | ++-----------------------------------+-------------------------+ + + +10-state accuracy +................. + +The network predicts relative solvent accessibility in 10 states, with +state i (i = 0-9) corresponding to a relative solvent accessibility of +i*i %. The 10-state accuracy of the network is: + + Q10 = 24.5% + +.......................................................................... + +These percentages are defined by: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +| number of correctly predicted residues +|Q3 = --------------------------------------- (*100) +| number of all residues +| +| no of res. correctly predicted to be buried +|Qburied (% of obs) = ------------------------------------------- (*100) +| no of all res. observed to be buried +| +| +| no of res. correctly predicted to be buried +|Qburied (% of pred)= ------------------------------------------- (*100) +| no of all residues predicted to be buried + +.......................................................................... + +Averaging over single chains +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The most reasonable way to compute the overall accuracies is the above +quoted percentage of correctly predicted residues. However, since the +user is mainly interested in the expected performance of the prediction +for a particular protein, the mean value when averaging over protein +chains might be of help as well. Computing first the correlation +between observed and predicted accessibility for each protein chan, and +then averaging over all 238 chains yields the following average: + ++-------------------------------====--+ +| corr/averaged over chains = 0.53 | ++-------------------------------====--+ +| standard deviation = 0.11 | ++-------------------------------------+ + +.......................................................................... + +Further details of performance accuracy +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The accuracy matrix in detail: +.............................. + +-------+----------------------------------------------------+----------- +\ PHD | 0 1 2 3 4 5 6 7 8 9 | SUM %obs +-------+----------------------------------------------------+----------- +OBS 0 | 8611 140 8 44 82 169 772 334 27 0 | 10187 16.6 +OBS 1 | 4367 164 0 50 106 231 738 346 44 3 | 6049 9.8 +OBS 2 | 3194 168 1 68 125 303 951 513 42 7 | 5372 8.7 +OBS 3 | 2760 159 8 80 136 327 1246 746 58 19 | 5539 9.0 +OBS 4 | 2312 144 2 72 166 396 1615 1245 124 19 | 6095 9.9 +OBS 5 | 1873 96 3 84 138 425 1979 1834 187 27 | 6646 10.8 +OBS 6 | 1387 67 1 60 80 278 2237 2627 231 51 | 7019 11.4 +OBS 7 | 1082 35 0 32 56 225 1871 3107 302 60 | 6770 11.0 +OBS 8 | 660 25 0 27 43 136 1206 2374 325 87 | 4883 7.9 +OBS 9 | 325 20 2 27 29 74 648 1159 366 214 | 2864 4.7 +-------+----------------------------------------------------+----------- +SUM |26571 1018 25 544 961 2564 13263 14285 1706 487 | +%pred | 43.3 1.7 0.0 0.9 1.6 4.2 21.6 23.3 2.8 0.8 | +-------+----------------------------------------------------+----------- + +Note: This table is to be read in the following manner: + 8611 of all residues predicted to be in exposed by 0%, were + observed with 0% relative accessibility. However, 325 of all + residues predicted to have 0% are observed as completely exposed + (obs = 9 -> rel. acc. >= 81%). The term "observed" refers to the + DSSP compilation of area of solvent accessibility calculated from + 3D coordinates of experimentally determined structures (Diction- + ary of Secondary Structure of Proteins: Kabsch & Sander (1983) + Biopolymers, 22, 2577-2637). + + +Accuracy for each amino acid: +............................. + ++---+------------------------------+-----+-------+------+ +|AA | Q3 b%o b%p i%o i%p e%o e%p | Q10 | corr | N | ++---+------------------------------+-----+-------+------+ +| A | 59.0 87 60 2 38 66 57 | 31 | 0.530 | 5054 | +| C | 62.0 91 67 5 39 25 21 | 34 | 0.244 | 893 | +| D | 56.5 21 45 6 49 94 57 | 20 | 0.321 | 3536 | +| E | 60.8 9 40 3 41 98 61 | 21 | 0.347 | 3743 | +| F | 63.3 94 67 9 46 29 37 | 27 | 0.366 | 2436 | +| G | 52.1 75 51 1 31 67 53 | 22 | 0.405 | 4787 | +| H | 50.9 63 53 23 45 71 50 | 18 | 0.442 | 1366 | +| I | 64.9 95 68 6 41 30 38 | 34 | 0.360 | 3437 | +| K | 66.6 2 11 2 37 98 67 | 23 | 0.267 | 3652 | +| L | 61.6 93 65 8 44 31 40 | 31 | 0.368 | 5016 | +| M | 60.1 92 64 5 39 45 44 | 29 | 0.452 | 1371 | +| N | 55.5 45 45 8 38 87 59 | 17 | 0.410 | 2923 | +| P | 53.0 48 48 9 39 83 56 | 18 | 0.364 | 2920 | +| Q | 54.3 27 44 7 44 92 56 | 20 | 0.344 | 2225 | +| R | 49.9 15 47 36 47 76 51 | 18 | 0.372 | 2765 | +| S | 55.6 69 53 3 51 81 56 | 22 | 0.464 | 3981 | +| T | 51.8 61 51 8 38 78 53 | 21 | 0.432 | 3740 | +| V | 61.1 93 65 5 40 39 42 | 34 | 0.418 | 4156 | +| W | 56.2 85 62 20 49 29 27 | 21 | 0.318 | 891 | +| Y | 49.7 73 52 33 49 36 38 | 19 | 0.359 | 2301 | ++---+------------------------------+-----+-------+------+ + +Abbreviations: + +AA: amino acid in one-letter code +b%o, i%o, e%o: = Qburied, Qintermediate, Qexposed (% of observed), + i.e. percentage of correct prediction in each state, see above +b%p, i%p, e%p: = Qburied, Qintermediate, Qexposed (% of predicted), + i.e. probability of correct prediction in each state, see above +b%o: = Qburied (% of observed), see above +Q10: percentage of correctly predicted residues in each of the 10 + states of predicted relative accessibility. +corr: correlation between predicted and observed rel. acc. +N: number of residues in data set + + +Accuracy for different secondary structure: +........................................... + ++--------+------------------------------+----+-------+-------+ +| type | Q3 b%o b%p i%o i%p e%o e%p |Q10 | corr | N | ++--------+------------------------------+----+-------+-------+ +| helix | 59.5 79 64 8 44 80 56 | 27 | 0.574 | 20100 | +| strand | 61.3 84 73 9 46 69 37 | 35 | 0.524 | 13356 | +| loop | 54.4 64 43 11 44 78 61 | 18 | 0.442 | 27968 | ++--------+------------------------------+----+-------+-------+ + +Abbreviations as before. + + + +Position-specific reliability index +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The network predicts the 10 states for relative accessibility using real +numbers from the output units. The prediction is assigned by choosing +the maximal unit ("winner takes all"). However, the real numbers +contain additional information. +E.g. the difference between the maximal and the second largest output +unit (with the constraint that the second largest output is compiled +among all units at least 2 positions off the maximal unit) can be used +to derive a "reliability index". This index is given for each residue +along with the prediction. The index is scaled to have values between +0 (lowest reliability), and 9 (highest). +The accuracies (Q3, corr, asf.) to be expected for residues with values +above a particular value of the index are given below as well as the +fraction of such residues (%res).: + ++---+------------------------------+----+-------+-------+ +|RI | Q3 b%o b%p i%o i%p e%o e%p |Q10 | corr | %res | ++---+------------------------------+----+-------+-------+ +| 0 | 57.5 77 60 9 44 78 56 | 24 | 0.535 | 100.0 | +| 1 | 59.1 76 63 9 45 82 57 | 25 | 0.560 | 91.2 | +| 2 | 61.7 79 66 4 47 87 58 | 27 | 0.594 | 77.1 | +| 3 | 66.6 87 70 1 51 89 63 | 30 | 0.650 | 57.1 | +| 4 | 70.0 89 72 0 83 91 67 | 32 | 0.686 | 45.8 | +| 5 | 72.9 92 75 0 0 93 70 | 34 | 0.722 | 35.6 | +| 6 | 76.3 95 77 0 0 93 75 | 36 | 0.769 | 24.7 | +| 7 | 79.0 97 79 0 0 93 78 | 39 | 0.803 | 16.0 | +| 8 | 80.9 98 80 0 0 91 81 | 43 | 0.824 | 9.6 | +| 9 | 81.2 99 80 0 0 88 83 | 45 | 0.828 | 5.9 | ++---+------------------------------+----+-------+-------+ + +Abbreviations as before. + +The above table gives the cumulative results, e.g. 45.8% of all +residues have a reliability of at least 4. The correlation for this +most reliably predicted half of the residues is 0.686, i.e. a value +comparable to what could be expected if homology modelling were +possible. For this subset of 45.8% of all residues, 89% of the buried +residues are correctly predicted, and 72% of all residues predicted to +be buried are correct. + +.......................................................................... + +The following table gives the non-cumulative quantities, i.e. the +values per reliability index range. These numbers answer the question: +how reliable is the prediction for all residues labeled with the +particular index i. + ++---+------------------------------+----+-------+-------+ +|RI | Q3 b%o b%p i%o i%p e%o e%p |Q10 | corr | %res | ++---+------------------------------+----+-------+-------+ +| 0 | 40.9 79 40 16 41 21 40 | 14 | 0.175 | 8.8 | +| 1 | 45.4 61 46 28 44 48 44 | 17 | 0.278 | 14.1 | +| 2 | 47.4 53 52 10 46 80 44 | 19 | 0.343 | 19.9 | +| 3 | 52.9 75 59 4 50 77 47 | 23 | 0.439 | 11.4 | +| 4 | 60.0 81 63 0 83 84 56 | 25 | 0.547 | 10.1 | +| 5 | 65.2 82 70 0 0 93 62 | 28 | 0.607 | 10.9 | +| 6 | 71.3 90 72 0 0 94 70 | 31 | 0.692 | 8.8 | +| 7 | 76.0 94 76 0 0 95 75 | 34 | 0.762 | 6.3 | +| 8 | 80.5 97 81 0 0 94 79 | 39 | 0.808 | 3.8 | +| 9 | 81.2 99 80 0 0 88 83 | 45 | 0.828 | 5.9 | ++---+------------------------------+----+-------+-------+ + +For example, for residues with RI = 4 83% of all predicted intermediate +residues are correctly predicted as such. + + + + + + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Prediction of helical transmembrane segments by PHDhtm: + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + Author: Burkhard Rost + EMBL, Heidelberg, FRG + Meyerhofstrasse 1, 69 117 Heidelberg + Internet: Rost@EMBL-Heidelberg.DE + + All rights reserved. + + + + +About the network method +~~~~~~~~~~~~~~~~~~~~~~~ + +The PHD mail server is described in: + Rost, Burkhard; Sander, Chris; Schneider, Reinhard: + PHD - an automatic mail server for protein secondary structure + prediction. + CABIOS, 1994, 10, 53-60. + +To be quoted for publications of PHDhtm output: + Rost, Burkhard; Casadio, Rita; Fariselli, Piero; Sander, Chris: + Prediction of helical transmembrane segments at 95% accuracy. + Protein Science, 1995, 4, 521-533. + + + +Estimated Accuracy of Prediction +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +A cross validation test on 69 helical trans-membrane proteins (in total +about 30,000 residues) with less than 25% pairwise sequence identity +gave the following results: + +++================++-----------------------------------------+ +|| Qtotal = 94.7% || ("overall two state accuracy") | +++================++-----------------------------------------+ + ++----------------------------+-----------------------------+ +| Qhelix (% of observed)=92% | Qhelix (% of predicted)=83% | +| Qloop (% of observed)=96% | Qloop (% of predicted)=97% | ++----------------------------+-----------------------------+ + +.......................................................................... + +These percentages are defined by: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +| number of correctly predicted residues +|Qtotal = --------------------------------------- (*100) +| number of all residues +| +| no of res correctly predicted to be in helix +|Qhelix (% of obs) = -------------------------------------------- (*100) +| no of all res observed to be in helix +| +| +| no of res correctly predicted to be in helix +|Qhelix (% of pred)= -------------------------------------------- (*100) +| no of all residues predicted to be in helix + +.......................................................................... + +Further measures of performance +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Matthews correlation coefficient: + ++---------------------------------------------+ +| Chelix = 0.84, Cloop = 0.84 | ++---------------------------------------------+ +.......................................................................... + +Average length of predicted secondary structure segments: + +| +------------+----------+ +| | predicted | observed | ++-----------+------------+----------+ +| Lhelix = | 24.6 | 22.2 | ++-----------+------------+----------+ +.......................................................................... + +The accuracy matrix in detail: + ++---------------------------------+ +| number of residues with H, L | ++---------+------+-------+--------+ +| |net H | net L |sum obs | ++---------+------+-------+--------+ +| obs H | 5214 | 492 | 5706 | +| obs L | 1050 | 22423 | 23473 | ++---------+------+-------+--------+ +| sum Net | 6264 | 22915 | 29179 | ++---------+------+-------+--------+ + +Note: This table is to be read in the following manner: + 5214 of all residues predicted to be in a helical trans-membrane + region, were observed to be in the lipid bilayer, 1050 however + were observed either inside or outside of the protein, i.e. in + loop (or non-membrane) regions. The term "observed" refers to DSSP + assignment of secondary structure calculated from 3D coordinates + of experimentally determined structures (Dictionary of Secondary + Structure of Proteins: Kabsch & Sander (1983) Biopolymers, 22, + 2577-2637) where these were available. For all other proteins, + the assignment of trans-membrane segments has been taken from the + Swissprot data bank (Bairoch, A.; Boeckmann, B.: The SWISS-PROT + protein sequence data bank. Nucl. Acids Res. 20: 2019-2022, 1992). + +.......................................................................... + +Overlap between predicted and observed segments: + ++-----------------+---------------+----------------+ +| segment overlap | % of observed | % of predicted | +| Sov helix | 95.6% | 95.5% | +| Sov loop | 83.6% | 97.2% | ++-----------------+---------------+----------------+ +| Sov total | 86.0% | 96.8% | ++-----------------+---------------+----------------+ + + Definition of Sov in: Rost et al., JMB, 1994, 235, 13-26. + + As helical trans-membrane segments are longer than globular heli- + ces, correctly predicted segments can easily be made out. PHDhtm + misses 5 out of 258 observed segments, predicts 6 where non is + observed and 3 times the predicted helical segment overlaps two + observed regions. Thus, in total more than 95% of all segments + are correctly predicted. + +.......................................................................... + +Entropy of prediction (information measure): + ++-----------------+ +| I = 0.64 | ++-----------------+ + + (For comparison: homology modelling of globular proteins in three + states: I=0.62.) + Definition of Sov in: Rost et al., JMB, 1994, 235, 13-26. + + + +Position-specific reliability index +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +The network predicts two states: helical trans-membrane region and rest +using two output units. The prediction is assigned by choosing the ma- +ximal unit ("winner takes all"). However, the real numbers of the out- +put units contain additional information. +E.g. the difference between the two output units can be used to derive +a "reliability index". This index is given for each residue along with +the prediction. The index is scaled to have values between 0 (lowest +reliability), and 9 (highest). +The accuracies (Qtot) to be expected for residues with values above a +particular value of the index are given below as well as the fraction +of such residues (%res).: + ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ +| index| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | +| %res |100.0| 98.8| 97.3| 95.9| 94.1| 92.3| 89.9| 86.2| 75.0| 66.8| ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ +| | | | | | | | | | | | +| Qtot | 94.7| 95.2| 95.6| 96.2| 96.7| 97.2| 97.7| 98.4| 99.4| 99.8| +| | | | | | | | | | | | ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ +| H%obs| 91.8| 92.9| 93.8| 94.4| 95.0| 95.7| 96.2| 96.8| 95.5| 78.7| +| L%obs| 95.3| 95.7| 96.1| 96.6| 97.0| 97.5| 98.1| 98.8| 99.7|100.0| +| | | | | | | | | | | | +| H%prd| 82.7| 83.8| 85.0| 86.7| 88.1| 89.7| 91.4| 93.8| 96.3| 97.1| +| L%prd| 97.9| 98.3| 98.5| 98.7| 98.8| 99.0| 99.2| 99.4| 99.7| 99.9| ++------+-----+-----+-----+-----+-----+-----+-----+-----+-----+-----+ + +The above table gives the cumulative results, e.g. 92.3% of all +residues have a reliability of at least 5. The overall two-state +accuracy for this subset is 97.2%. For this subset, e.g., 95.7% of +the observed helical trans-membrane residues are correctly predicted, +and 89.7% of all residues predicted to be in helical trans-membrane +segment are correct. + + + + + + + +The resulting network (PHD) prediction is: +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +________________________________________________________________________________ + + + + PHD: Profile fed neural network systems from HeiDelberg + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + Prediction of: + secondary structure, by PHDsec + solvent accessibility, by PHDacc + and helical transmembrane regions, by PHDhtm + + Author: + Burkhard Rost + EMBL, 69012 Heidelberg, Germany + Internet: Rost@EMBL-Heidelberg.DE + + All rights reserved. + + + + The network systems are described in: + + PHDsec: B Rost & C Sander: JMB, 1993, 232, 584-599. + B Rost & C Sander: Proteins, 1994, 19, 55-72. + PHDacc: B Rost & C Sander: Proteins, 1994, 20, 216-226. + PHDhtm: B Rost et al.: Prot. Science, 1995, 4, 521-533. + + + + Some statistics + ~~~~~~~~~~~~~~~ + + Percentage of amino acids: + +--------------+--------+--------+--------+--------+--------+ + | AA: | L | A | S | G | I | + | % of AA: | 13.0 | 10.0 | 9.7 | 8.9 | 8.6 | + +--------------+--------+--------+--------+--------+--------+ + | AA: | V | R | T | F | D | + | % of AA: | 7.8 | 5.2 | 4.5 | 4.5 | 4.5 | + +--------------+--------+--------+--------+--------+--------+ + | AA: | N | Q | E | P | K | + | % of AA: | 4.1 | 3.0 | 3.0 | 2.6 | 2.6 | + +--------------+--------+--------+--------+--------+--------+ + | AA: | Y | M | W | H | C | + | % of AA: | 1.9 | 1.9 | 1.5 | 1.5 | 1.5 | + +--------------+--------+--------+--------+--------+--------+ + + Percentage of secondary structure predicted: + +--------------+--------+--------+--------+ + | SecStr: | H | E | L | + | % Predicted: | 43.9 | 16.7 | 39.4 | + +--------------+--------+--------+--------+ + + According to the following classes: + all-alpha: %H>45 and %E< 5; all-beta : %H<5 and %E>45 + alpha-beta : %H>30 and %E>20; mixed: rest, + this means that the predicted class is: mixed class + + + + PHD output for your protein + ~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + Tue Nov 24 17:44:57 1998 + Jury on: 10 different architectures (version 5.94_317 ). + Note: differently trained architectures, i.e., different versions can + result in different predictions. + + + + About the protein + ~~~~~~~~~~~~~~~~~ + + HEADER /home/phd/server/work/predict_h25873-220 + COMPND + SOURCE + AUTHOR + SEQLENGTH 269 + NCHAIN 1 chain(s) in predict_h25873-22040 data set + NALIGN 48 + (=number of aligned sequences in HSSP file) + + + + Abbreviations: PHDsec + ~~~~~~~~~~~~~~~~~~~~~ + + sequence: + AA : amino acid sequence + secondary structure: + HEL: H=helix, E=extended (sheet), blank=other (loop) + PHD: Profile network prediction HeiDelberg + Rel: Reliability index of prediction (0-9) + detail: + prH: 'probability' for assigning helix + prE: 'probability' for assigning strand + prL: 'probability' for assigning loop + note: the 'probabilites' are scaled to the interval 0-9, e.g., + prH=5 means, that the first output node is 0.5-0.6 + subset: + SUB: a subset of the prediction, for all residues with an expected + average accuracy > 82% (tables in header) + note: for this subset the following symbols are used: + L: is loop (for which above " " is used) + ".": means that no prediction is made for this residue, as the + reliability is: Rel < 5 + + Abbreviations: PHDacc + ~~~~~~~~~~~~~~~~~~~~~ + + SS : secondary structure + HEL: H=helix, E=extended (sheet), blank=other (loop) + solvent accessibility: + 3st: relative solvent accessibility (acc) in 3 states: + b = 0-9%, i = 9-36%, e = 36-100%. + PHD: Profile network prediction HeiDelberg + Rel: Reliability index of prediction (0-9) + O_3: observed relative acc. in 3 states: B, I, E + note: for convenience a blank is used intermediate (i). + P_3: predicted relative accessibility in 3 states + 10st:relative accessibility in 10 states: + = n corresponds to a relative acc. of n*n % + subset: + SUB: a subset of the prediction, for all residues with an expected + average correlation > 0.69 (tables in header) + note: for this subset the following symbols are used: + "I": is intermediate (for which above " " is used) + ".": means that no prediction is made for this residue, as the + reliability is: Rel < 4 + + + Abbreviations: PHDhtm + ~~~~~~~~~~~~~~~~~~~~~ + + secondary structure: + HL: T=helical transmembrane region, blank=other (loop) + PHD: Profile network prediction HeiDelberg + PHDF:filtered prediction, i.e., too long transmembrane segments + are split, too short ones are deleted + Rel: Reliability index of prediction (0-9) + detail: + prH: 'probability' for assigning helical transmembrane region + prL: 'probability' for assigning loop + note: the 'probabilites' are scaled to the interval 0-9, e.g., + prH=5 means, that the first output node is 0.5-0.6 + subset: + SUB: a subset of the prediction, for all residues with an expected + average accuracy > 82% (tables in header) + note: for this subset the following symbols are used: + L: is loop (for which above " " is used) + ".": means that no prediction is made for this residue, as the + reliability is: Rel < 5 + + + + protein: predict length 269 + + ....,....1....,....2....,....3....,....4....,....5....,....6 + AA |MASEIKKKLFWRAVVAEFLAMTLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSI| + PHD sec | HHHHHHHHHHHHHHHHHHHHHHHHHHEE HHHHHHHHHHHHH| + Rel sec |998443148899999999999998997676530312469989998623353579999999| + detail: + prH sec |001223468899999999999998888777653112210000000145566788999999| + prE sec |000011000000000000000001001111233542100000000000323211000000| + prL sec |998665420100000000000000000011112244578988998753100000000000| + subset: SUB sec |LLL.....HHHHHHHHHHHHHHHHHHHHHHH......LLLLLLLLL...H.HHHHHHHHH| + + ACCESSIBILITY + 3st: P_3 acc |eeeebee bbb bbbbbbbbbbbbbbbbbbbbbebeee eeeeeeeeebbbbbbbbbbbb| + 10st: PHD acc |997706650005000000000000000000000607775779776677000000000000| + Rel acc |735421110541467608662789996343122133420454330023453975664547| + subset: SUB acc |e.ee.....bb.bbbb.bbb.bbbbbb.b.......e..eee......bb.bbbbbbbbb| + ....,....7....,....8....,....9....,....10...,....11...,....12 + AA |ATLAQSVGHISGAHSNPAVTLGLLLSCQISILRAVMYIIAQCVGAIVASAILSGITSSLL| + PHD sec |HHHHHHHHHE HHHHEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH | + Rel sec |999996412122653167703135552356779999999999999999999998467213| + detail: + prH sec |998986544334223477843456665567779999999999999999999998611343| + prE sec |001001123420010000145432101221110000000000000000000000000000| + prL sec |000001232245765521000000123210000000000000000000000000278555| + subset: SUB sec |HHHHHH......LL..HHH....HHH..HHHHHHHHHHHHHHHHHHHHHHHHHH.LL...| + + ACCESSIBILITY + 3st: P_3 acc |bbbbebbbebbbbbb bbbbbbbbbbbebbbbbbbbbbbbbbbbbbbbbbbbeebbeeeb| + 10st: PHD acc |000060006000000500000000000600000000000000000000000067006760| + Rel acc |456515321655013144869663400154551757478936465465467713401400| + subset: SUB acc |bbbb.b...bbb....bbbbbbb.b...bbbb.bbbbbbb.bbbbbbbbbbb..b..e..| + ....,....13...,....14...,....15...,....16...,....17...,....18 + AA |ENSLGRNDLARGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSAPLAIGLSVALGH| + PHD sec | HHH EEEEEEEEEEEEEEEEEEE E E HHHHHH| + Rel sec |359985212134223651899898866789799875436658889963211351457756| + detail: + prH sec |320002345432332111000000000000100000221120000000001113567767| + prE sec |100000000000011014899888877789789886100000000013544222221111| + prL sec |568986543466545763100000011100000112567768889975454564210111| + subset: SUB sec |.LLLLL.........LL.EEEEEEEEEEEEEEEEEE..LLLLLLLLL.....L..HHHHH| + + ACCESSIBILITY + 3st: P_3 acc |eeebbbebbbeebeebeebbbbbbbbbbbbbbbbbbbeeeeeeeebbbbbbbbbbbbbbb| + 10st: PHD acc |677000600077076077000000000000000000077767767000000000000000| + Rel acc |133100124043040233247198656399879530035414413123255869586654| + subset: SUB acc |........b.e..e.....bb.bbbbb.bbbbbb....ee.ee......bbbbbbbbbbb| + ....,....19...,....20...,....21...,....22...,....23...,....24 + AA |LLAIDYTGCGINPARSFGSAVLTRNFSNHWIFWVGPFIGSALAVLIYDFILAPRSSDFTD| + PHD sec |HEEEE E HHHEEEE EEEEEE HHHHHHHHHHHHHEEEEE | + Rel sec |321341126989622145152653534229996251699999999973147525556642| + detail: + prH sec |521100000000145432463121122000000114789999999875421111121124| + prE sec |244564431000000000015765121358997510000000000013467642110000| + prL sec |233234457889754567411012655530002364200000000010010136667765| + subset: SUB sec |........LLLLL....H.H.EE.L....EEEE.L.HHHHHHHHHHH...EE.LLLLL..| + + ACCESSIBILITY + 3st: P_3 acc |bbbbebbbbbbebb bbbbbbbbeebeebbbbbbbbbbbbbbbbbbbbbbbbeeeee ee| + 10st: PHD acc |000060000006005000000007606600000000000000000000000076777577| + Rel acc |754424240102242141047612131118967874356346635751777031345044| + subset: SUB acc |bbbb.b.b.....b..b..bbb.......bbbbbbb.bb.bbb.bbb.bbb....ee.ee| + ....,....25...,....26...,....27...,....28...,....29...,....30 + AA |RMKVWTSGQVEEYDLDADDINSRVEMKPK| + PHD sec |HHHHHH | + Rel sec |66775259975467555457776422699| + detail: + prH sec |77887520012221222221111100000| + prE sec |00000000000000000000001233200| + prL sec |11112379987678777678887655799| + subset: SUB sec |HHHHH.LLLLL.LLLLL.LLLLL...LLL| + + ACCESSIBILITY + 3st: P_3 acc |ebebbeeeeeeeeeeeeeeeeeebeeeee| + 10st: PHD acc |60700787677777677777767067789| + Rel acc |10411563134335144444514212559| + subset: SUB acc |..e..ee...e..e.eeeeee.e...eee| + + + PHDhtm Helical transmembrane prediction + note: PHDacc and PHDsec are reliable for water- + soluble globular proteins, only. Thus, + please take the predictions above with + particular caution wherever transmembrane + helices are predicted by PHDhtm! + + + PHDhtm +--- +--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION: SYMBOLS +--- AA : amino acid in one-letter code +--- PHD htm : HTM's predicted by the PHD neural network +--- system (T=HTM, ' '=not HTM) +--- Rel htm : Reliability index of prediction (0-9, 0 is low) +--- detail : Neural network output in detail +--- prH htm : 'Probability' for assigning a helical trans- +--- membrane region (HTM) +--- prL htm : 'Probability' for assigning a non-HTM region +--- note: 'Probabilites' are scaled to the interval +--- 0-9, e.g., prH=5 means, that the first +--- output node is 0.5-0.6 +--- subset : Subset of more reliable predictions +--- SUB htm : All residues for which the expected average +--- accuracy is > 82% (tables in header). +--- note: for this subset the following symbols are used: +--- L: is loop (for which above ' ' is used) +--- '.': means that no prediction is made for this, +--- residue as the reliability is: Rel < 5 +--- other : predictions derived based on PHDhtm +--- PHDFhtm : filtered prediction, i.e., too long HTM's are +--- split, too short ones are deleted +--- PHDRhtm : refinement of neural network output +--- PHDThtm : topology prediction based on refined model +--- symbols used: +--- i: intra-cytoplasmic +--- T: transmembrane region +--- o: extra-cytoplasmic +--- +--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION + ....,....1....,....2....,....3....,....4....,....5....,....6 + AA |MASEIKKKLFWRAVVAEFLAMTLFVFISIGSALGFNYPLERNQTLVQDNVKVSLAFGLSI| + PHD htm | TTTTTTTTTTTTTTTTTTT TTTTTTTTTTTT| + detail: | | + prH htm |000000000001136788999999999988875321110000000123678889999988| + prL htm |999999999998863211000000000011124678889999999876321110000011| + other: | | + PHDFhtm | TTTTTTTTTTTTTTTTTTT TTTTTTTTTTT| + PHDRhtm | TTTTTTTTTTTTTTTTTT TTTTTTTTTTT| + PHDThtm |iiiiiiiiiiiiiiTTTTTTTTTTTTTTTTTToooooooooooooooooTTTTTTTTTTT| + subset: | | + SUB htm |............................................................| + ....,....7....,....8....,....9....,....10...,....11...,....12 + AA |ATLAQSVGHISGAHSNPAVTLGLLLSCQISILRAVMYIIAQCVGAIVASAILSGITSSLL| + PHD htm |TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT | + detail: | | + prH htm |888888877777666677788888888888888888888888888888888876543211| + prL htm |111111122222333322211111111111111111111111111111111123456788| + other: | | + PHDFhtm |TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT | + PHDRhtm |TTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTT | + PHDThtm |TTTTTTTTiiiiiiiiiiiiiTTTTTTTTTTTTTTTTTTTTTTTTToooooooooooooo| + subset: | | + SUB htm |............................................................| + ....,....13...,....14...,....15...,....16...,....17...,....18 + AA |ENSLGRNDLARGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSAPLAIGLSVALGH| + PHD htm | TTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTT| + detail: | | + prH htm |000000000001234567788888999988887643211111111235788899998888| + prL htm |999999999998765432211111000011112356788888888764211100001111| + other: | | + PHDFhtm | TTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTT| + PHDRhtm | TTTTTTTTTTTTTTTTTT TTTTTTTTTTTT| + PHDThtm |ooooooooooooooooTTTTTTTTTTTTTTTTTTiiiiiiiiiiiiiiTTTTTTTTTTTT| + subset: | | + SUB htm |............................................................| + ....,....19...,....20...,....21...,....22...,....23...,....24 + AA |LLAIDYTGCGINPARSFGSAVLTRNFSNHWIFWVGPFIGSALAVLIYDFILAPRSSDFTD| + PHD htm |TTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT | + detail: | | + prH htm |888887765443432233334566777777788888888888888888887542100000| + prL htm |111112234556567766665433222222211111111111111111112457899999| + other: | | + PHDFhtm |TTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT | + PHDRhtm |TTTTTT TTTTTTTTTTTTTTTTTTT | + PHDThtm |TTTTTToooooooooooooooooooooooooTTTTTTTTTTTTTTTTTTTiiiiiiiiii| + subset: | | + SUB htm |............................................................| + ....,....25...,....26...,....27...,....28...,....29...,....30 + AA |RMKVWTSGQVEEYDLDADDINSRVEMKPK| + PHD htm | | + detail: | | + prH htm |00000000000000000000000000000| + prL htm |99999999999999999999999999999| + other: | | + PHDFhtm | | + PHDRhtm | | + PHDThtm |iiiiiiiiiiiiiiiiiiiiiiiiiiiii| + subset: | | + SUB htm |.............................| +--- +--- PhdTopology REFINEMENT AND TOPOLOGY PREDICTION END +--- + +________________________________________________________________________________ + + + +________________________________________________________________________________ + + +----------------------------------------------------------------------------- +--- PredictProtein: NEWS from January, 1997 --- +--- --- +--- Dear user, --- +--- --- +--- as of January 1, 1997, EMBL has effectively decided to not --- +--- support the PredictProtein service by personal resources. I do --- +--- maintain the program, so to speak, in my private time. However, --- +--- my contract obliges me to do science, instead. Unfortunately, --- +--- the computer environment at EMBL is at the same time starting --- +--- to become increasingly unstable. Consequence of these two re- --- +--- cent developments is that the PredictProtein service is not as --- +--- stable as it was. --- +--- --- +--- I apologise for the problems this may cause. In particular, --- +--- I apologise for my inability to reply to the 20-30 daily, per- --- +--- sonal mails, and suggest to re-submit requests after 24 hours! --- +--- --- +--- Hoping that I shall find a more convenient solution for the --- +--- future of the PredictProtein I remain with my best regards, --- +--- --- +--- Burkhard Rost --- +----------------------------------------------------------------------------- +--- PredictProtein: NEWS from April, 1998 --- +--- --- +-------------------------------- --- +--- MOVING PredictProtein --- +--- There appears to be light on the horizon! PP will may be having --- +--- many hickups over the next months (as I shall leave EMBL). How- --- +--- ever, the server seems to have a fair chance of survival thanks --- +--- to a major support that is being raised by Columbia University, --- +--- New York, U.S.A.). I hope that this will settle the issue for --- +--- the years to come ... --- +-------------------------------- --- +--- WARNING --- +--- After a major rewriting of most of the PP code over the last, --- +--- I am afraid that not all errors have been traced by me, yet. --- +--- Thus, please have mercy and report any bug you'll encounter! --- +--- THANKS, Burkhard Rost --- +-------------------------------- --- +--- NEW PREDICTION DEFAULTS --- +--- * Coiled-coil regions: now by default the program COILS written by --- +--- Andrei Lupas is run on your sequence. An output is returned if a --- +--- coiled-coil region has been detected. --- +--- * Functional sequence motifs: now by default the PROSITE database --- +--- written by Amos Bairoch, Philip Bucher and Kay Hofmann is scanned --- +--- for sequence motifs. An output is returned if any motif has been --- +--- detected. --- +-------------------------------- --- +--- see http://www.embl-heidelberg.de/predictprotein/ppNews.html --- +--- for a description of the following new options. --- +--- NEW INPUT OPTION --- +--- * Your input sequence(s) in FASTA-list format ("# FASTA list ") --- +--- NEW OUTPUT OPTIONS --- +--- * Return also BLASTP output ("return blast") --- +--- * Return prediction additionally in RDB format ("return phd rdb") --- +--- * Return topits hssp ("return topits hssp") --- +--- * Return topits strip ("return topits strip") --- +--- * Return topits own ("return topits own") --- +--- * Return no coils ("return no coils") --- +--- * Return no prosite ("return no prosite") --- +----------------------------------------------------------------------------- +%</AQP1PHD> +% \end{macrocode} +% \begin{macrocode} +%<*AQPHMMsgl> +>HP: 269 AQP1 IN 6 14 33 54 73 94 112 139 156 165 184 211 230 +>HP: 271 AQP2 IN 6 17 35 44 65 86 104 131 148 157 176 203 224 +>HP: 285 AQP3 IN 6 22 41 50 72 103 122 153 172 185 207 238 260 +>HP: 323 AQP4 IN 6 37 57 70 92 123 147 160 177 186 205 232 254 +>HP: 265 AQP5 IN 6 13 32 59 78 87 110 131 149 158 177 204 228 +%</AQPHMMsgl> +% \end{macrocode} +% \begin{macrocode} +%<*AQPHMMext> +Protein: AQP1 +Length: 269 +N-terminus: IN +Number of transmembrane helices: 6 +Transmembrane helices: 14-33 54-73 94-112 139-156 165-184 211-230 + +Total entropy of the model: 17.0025 +Entropy of the best path: 17.0049 + +The best path: + + seq MASEIKKKLF WRAVVAEFLA MTLFVFISIG SALGFNYPLE RNQTLVQDNV 50 + pred IIIIiiiiii iiiHHHHHHH HHHHHHHHHH HHHooooooo oooooooooo + + seq KVSLAFGLSI ATLAQSVGHI SGAHSNPAVT LGLLLSCQIS ILRAVMYIIA 100 + pred oooHHHHHHH HHHHHHHHHH HHHiiiiiii iiiiiiiiii iiiHHHHHHH + + seq QCVGAIVASA ILSGITSSLL ENSLGRNDLA RGVNSGQGLG IEIIGTLQLV 150 + pred HHHHHHHHHH HHoooooooo oooooooooo ooooooooHH HHHHHHHHHH + + seq LCVLATTDRR RRDLGGSAPL AIGLSVALGH LLAIDYTGCG INPARSFGSA 200 + pred HHHHHHiiii iiiiHHHHHH HHHHHHHHHH HHHHoooooo oooooooooo + + seq VLTRNFSNHW IFWVGPFIGS ALAVLIYDFI LAPRSSDFTD RMKVWTSGQV 250 + pred oooooooooo HHHHHHHHHH HHHHHHHHHH iiiiiiiiii iiiiiIIIII + + seq EEYDLDADDI NSRVEMKPK 269 + pred IIIIIIIIII IIIIIIIII + +Protein: AQP2 +Length: 271 +N-terminus: IN +Number of transmembrane helices: 6 +Transmembrane helices: 17-35 44-65 86-104 131-148 157-176 203-224 + +Total entropy of the model: 17.0017 +Entropy of the best path: 17.0046 + +The best path: + + seq MWELRSIAFS RAVLAEFLAT LLFVFFGLGS ALQWASSPPS VLQIAVAFGL 50 + pred IIIIIIiiii iiiiiiHHHH HHHHHHHHHH HHHHHooooo oooHHHHHHH + + seq GIGILVQALG HVSGAHINPA VTVACLVGCH VSFLRAAFYV AAQLLGAVAG 100 + pred HHHHHHHHHH HHHHHiiiii iiiiiiiiii iiiiiHHHHH HHHHHHHHHH + + seq AAILHEITPV EIRGDLAVNA LHNNATAGQA VTVELFLTMQ LVLCIFASTD 150 + pred HHHHoooooo oooooooooo oooooooooo HHHHHHHHHH HHHHHHHHii + + seq ERRGDNLGSP ALSIGFSVTL GHLLGIYFTG CSMNPARSLA PAVVTGKFDD 200 + pred iiiiiiHHHH HHHHHHHHHH HHHHHHoooo oooooooooo oooooooooo + + seq HWVFWIGPLV GAIIGSLLYN YLLFPSAKSL QERLAVLKGL EPDTDWEERE 250 + pred ooHHHHHHHH HHHHHHHHHH HHHHiiiiii iiiiiiiiiI IIIIIIIIII + + seq VRRRQSVELH SPQSLPRGSK A 271 + pred IIIIIIIIII IIIIIIIIII I + +Protein: AQP3 +Length: 285 +N-terminus: IN +Number of transmembrane helices: 6 +Transmembrane helices: 22-41 50-72 103-122 153-172 185-207 238-260 + +Total entropy of the model: 17.0059 +Entropy of the best path: 17.0075 + +The best path: + + seq MNRCGEMLHI RYRLLRQALA ECLGTLILVM FGCGSVAQVV LSRGTHGGFL 50 + pred IIIIIIiiii iiiiiiiiii iHHHHHHHHH HHHHHHHHHH HooooooooH + + seq TINLAFGFAV TLAILVAGQV SGAHLNPAVT FAMCFLAREP WIKLPIYTLA 100 + pred HHHHHHHHHH HHHHHHHHHH HHiiiiiiii iiiiiiiiii iiiiiiiiii + + seq QTLGAFLGAG IVFGLYYDAI WAFAGNELVV SGPNGTAGIF ATYPSGHLDM 150 + pred iiHHHHHHHH HHHHHHHHHH HHoooooooo oooooooooo oooooooooo + + seq VNGFFDQFIG TAALIVCVLA IVDPYNNPVP RGLEAFTVGL VVLVIGTSMG 200 + pred ooHHHHHHHH HHHHHHHHHH HHiiiiiiii iiiiHHHHHH HHHHHHHHHH + + seq FNSGYAVNPA RDFGPRLFTA LAGWGSEVFT TGQNWWWVPI VSPLLGSIGG 250 + pred HHHHHHHooo oooooooooo oooooooooo oooooooHHH HHHHHHHHHH + + seq VFVYQLMIGC HLEQPPPSTE AENVKLAHMK HKEQI 285 + pred HHHHHHHHHH iiiiiiiiii iiiiiIIIII IIIII + +Protein: AQP4 +Length: 323 +N-terminus: IN +Number of transmembrane helices: 6 +Transmembrane helices: 37-57 70-92 123-147 160-177 186-205 232-254 + +Total entropy of the model: 17.0058 +Entropy of the best path: 17.0091 + +The best path: + + seq MSDGAAARRW GKCGPPCSRE SIMVAFKGVW TQAFWKAVTA EFLAMLIFVL 50 + pred IIIIIIIIII IIIIIIIIII Iiiiiiiiii iiiiiiHHHH HHHHHHHHHH + + seq LSVGSTINWG GSENPLPVDM VLISLCFGLS IATMVQCFGH ISGGHINPAV 100 + pred HHHHHHHooo oooooooooH HHHHHHHHHH HHHHHHHHHH HHiiiiiiii + + seq TVAMVCTRKI SIAKSVFYIT AQCLGAIIGA GILYLVTPPS VVGGLGVTTV 150 + pred iiiiiiiiii iiiiiiiiii iiHHHHHHHH HHHHHHHHHH HHHHHHHooo + + seq HGNLTAGHGL LVELIITFQL VFTIFASCDS KRTDVTGSVA LAIGFSVAIG 200 + pred oooooooooH HHHHHHHHHH HHHHHHHiii iiiiiHHHHH HHHHHHHHHH + + seq HLFAINYTGA SMNPARSFGP AVIMGNWENH WIYWVGPIIG AVLAGALYEY 250 + pred HHHHHooooo oooooooooo oooooooooo oHHHHHHHHH HHHHHHHHHH + + seq VFCPDVELKR RLKEAFSKAA QQTKGSYMEV EDNRSQVETE DLILKPGVVH 300 + pred HHHHiiiiii iiiiiiiiiI IIIIIIIIII IIIIIIIIII IIIIIIIIII + + seq VIDIDRGDEK KGKDSSGEVL SSV 323 + pred IIIIIIIIII IIIIIIIIII III + +Protein: AQP5 +Length: 265 +N-terminus: IN +Number of transmembrane helices: 6 +Transmembrane helices: 13-32 59-78 87-110 131-149 158-177 204-228 + +Total entropy of the model: 17.0020 +Entropy of the best path: 17.0052 + +The best path: + + seq MKKEVCSLAF FKAVFAEFLA TLIFVFFGLG SALKWPSALP TILQISIAFG 50 + pred IIIIIIIIii iiHHHHHHHH HHHHHHHHHH HHoooooooo oooooooooo + + seq LAIGTLAQAL GPVSGGHINP AITLALLIGN QISLLRAVFY VAAQLVGAIA 100 + pred ooooooooHH HHHHHHHHHH HHHHHHHHii iiiiiiHHHH HHHHHHHHHH + + seq GAGILYWLAP LNARGNLAVN ALNNNTTPGK AMVVELILTF QLALCIFSST 150 + pred HHHHHHHHHH oooooooooo oooooooooo HHHHHHHHHH HHHHHHHHHi + + seq DSRRTSPVGS PALSIGLSVT LGHLVGIYFT GCSMNPARSF GPAVVMNRFS 200 + pred iiiiiiiHHH HHHHHHHHHH HHHHHHHooo oooooooooo oooooooooo + + seq PSHWVFWVGP IVGAMLAAIL YFYLLFPSSL SLHDRVAVVK GTYEPEEDWE 250 + pred oooHHHHHHH HHHHHHHHHH HHHHHHHHii iiiiiiiiii iiiIIIIIII + + seq DHREERKKTI ELTAH 265 + pred IIIIIIIIII IIIII +%</AQPHMMext> +% \end{macrocode} +% \begin{macrocode} +%<*TCoffee> +T-COFFEE, Version_5.31(Fri Oct 26 17:01:36 2007) +Cedric Notredame +CPU TIME:1 sec. +SCORE=54 +* + BAD AVG GOOD +* +AQP1.PRO : 55 +AQP2.PRO : 58 +AQP3.PRO : 46 +AQP4.PRO : 55 +AQP5.PRO : 58 +cons : 54 + +AQP1.PRO 1 65------------------------3777666677777766666666556666666554 36 +AQP2.PRO 1 -2------------------------2776667777777777777667666666666654 35 +AQP3.PRO 1 5---------9644-----33322111------457777665555556555657555544 40 +AQP4.PRO 1 63DGAAARRW9644PPCSR33322113667667677777666666666666767666665 60 +AQP5.PRO 1 65------------------------4877667667777777776666666667666665 36 +cons 1 54--------9644-----33322113777667667777766666666666666666554 60 + + +AQP1.PRO 37 111221111223454555555555444444444554455555555544544445555444 96 +AQP2.PRO 36 ---33----323444444444444444454444455556666555555555455565555 88 +AQP3.PRO 41 111211----11444444444433333232333344455565555544444445555444 96 +AQP4.PRO 61 ---331111223554555555544444454455555666666666555555455555555 117 +AQP5.PRO 37 ---43----323555555555554444454455555555666555555555555565555 89 +cons 61 111331111323454545444444444444444455555665555555555455555555 120 + + +AQP1.PRO 97 5555555556555655555----------4444445555555555555555-----5555 141 +AQP2.PRO 89 6556666666666665555----------5555555566666666666666-----5556 133 +AQP3.PRO 97 4445555555555554443YYDAIWAFAG2322222333333344443454LDMVN4445 156 +AQP4.PRO 118 5556666666666665544----------4445545555555555665666-----6666 162 +AQP5.PRO 90 5555555556666665554----------4455555666666666666677-----6676 134 +cons 121 5555556666666655554----------4444444555555555555566-----5566 180 + + +AQP1.PRO 142 6677777777777766666666-5666656666666555666556677777778777766 200 +AQP2.PRO 134 5566777777777766666555-5565556666666555556556788888888888777 192 +AQP3.PRO 157 7666777777777777765444V3454455554444322222224577777777777665 216 +AQP4.PRO 163 7777777777777777776666-5555555555666555555555677777777777766 221 +AQP5.PRO 135 7777888788887777776666-5666666666666555555556677777777777776 193 +cons 181 7677777777777777666555-5565555565556544555555677777777777766 240 + + +AQP1.PRO 201 7766--666---------66666666665555666666555566544455555220111- 248 +AQP2.PRO 193 7766--666---------6666666665555555555555556664456666633-222- 239 +AQP3.PRO 217 5544LA2220EVFTTGQN223333434333334433332322------------------ 258 +AQP4.PRO 222 6555--555---------55655666656666655555555454-33345544100111- 268 +AQP5.PRO 194 6666--5440--------5555556655555555555544445664444555533-222T 242 +cons 241 6665--5550--------55555555555555555555444455544455555220221- 300 + + +AQP1.PRO 249 22222--2111111111----11000----------------------------3 269 +AQP2.PRO 240 33333--42222222223--3333333233322-------------------223 271 +AQP3.PRO 259 --------------------2111222122211122-111112221-------12 285 +AQP4.PRO 269 11111KG22111111123VE3222333233322122D111112221SSGEVL224 323 +AQP5.PRO 243 23333--33222223334--3333333---------------------------- 265 +cons 301 23322--32222222223--3222223233322122-111112221------223 355 +%</TCoffee> +% \end{macrocode} +% \begin{macrocode} +%<*Standard> +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% Standard genetic code definitions %%%%% +%%%%% %%%%% +%%%%% (The last codon of each list is used for backtranslations %%%%% +%%%%% from protein to DNA sequences---therefore the wobbles) %%%%% +%%%%% %%%%% +%%%%% These definitions are default in TeXshade. %%%%% +%%%%% There is no need to load them. This is an example file only. %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +\codon{A}{GCA,GCG,GCC,GCT,GCU,GCN} +\codon{C}{TGC,TGT,UGC,UGU,TGY} +\codon{D}{GAC,GAT,GAU,GAY} +\codon{E}{GAA,GAG,GAR} +\codon{F}{TTC,TTT,UUC,UUU,TTY} +\codon{G}{GGA,GGG,GGC,GGT,GGU,GGN} +\codon{H}{CAC,CAT,CAY} +\codon{I}{ATA,ATC,ATT,AUA,AUC,AUU,ATH} +\codon{K}{AAA,AAG,AAG,AAR} +\codon{L}{CTA,CTG,CTC,CTT,TTA,TTG,CUG,CUG,CUC,CUU,UUA,UUG,YTN} +\codon{M}{ATG,AUG,ATG} +\codon{N}{AAC,AAT,AAU,AAY} +\codon{P}{CCA,CCG,CCC,CCT,CCU,CCN} +\codon{Q}{CAA,CAG,CAR} +\codon{R}{AGA,AGG,CGA,CGG,CGC,CGT,CGU,MGN} +\codon{S}{TCT,TCC,TCG,TCA,AGT,AGC,UCU,UCC,UCG,UCA,AGU,WSN} +\codon{T}{ACT,ACC,ACG,ACA,ACU,ACN} +\codon{V}{GTA,GTG,GTC,GTT,GUA,GUG,GUC,GUU,GTN} +\codon{W}{TGG,UGG,TGG} +\codon{Y}{TAC,TAT,UAC,UAU,TAY} +\codon{.}{TAA,TAG,TGA,UAA,UAG,UGA,TRR} +%</Standard> +% \end{macrocode} +% \begin{macrocode} +%<*Ciliate> +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% Ciliate macronuclear genetic code definitions %%%%% +%%%%% %%%%% +%%%%% Only exchanges compared to the standard code must be defined. %%%%% +%%%%% %%%%% +%%%%% (The last codon of the list is used for backtranslations %%%%% +%%%%% from protein to DNA sequences---therefore the wobbles) %%%%% +%%%%% %%%%% +%%%%% %%%%% +%%%%% Activate these definitions for your alignment by the following %%%%% +%%%%% command in the texshade environment: %%%%% +%%%%% %%%%% +%%%%% \geneticcode{ciliate} %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +\codon{Q}{TAA,TAG,UAA,UAG,YAR} +%</Ciliate> +% \end{macrocode} +% \Finale +\endinput diff --git a/macros/latex/contrib/texshade/texshade.ins b/macros/latex/contrib/texshade/texshade.ins new file mode 100644 index 0000000000..73f08c8f6d --- /dev/null +++ b/macros/latex/contrib/texshade/texshade.ins @@ -0,0 +1,73 @@ +%% +%% docstrip install file for texshade.sty +%% +%% Copyright 1999-2011 Eric Beitz +%% +\def\batchfile{texshade.ins} + +\input docstrip + +\askforoverwritefalse +\keepsilent + +\declarepreamble\texshade + +LaTeX package for typesetting nucleotide and peptide alignments + +Copyright (C) 1999-2011 Eric Beitz +See the file texshade.txt + +\endpreamble + +\generate{\usepreamble\texshade% + \file{texshade.sty}{\from{texshade.dtx}{texshade}}} + +\generate{\usepreamble\empty \usepostamble\empty% + \file{texshade.def}{\from{texshade.dtx}{definitions}} + \file{AQPDNA.MSF}{\from{texshade.dtx}{AQPDNA}} + \file{AQPpro.MSF}{\from{texshade.dtx}{AQPpro}} + \file{AQP2spec.ALN}{\from{texshade.dtx}{AQP2spec}} + \file{AQP1.top}{\from{texshade.dtx}{AQP1topo}} + \file{AQP1.phd}{\from{texshade.dtx}{AQP1PHD}} + \file{AQP_HMM.sgl}{\from{texshade.dtx}{AQPHMMsgl}} + \file{AQP_HMM.ext}{\from{texshade.dtx}{AQPHMMext}} + \file{AQP_TC.asc}{\from{texshade.dtx}{TCoffee}} + \file{standard.cod}{\from{texshade.dtx}{Standard}} + \file{ciliate.cod}{\from{texshade.dtx}{Ciliate}}} + +\Msg{**************************************************************} +\Msg{*} +\Msg{* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!} +\Msg{* !!! Have you used a docstrip version 2.4 or later?} +\Msg{* !!!} +\Msg{* !!! IF NOT GO AND GET A RECENT VERSION!} +\Msg{* !!!} +\Msg{* !!! The documentation will not run through TeX with} +\Msg{* !!! your files extracted by an old docstrip version!} +\Msg{* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!} +\Msg{*} +\Msg{* To finish the installation you have to move the following} +\Msg{* files into a directory searched by LaTeX:} +\Msg{*} +\Msg{* \space\space texshade.sty} +\Msg{* \space\space texshade.def} +\Msg{* \space\space standard.cod} +\Msg{* \space\space ciliate.cod} +\Msg{*} +\Msg{* To produce the documentation run the following file twice} +\Msg{* through LaTeX:} +\Msg{*} +\Msg{* \space\space texshade.dtx} +\Msg{*} +\Msg{* Make sure that the following files are present in the same} +\Msg{* directory as texshade.dtx (needed for texing the doc):} +\Msg{*} +\Msg{* \space\space AQPDNA.MSF} +\Msg{* \space\space AQPpro.MSF} +\Msg{* \space\space APQ2spec.ALN} +\Msg{* \space\space AQP1.top} +\Msg{* \space\space APQ1.phd} +\Msg{*} +\Msg{* Happy TeXing!} +\Msg{*} +\Msg{**************************************************************} diff --git a/macros/latex/contrib/texshade/texshade.pdf b/macros/latex/contrib/texshade/texshade.pdf Binary files differnew file mode 100644 index 0000000000..f423a08595 --- /dev/null +++ b/macros/latex/contrib/texshade/texshade.pdf diff --git a/macros/latex/contrib/texshade/tsfaq.pdf b/macros/latex/contrib/texshade/tsfaq.pdf Binary files differnew file mode 100644 index 0000000000..53b9b89528 --- /dev/null +++ b/macros/latex/contrib/texshade/tsfaq.pdf diff --git a/macros/latex/contrib/texshade/tsfaq.tex b/macros/latex/contrib/texshade/tsfaq.tex new file mode 100644 index 0000000000..0ab7a0ec37 --- /dev/null +++ b/macros/latex/contrib/texshade/tsfaq.tex @@ -0,0 +1,432 @@ +\documentclass[12pt]{article} + + +\begin{document} + + +\noindent +Eric Beitz \hfill March 2005 + +\section*{\TeX{}shade: frequently asked questions } +\bigskip + +This is the sixth update of the FAQ list for \TeX{}shade. Feel free to +contact me if you have problems, questions or suggestions about the +package. I will post them and provide hopefully helpful hints in +future issues of this list. +\bigskip + +\noindent +\qquad email: \texttt{eric.beitz@uni-tuebingen.de} +\smallskip + +\noindent +\TeX{}shade: +\texttt{http://homepages.uni-tuebingen.de/beitz/tse.html} + + +\subsection*{A. Increasing \TeX{}'s memory settings} +\medskip + + If you are using \TeX{}shade to align several large sequences (about 1000 + residues/sequence), LaTeX will probably stop compiling and quit with one + of the following messages: + \texttt{!\ TeX capacity exceeded, sorry [main memory size=384000]} or + \texttt{!\ TeX capacity exceeded, sorry [stack size=300]}. + +Due to several requests I want to start a list of protocols how +to increase the standard \TeX{} memory settings for bigger +alignments. Please contribute to this list by sending me the +procedure for your particular system. + +\begin{enumerate} + + \item + + \textbf{Oz\TeX{} 4.0 for the Macintosh:} + + Find the file `OzTeX:TeX:Configs:Default'. This file contains + all memory settings. Look for the section + `\% TeX parameters' and increase the values that \TeX{} complains + about during the run. You will have to restart Oz\TeX{} before the + changes are active. + + For older versions of Oz\TeX{} the configuration file has the + same name but the path is somewhat different. + + + \item + + \textbf{te\TeX{} for *NIX:} (contributed by Joerg Daehn) + + Find the file: `/usr/share/texmf/web2c/texmf.cnf' or + + use \verb|locate texmf.cnf| at the command prompt to find it. + + Login as super user. Backup `texmf.cnf' in case you destroy something and + then open the `texmf.cnf' file in your favorite text editor and use its + search function to locate \verb|main_memory|. This variable is set to 384000. + Change this to some higher value, i.e. 4000000 (works fine for me!). The + total amount of memory should not exceed 8000000, so check the other + values in that section. + + Next, you want to change the stack size. Search for \verb|stack_size|. This + will be set to 300. I changed it to 4000 and it works fine. + + There might be complains by \TeX{} about further specific parameters such + as \verb|stack_size|. You find all those in the same file. + + After this you have to run `texconfig init'. + + Logout as root. + + After this all should be set for large alignments. Happy \TeX{}ing! + + The information on how to achieve this was derived from a mail in the + te\TeX{} mail archive. The original question was posted by Pascal Francq and + answered by Rolf Nieprasch. + + + \item + + \textbf{MiK\TeX{} for Windows:} + + The MiK\TeX{} documentation describes very detailed how the memory + settings can be changed. In brief, you must locate the + configuration file `miktex/config/miktex.ini'. In the [MiKTeX] + section of this file you find all the parameters you need, e.\,g.\ + \verb|mem_min|, \verb|mem_max|, \verb|buf_size|, \verb|stack_size| etc. + + It appears, that the standard settings of MiK\TeX{} are bigger + than that of other \TeX{} installations, so it may not always be necessary + to increase the values. + + +\end{enumerate} + + +\subsection*{B. Problems using \TeX{}shade} +\medskip + +\begin{enumerate} + + \item + + \textbf{I cannot \TeX{} the manual because I get the error + message `\texttt{!\ TeX capacity exceeded, sorry \ldots}'.} + + \TeX{}shade needs a lot of memory for setting and shading + alignments. The manual is a good test for your memory settings + because it uses many alignments and fingerprints, which are + in particular memory consuming. If you do not know how to increase + \TeX's memory settings, and you do not know a \TeX{} wizard either, then + visit the \TeX{}shade homepage at + \texttt{http://homepages.uni-tuebingen.de/beitz/tse.html} for + downloading the manual in either of three formats: DVI, PDF or + PostScript. + + + \item + + \textbf{I can set my alignment only when I reduce the number of + base-pairs by about 11,000. Otherwise I get the `\texttt{!\ TeX + capacity exceeded, sorry \ldots}' error.} + + There are several parameters defining \TeX's + usable space. If you are a \TeX{} wizard (or you know one) + increase the values that + \TeX{}shade complains about during the run in order to set + bigger alignments. But do not be disappointed when your \TeX{} + system will not set an alignment containing thousands of residues. + There is definitely an upper limit (probably the new \LaTeX3 will + allow you to use even more memory). Setting alignments is a big job for a + typesetting system! + + + \item + + \textbf{I want to align 80 sequences but I get the + `\texttt{!\ No room for a new count}' message.} + + For each sequence two counter variables are used by \TeX{}shade, + further 14 counters for other purposes are needed (and \TeX{} + can handle only 255 counters). This limits the amount of sequences + to about 100 in theory. But \LaTeX{} itself and each of + the loaded packages allocates more counters further reducing the maximum + number of sequences. + + + \item + + \textbf{I receive error messages `\texttt{!\ Missing \$ inserted}' + when \TeX{}ing my alignment. What is wrong?} + + At least one of the sequence names in the alignment file contains an + underscore `\_' symbol. This makes \TeX{} to believe you missed to + enter math mode because subscript initiated by an underscore is + only allowed in math. You need to change the sequence name(s) either in the + alignment file using the `find \& replace' option of your editor or + by using the \verb|\nameseq| command in the \TeX{}shade environment. + Nevertheless, subscript and superscript are permitted in sequence names, + e.\,g. \verb|\nameseq{1}{Name$_{sub}^{super}$}| will result in + Name$_{sub}^{super}$. + + Since v1.3b \TeX{}shade{} is much more tolerant concering special + characters. Get it and read the section about sequence names. + + + \item + + \textbf{My sequence names start out with a number in the + alignment file. Why are they ignored by \TeX{}shade?} + + \TeX{}shade analyzes the first character of each line in the + alignment file in order to decide whether it is a comment, a + ruler or a sequence line etc. All lines starting out with a + non-letter character are interpreted as non-sequence lines. Hence, + you have to change those names in the alignment file. If you + want to have sequence names starting with a number you can + use the \verb|\nameseq| command in the \TeX{}shade environment to + introduce the number, e.\,g. \verb|\nameseq{1}{57th sequence}|. + + + \item + + \textbf{Only a fraction of the residues which are supposed to be + shaded actually are. Why?} + + Make sure that \TeX{}shade knows when protein sequences are to be + set. Align\-ments in the ALN-format do not contain information about the + sequence type (DNA or protein). In such cases DNA sequences are + assumed by \TeX{}shade leading to a shading of only A's, C's, G's, + R's, T's and Y's. A simple solution is to say \verb|\seqtype{P}| in the + \verb|texshade| environment. + + + \item + + \textbf{Functional shading does not work and I get an error message. Why?} + + Same problem as discussed in the point before this one. Functional + shading is permitted only on protein sequences. So, tell \TeX{}shade + that you are using a protein alignment. + + + \item + + \textbf{There is an incompatiblity between \TeX{}shade (v1.2) + and the multi-language package `\texttt{babel}'!} + + You are right! The command \verb|\language| is defined in both + packages which leads to error messages. This bug is fixed since + the release of \TeX{}shade version 1.3 from March 2000. In this + version \verb|\language| is replaced by two commands: + \verb|\germanlanguage| and \verb|\englishlanguage|. + + \item + + \textbf{\TeX{}shade crashes when dashes ``-'' are used as gap + symbols in alignment input files.} + + Yes. Be careful with all kinds of characters that are ``active'' + in \TeX{}, such as \verb|$ _ ^ & % " \|. The dash is not really active + but two or three consecutive dashes are amalgamated to one longer + dash in \TeX. Having those characters in an input file might result + in unforeseen errors or even crashes. + + \item + + \textbf{I have problems using PHD predictions in \TeX{}shade. An + empty \texttt{.top} or \texttt{.sec} file is created.} + + When you do the PHD run do not restrict the calculation to either + secondary structure or topology prediction. Turn on everything. + Otherwise the output will have some ambiguous lines which can not + be interpreted by \TeX{}shade. Result is an empty + \texttt{.top} or \texttt{.sec} file. + +\end{enumerate} + + + +\subsection*{C. Changing the output} +\medskip + +\begin{enumerate} + + \item + + \textbf{How can I force \TeX{}shade to print more residues per line?} + + Use the \verb|\residuesperline*| command with the `\verb|*|' extension. + This will allow you to set any number of residues per line that is + desired, e.\,g. \verb|\residuesperline*{97}|. But then expect numerous + `\texttt{!\ Overfull hbox}' errors due to printing lines that + are broader than the preset \verb|\textwidth|. The same command + without the `\verb|*|' will calculate the highest number of residues + fitting in one line and round it to be divisible by five. + + + \item + + \textbf{Is it possible to add a caption to the \TeX{}shade output?} + + Yes, it is. Since \TeX{}shade v1.5 the \verb|\showcaption| + command is + available to add captions on the top or the bottom of the + alignment. The caption behaves exactly as a figure caption + including the style, numbering and appearance in the list of + figures. + \medskip + + Example: \verb|\showcaption{Nice alignment!}|. + + + \item + + \textbf{I want a short version of the caption for the `List of + Figures'. Is this possible?} + + Yes, with \TeX{}shade v1.9 short captions have been introduced. + In addition to \verb|showcaption| use the command + \verb|shortcaption{|\emph{text}\verb|}|. + \medskip + + Example: \verb|\showcaption{Nice alignment!}|\ + \verb|\shortcaption{Nice}|. + + + \item + + \textbf{My alignment file contains the letters `B' and `Z' for + Asx and Glx, respectively. How can I apply a special shading for + these?} + + Use \verb|\funcgroup| to define `B' and `Z' as functional groups + and assign the colors and the printing style, e.\,g. + \medskip + + \verb|\funcgroup{B}{White}{Blue}{upper}{up}| + \smallskip + + \verb|\funcgroup{Z}{White}{Red}{upper}{up}| + \medskip + + or add the new residues to an existing group, e.\,g. + \medskip + + \verb|\funcgroup{acidic/amide}{DENQBZ}{Black}{Green}{upper}{up}|. + + + \item + + \textbf{How can I build a legend using the `\texttt{shadebox}' + command?} + + The \verb|\shadebox| command simply prints a color-filled box at + the very location it occurs in the text. This means you have to + use \verb|\shadebox| in the normal text after the \TeX{}shade environment + or inside the caption. You find a minimal example below: + \medskip + + \qquad\vbox{% + \verb|\begin{texshade}{alignmentfile.MSF}| + \medskip + + \qquad \verb|\showcpation{Red box: \shadebox{Red}}| + \medskip + + \qquad \emph{further commands, if needed} + \medskip + + \verb|\end{texshade}| + } + + \medskip + + Legend: + + \qquad\verb|\shadebox{conserved}|: conserved residues + + \qquad\verb|\shadebox{White}|: boring residues + + \qquad\verb|\shadebox{Red}|: exciting residues + + + + \item + + \textbf{I do not like the spacing between the feature lines. How + can I change it?} + + Employ the respective space controlling command from the + following list \verb|\ttopspace|, + \verb|\topspace|, \verb|\bottomspace|, \verb|\bbottomspace|. + Those are available since \TeX{}shade v1.5 (see manual). + + + + \item + + \textbf{How can I change gap and match symbols in diverse mode?} + + Since \TeX{}shade version 1.7, standard definitions for \verb|diverse| + mode are: + + \begin{verbatim} + \nomatchresidues{Black}{White}{lower}{up} + \similarresidues{Black}{White}{lower}{up} + \conservedresidues{Black}{White}{{.}}{up} + \allmatchresidues{Black}{White}{{.}}{up} + \gapchar{-} + \end{verbatim} + + After calling \verb|\shadingmode{diverse}| these commands can be + used to redefine the \verb|diverse| mode settings (mind the double + curly braces around the dot-symbol!). + + + + \item + + \textbf{I want to rotate the alignment on the page. Is this possible?} + + Yes. Stefan Vogt has found this solution: use pdflscape.sty and + activate it in the preamble with \verb|\usepackage{pdflscape}|. Then + put your \TeX{}shade environment inside a \verb|landscape|-environment. + You also need to adjust the number of residues per line with + \verb|\residuesperline*{number}| to make them fill the rotated page. + \medskip + + \qquad\vbox{% + \verb|\begin{landscape}| + + \verb|\centering| + + \qquad \verb|\begin{texshade}{alignmentfile.MSF}| + + \qquad \verb|\residuesperline*{|\emph{number}\verb|}| + \medskip + + \qquad \qquad \emph{further commands, if needed} + \medskip + + \qquad \verb|\end{texshade}| + + \verb|\end{landscape}| + } + + + + \item + + \textbf{I want use the \TeX{}shade and \TeX{}topo logos in my text. How?} + + Use the commands: \verb|\TeXshade| and \verb|\TeXtopo|. + + +\end{enumerate} + + + +\end{document}
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