diff options
| author | Karl Berry <karl@freefriends.org> | 2007-02-22 19:55:42 +0000 |
|---|---|---|
| committer | Karl Berry <karl@freefriends.org> | 2007-02-22 19:55:42 +0000 |
| commit | f8e28122b906902277cfad964b78f7c4cbb83c20 (patch) | |
| tree | 9d4da0d08aebb73a7b7863d902d9bd11c7a01999 | |
| parent | 2f5894cda3e5c9c65f3a7c15097ccab670381247 (diff) | |
texshadow 1.16 (19feb07)
git-svn-id: svn://tug.org/texlive/trunk@3983 c570f23f-e606-0410-a88d-b1316a301751
| -rw-r--r-- | Master/texmf-dist/doc/latex/texshade/README | 14 | ||||
| -rw-r--r-- | Master/texmf-dist/doc/latex/texshade/texshade.pdf | bin | 594129 -> 606956 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/latex/texshade/tsfaq.pdf | bin | 77546 -> 72967 bytes | |||
| -rw-r--r-- | Master/texmf-dist/doc/latex/texshade/tsfaq.tex | 8 | ||||
| -rw-r--r-- | Master/texmf-dist/source/latex/texshade/texshade.dtx | 1008 | ||||
| -rw-r--r-- | Master/texmf-dist/source/latex/texshade/texshade.ins | 4 | ||||
| -rw-r--r-- | Master/texmf-dist/tex/latex/texshade/texshade.def | 4 | ||||
| -rw-r--r-- | Master/texmf-dist/tex/latex/texshade/texshade.sty | 824 | ||||
| -rw-r--r-- | Master/texmf-dist/tpm/texshade.tpm | 8 |
9 files changed, 1567 insertions, 303 deletions
diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README index 0fca2e6ccd3..10db0a70f20 100644 --- a/Master/texmf-dist/doc/latex/texshade/README +++ b/Master/texmf-dist/doc/latex/texshade/README @@ -1,4 +1,4 @@ - TeXshade v1.15 + TeXshade v1.16 >> >> A LaTeX package for setting nucleotide and peptide alignments. >> @@ -26,7 +26,7 @@ >> ding modes. TeXshade combines highest flexibility and the >> habitual TeX output quality--with reasonable time expenditure. >> - Copyright (C) 1999 - 2006 Eric Beitz + Copyright (C) 1999 - 2007 Eric Beitz @@ -88,7 +88,7 @@ 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/) + http://www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html) The resulting file "texshade.dvi" can be viewed and printed using a DVI-viewer which is able to display embedded PostScript. Another @@ -124,11 +124,11 @@ 3 - CONTACT - E-Mail: eric.beitz@uni-tuebingen.de - WWW: http://homepages.uni-tuebingen.de/beitz/ + E-Mail: ebeitz@pharmazie.uni-kiel.de + WWW: www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotech.html (On-line documentation and updates) - Address: Eric Beitz, Universit"at T"ubingen, Pharmazeutische Chemie, - Auf der Morgenstelle 8, D-72076 T"ubingen (Germany) + Address: Eric Beitz, University of Kiel, Pharmaceutical Chemistry, + Gutenbergstrasse 76, D-24118 Kiel (Germany) diff --git a/Master/texmf-dist/doc/latex/texshade/texshade.pdf b/Master/texmf-dist/doc/latex/texshade/texshade.pdf Binary files differindex 3ac7cb76492..9cb02ac5cb5 100644 --- a/Master/texmf-dist/doc/latex/texshade/texshade.pdf +++ b/Master/texmf-dist/doc/latex/texshade/texshade.pdf diff --git a/Master/texmf-dist/doc/latex/texshade/tsfaq.pdf b/Master/texmf-dist/doc/latex/texshade/tsfaq.pdf Binary files differindex 53b9b895288..b427f881113 100644 --- a/Master/texmf-dist/doc/latex/texshade/tsfaq.pdf +++ b/Master/texmf-dist/doc/latex/texshade/tsfaq.pdf diff --git a/Master/texmf-dist/doc/latex/texshade/tsfaq.tex b/Master/texmf-dist/doc/latex/texshade/tsfaq.tex index 0ab7a0ec378..94d6b73193d 100644 --- a/Master/texmf-dist/doc/latex/texshade/tsfaq.tex +++ b/Master/texmf-dist/doc/latex/texshade/tsfaq.tex @@ -5,24 +5,24 @@ \noindent -Eric Beitz \hfill March 2005 +Eric Beitz \hfill February 2007 \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 +package. I will post them and provide hints in future issues of this list. \bigskip \noindent -\qquad email: \texttt{eric.beitz@uni-tuebingen.de} +\qquad email: \texttt{ebeitz@pharmazie.uni-kiel.de} \smallskip \noindent \TeX{}shade: -\texttt{http://homepages.uni-tuebingen.de/beitz/tse.html} +\verb|www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html| \subsection*{A. Increasing \TeX{}'s memory settings} diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx index 50faa1265d9..8bbff957b77 100644 --- a/Master/texmf-dist/source/latex/texshade/texshade.dtx +++ b/Master/texmf-dist/source/latex/texshade/texshade.dtx @@ -10,7 +10,7 @@ % `texshade.txt' for further information! % % -% Copyright (C) 1999-2006 Eric Beitz +% Copyright (C) 1999-2007 Eric Beitz % See the file texshade.txt % % \fi @@ -265,6 +265,24 @@ % 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/' - click on `Beitz' +% } +% % % \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 @@ -296,14 +314,14 @@ % 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 T\"ubingen, -% Pharmaceutical Chemistry, Morgenstelle 8, -% D-72076 T\"ubingen, Germany; -% send electronic mail to \texttt{eric.beitz@uni-tuebingen.de}; +% \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{http://homepages.uni-tuebingen.de/beitz/}}} -% \date{v1.15; 2006/06/27\\} +% \texttt{www.pharmazie.uni-kiel.de/chem/} -- click on `Beitz'}} +% \date{v1.16; 2007/02/18\\} % \maketitle % \begin{abstract} % Setting alignments of nucleotides and peptides for publication @@ -380,6 +398,27 @@ % % \subsection{Version History} % +% \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 % @@ -392,7 +431,7 @@ % \medskip % % \emph{Introduction:} In order to better recognize relevant positions -% in a subfamily logo [13], a bit-value can now be set by |\relevance| +% 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|. @@ -421,7 +460,7 @@ % 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}) [13]. +% implemented, i.e. subfamily logos (p.\pageref{Lshowsubfamilylogo}) [14]. % \bigskip % % \textbf{v1.12 2005/09/20} @@ -993,7 +1032,8 @@ % \featureslarge % \feature{top}{1}{77..109}{}{AQP2 species variants} % \namesrm\namessl -% \hidenumbering\showruler{top}{1} +% \hidenumbering +% \showruler{top}{1} % \shownames{left} % \nameseq{1}{Bos taurus} % \nameseq{2}{Canis familiaris} @@ -1177,10 +1217,17 @@ % \item [\textbf{rasmol}:] similar to |[chemical]| but with % shading following the rasmol % color scheme \label{ras} +% \bigskip +% +% \bigskip % % \begin{texshade}{AQPpro.MSF} % \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} @@ -1192,6 +1239,10 @@ % \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} @@ -1499,7 +1550,7 @@ % \label{sublogo} % % The following output is derived from the calculation of a -% subfamily logo [13]. Such logos display relevant deviations 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). @@ -2294,7 +2345,12 @@ % If a color scale is named the consensus will be shaded according % to the level of sequence conservation. For an example see page % \pageref{shadecons}. You can find more information on color scales -% on page \pageref{Lgraphs}. +% on page \pageref{Lgraphs}. These scales 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 @@ -2484,7 +2540,7 @@ % % Subfamily logos provide a novel tool to visualize % subfamily-specific sequence deviations at alignment positions with -% a high information content in an intuitive way [13]. +% 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 @@ -2683,6 +2739,7 @@ % \label{Lshowruler}\label{Lhideruler} % \label{Lrulersteps}\label{Lrulercolor} % \label{Lrotateruler}\label{Lunrotateruler} +% \label{Lnamerulerpos} % 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} @@ -2697,7 +2754,10 @@ % 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}|}|. +% |\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}). % % \label{Lgapchar}\label{Lgaprule} % \label{Lgapcolors}\label{gapchar} @@ -3009,6 +3069,48 @@ % With the optional parameter the default line thickness of the frame can % be changed, example: |\frameblock{1}{10..20,50..70}{Red[2pt]}| % +% \subsubsection{Hiding blocks of the alignment (still experimental!)} +% +% \label{Lhideblock} +% \textit{Be aware that this feature is still highly experimental. There are many instances +% in which this command fails. Please be patient until everything is fixed.} +% +% Complete blocks of the alignment incl. all sequences, consensus and labels +% can be hidden, e.g.\ to eliminate uninteresting alignment stretches or +% to condense the output, by: +% \medskip +% +% \quad|\hideblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,| +% +% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{label}|[|\meta{color}|]}{|\meta{text}|[|\meta{color}|]}| +% \medskip +% +% Here, \meta{seqref} denotes the sequence by its number of name +% which is used to define the alignment positions \meta{start1}..\meta{stop1} +% etc.\ to be hidden. A symbol can be displayed as a +% \meta{label} of the alignment deletion, i.e.\ |circ|, |triangle|, |square|, +% or |none|. A color can be assigned to the label by the optional parameter +% \meta{color}. Further, an explanatory text can be displayed above the symbol +% \meta{text} with an optional \meta{color}. For how to change the appearance +% of the font see p.\pageref{Lsetfont}. +% \medskip +% +% Examples: +% +% \quad|\hideblock{1}{20..80}{circ}{condensed![Red]}| +% +% \quad|\hideblock{1}{20..80}{triangle[Red]}{hidden block}| +% +% \quad|\hideblock{AQP1}{20..80}{none[Blue]}{$\Delta$20-80)}| +% +% \quad|\hideblock{consensus}{20..80,100..150,200..220}{none}{}| +% \medskip +% +% It may be advisable to show a ruler (probably single-stepped, see p.\pageref{Lshowruler}) to +% further indicate the alignment deletion. Make sure that there are no +% feature definitions (also frames, emphs, shades, tints) starting or +% ending within the hidden block. This may cause messy sequence labels. +% % \subsubsection{Graphical labeling of sequence features} % % \label{feature} @@ -3489,7 +3591,7 @@ % \label{LincludePHDsec} % \label{LincludePHDtopo} % \label{LincludeHMMTOP} -% The DSSP [8], STRIDE [9], PHD [10] and HMMTOP [11] algorithms produce +% 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: @@ -3760,7 +3862,8 @@ % % The first parameter selects the text whose style is to be % changed. Possible first parameters are -% |numbering|, |names|, |residues|, |features|, |featurestyles| and |legend|. +% |numbering|, |names|, |residues|, |features|, |featurestyles|, +% |hideblock|, and |legend|. % \medskip % % The style is set by the second parameter: @@ -3838,7 +3941,7 @@ % Corresponding sets are provided for the % numbering (|\numberingrm| etc.), % featurestyles (|featurestylesrm| etc.), names (|\namesrm| etc.), -% residues (|\residuesrm| etc.) and +% residues (|\residuesrm| etc.), hideblock labels (|hideblockrm| etc.), and % legend texts (|legendrm| etc.). % % @@ -3869,7 +3972,7 @@ % |\ttdefault|. % % For further information see \textsc{Tomas Rokicki}'s -% |dvips| manual [12]. +% |dvips| manual [13]. % % % @@ -4326,6 +4429,7 @@ % \quad|\conservedresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}| % % \quad|\allmatchresidues{|\meta{res.col.}|}{|\meta{shad.col.}|}{|\meta{case}|}{|\meta{style}|}| +% \newpage % % \quad|\funcshadingstyle{|\meta{residue}|}{|\meta{res.col.}|}{|\meta{shad.color}|}| % @@ -4373,7 +4477,10 @@ % % \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}] % @@ -4536,6 +4643,9 @@ % % \quad|\unrotateruler| % \hfill[\pageref{Lunrotateruler}] +% +% \quad|\namerulerpos{|\meta{number}|}{|\meta{text}|[|\meta{color}|]}| +% \hfill[\pageref{Lnamerulerpos}] % % \quad|\gapchar{|\meta{symbol}|}| % \qquad (incl. |rule|) \hfill [\pageref{Lgapchar}] @@ -4589,7 +4699,7 @@ % % \quad|\orderseqs{|\meta{seq1}|,|\meta{seq2}|,|\ldots|,|\meta{seq n}|}| % \hfill[\pageref{Lorderseqs}] -% +% % \vspace{1.5\baselineskip} % % \textbf{Residues per line and further settings} @@ -4645,6 +4755,8 @@ % \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}| % [\pageref{Lshaderegion}] % +% \newpage +% % \quad|\shadeblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,| % % \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{res.col.}|}{|\meta{shad.col.}|}| @@ -4680,6 +4792,11 @@ % % \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{color}|[|\meta{length}|]}| % [\pageref{Lframeblock}] +% +% \quad|\hideblock{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,|\meta{start2}..\meta{stop2}|,| +% +% \hfill\ldots|,|\meta{start n}..\meta{stop n}|}{|\meta{label}|[|\meta{color}|]}{|\meta{text}|[|\meta{color}|]}| +% [\pageref{Lhideblock}] % % \quad|\feature{|\meta{position}|}{|\meta{seqref}|}{|\meta{start1}..\meta{stop1}|,| % @@ -4821,6 +4938,7 @@ % % \vspace{1.5\baselineskip} % +% \newpage % % \textbf{Displaying and building legends} % \medskip @@ -4845,7 +4963,6 @@ % % \vspace{1.5\baselineskip} % -% \newpage % % \textbf{Adding captions to the alignment} % \medskip @@ -4953,30 +5070,32 @@ % [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] \textsc{Kabsch, W.; Sander, C.} (1983) Dictionary of +% +% [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. % -% [9] \textsc{Frishman, D.; Argos, P.} (1995) Knowledge-based +% [10] \textsc{Frishman, D.; Argos, P.} (1995) Knowledge-based % protein secondary structure assignment. % \newblock \textit{Proteins: structure, function and % genetics}: \textbf{23}, 566--579. % -% [10] \textsc{Rost, B.; Sander, C.} (1994) +% [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. % -% [11] \textsc{Tusnady, G.E.; Simon, I.} (2001) +% [12] \textsc{Tusnady, G.E.; Simon, I.} (2001) % The HMMTOP transmembrane topology prediction server. % \newblock \textit{Bioinformatics}: \textbf{17}, 849-850. % -% [12] \textsc{Rokicki, T.} DVIPS: A \TeX{} driver. +% [13] \textsc{Rokicki, T.} DVIPS: A \TeX{} driver. % -% [13] \textsc{Beitz, E.} (2006) Subfamily logos: visualization of sequence +% [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. % @@ -5007,8 +5126,8 @@ % \begin{macrocode} %<*texshade> \NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{texshade}[2006/06/27 LaTeX TeXshade (v1.15)] -\message{Package `texshade', Version 1.15 of 2006/06/27.} +\ProvidesPackage{texshade}[2007/02/18 LaTeX TeXshade (v1.16)] +\message{Package `texshade', Version 1.16 of 2007/02/18.} \PassOptionsToPackage{dvips}{color} \PassOptionsToPackage{dvips}{graphicx} @@ -5049,6 +5168,7 @@ \newread\structurefile \newwrite\featurefile \newread\alignfile \newread\sublogofile +\newwrite\exp@rtfile \expandafter\ifx\csname blacktriangleright\endcsname\relax \openin\structurefile = amssymb.sty @@ -5482,122 +5602,185 @@ \xdef\consCG{50} \xdef\consCN{33} \xdef\consCD{17} \xdef\consCE{0} \xdef\consCQ{17} \xdef\consCH{33} \xdef\consCR{33} \xdef\consCK{0} \xdef\consCM{33} \xdef\consCI{33} \xdef\consCL{33} \xdef\consCV{33} \xdef\consCF{50} \xdef\consCY{50} \xdef\consCW{50} +\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\consSC{67} \xdef\consSS{100} \xdef\consST{83} \xdef\consSP{67} \xdef\consSA{83} \xdef\consSG{83} \xdef\consSN{83} \xdef\consSD{67} \xdef\consSE{50} \xdef\consSQ{50} \xdef\consSH{50} \xdef\consSR{50} \xdef\consSK{50} \xdef\consSM{33} \xdef\consSI{33} \xdef\consSL{33} \xdef\consSV{67} \xdef\consSF{50} \xdef\consSY{50} \xdef\consSW{33} +\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\consTC{33} \xdef\consTS{83} \xdef\consTT{100} \xdef\consTP{67} \xdef\consTA{83} \xdef\consTG{67} \xdef\consTN{67} \xdef\consTD{50} \xdef\consTE{50} \xdef\consTQ{50} \xdef\consTH{33} \xdef\consTR{50} \xdef\consTK{67} \xdef\consTM{50} \xdef\consTI{50} \xdef\consTL{33} \xdef\consTV{67} \xdef\consTF{33} \xdef\consTY{33} \xdef\consTW{17} +\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\consPC{33} \xdef\consPS{67} \xdef\consPT{67} \xdef\consPP{100} \xdef\consPA{83} \xdef\consPG{67} \xdef\consPN{33} \xdef\consPD{50} \xdef\consPE{50} \xdef\consPQ{50} \xdef\consPH{50} \xdef\consPR{50} \xdef\consPK{33} \xdef\consPM{33} \xdef\consPI{33} \xdef\consPL{50} \xdef\consPV{67} \xdef\consPF{50} \xdef\consPY{33} \xdef\consPW{33} +\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\consAC{33} \xdef\consAS{83} \xdef\consAT{83} \xdef\consAP{83} \xdef\consAA{100} \xdef\consAG{83} \xdef\consAN{50} \xdef\consAD{67} \xdef\consAE{67} \xdef\consAQ{50} \xdef\consAH{33} \xdef\consAR{33} \xdef\consAK{50} \xdef\consAM{50} \xdef\consAI{33} \xdef\consAL{33} \xdef\consAV{83} \xdef\consAF{50} \xdef\consAY{33} \xdef\consAW{33} +\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\consGC{50} \xdef\consGS{83} \xdef\consGT{67} \xdef\consGP{67} \xdef\consGA{83} \xdef\consGG{100} \xdef\consGN{50} \xdef\consGD{67} \xdef\consGE{67} \xdef\consGQ{33} \xdef\consGH{17} \xdef\consGR{50} \xdef\consGK{33} \xdef\consGM{17} \xdef\consGI{33} \xdef\consGL{33} \xdef\consGV{67} \xdef\consGF{33} \xdef\consGY{33} \xdef\consGW{50} +\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\consNC{33} \xdef\consNS{83} \xdef\consNT{67} \xdef\consNP{33} \xdef\consNA{50} \xdef\consNG{50} \xdef\consNN{100} \xdef\consND{83} \xdef\consNE{67} \xdef\consNQ{50} \xdef\consNH{67} \xdef\consNR{50} \xdef\consNK{67} \xdef\consNM{17} \xdef\consNI{33} \xdef\consNL{17} \xdef\consNV{33} \xdef\consNF{33} \xdef\consNY{50} \xdef\consNW{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\consDC{17} \xdef\consDS{67} \xdef\consDT{50} \xdef\consDP{50} \xdef\consDA{67} \xdef\consDG{67} \xdef\consDN{83} \xdef\consDD{100} \xdef\consDE{83} \xdef\consDQ{67} \xdef\consDH{50} \xdef\consDR{33} \xdef\consDK{50} \xdef\consDM{33} \xdef\consDI{17} \xdef\consDL{17} \xdef\consDV{50} \xdef\consDF{17} \xdef\consDY{33} \xdef\consDW{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\consEC{0} \xdef\consES{50} \xdef\consET{50} \xdef\consEP{50} \xdef\consEA{67} \xdef\consEG{67} \xdef\consEN{67} \xdef\consED{83} \xdef\consEE{100} \xdef\consEQ{67} \xdef\consEH{33} \xdef\consER{50} \xdef\consEK{67} \xdef\consEM{33} \xdef\consEI{17} \xdef\consEL{17} \xdef\consEV{67} \xdef\consEF{33} \xdef\consEY{17} \xdef\consEW{17} +\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\consQC{17} \xdef\consQS{50} \xdef\consQT{50} \xdef\consQP{50} \xdef\consQA{50} \xdef\consQG{33} \xdef\consQN{50} \xdef\consQD{67} \xdef\consQE{67} \xdef\consQQ{100} \xdef\consQH{67} \xdef\consQR{50} \xdef\consQK{67} \xdef\consQM{33} \xdef\consQI{17} \xdef\consQL{33} \xdef\consQV{33} \xdef\consQF{17} \xdef\consQY{33} \xdef\consQW{17} +\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\consHC{33} \xdef\consHS{50} \xdef\consHT{33} \xdef\consHP{50} \xdef\consHA{33} \xdef\consHG{17} \xdef\consHN{67} \xdef\consHD{50} \xdef\consHE{33} \xdef\consHQ{67} \xdef\consHH{100} \xdef\consHR{67} \xdef\consHK{50} \xdef\consHM{33} \xdef\consHI{33} \xdef\consHL{50} \xdef\consHV{17} \xdef\consHF{33} \xdef\consHY{50} \xdef\consHW{17} +\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\consRC{33} \xdef\consRS{50} \xdef\consRT{50} \xdef\consRP{50} \xdef\consRA{33} \xdef\consRG{50} \xdef\consRN{50} \xdef\consRD{33} \xdef\consRE{50} \xdef\consRQ{50} \xdef\consRH{67} \xdef\consRR{100} \xdef\consRK{83} \xdef\consRM{33} \xdef\consRI{33} \xdef\consRL{33} \xdef\consRV{33} \xdef\consRF{17} \xdef\consRY{17} \xdef\consRW{33} +\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\consKC{0} \xdef\consKS{50} \xdef\consKT{67} \xdef\consKP{33} \xdef\consKA{50} \xdef\consKG{33} \xdef\consKN{67} \xdef\consKD{50} \xdef\consKE{67} \xdef\consKQ{67} \xdef\consKH{50} \xdef\consKR{83} \xdef\consKK{100} \xdef\consKM{33} \xdef\consKI{33} \xdef\consKL{33} \xdef\consKV{50} \xdef\consKF{17} \xdef\consKY{17} \xdef\consKW{17} +\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\consMC{33} \xdef\consMS{50} \xdef\consMT{50} \xdef\consMP{33} \xdef\consMA{50} \xdef\consMG{17} \xdef\consMN{17} \xdef\consMD{33} \xdef\consME{33} \xdef\consMQ{33} \xdef\consMH{33} \xdef\consMR{33} \xdef\consMK{33} \xdef\consMM{100} \xdef\consMI{67} \xdef\consML{83} \xdef\consMV{67} \xdef\consMF{50} \xdef\consMY{33} \xdef\consMW{50} +\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\consIC{33} \xdef\consIS{33} \xdef\consIT{50} \xdef\consIP{33} \xdef\consIA{33} \xdef\consIG{33} \xdef\consIN{33} \xdef\consID{17} \xdef\consIE{17} \xdef\consIQ{17} \xdef\consIH{33} \xdef\consIR{33} \xdef\consIK{33} \xdef\consIM{67} \xdef\consII{100} \xdef\consIL{83} \xdef\consIV{33} \xdef\consIF{67} \xdef\consIY{50} \xdef\consIW{50} +\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\consLC{33} \xdef\consLS{33} \xdef\consLT{33} \xdef\consLP{50} \xdef\consLA{33} \xdef\consLG{33} \xdef\consLN{17} \xdef\consLD{17} \xdef\consLE{17} \xdef\consLQ{33} \xdef\consLH{50} \xdef\consLR{33} \xdef\consLK{33} \xdef\consLM{83} \xdef\consLI{83} \xdef\consLL{100} \xdef\consLV{33} \xdef\consLF{67} \xdef\consLY{50} \xdef\consLW{67} +\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\consVC{33} \xdef\consVS{67} \xdef\consVT{67} \xdef\consVP{67} \xdef\consVA{83} \xdef\consVG{67} \xdef\consVN{33} \xdef\consVD{50} \xdef\consVE{67} \xdef\consVQ{33} \xdef\consVH{17} \xdef\consVR{33} \xdef\consVK{50} \xdef\consVM{67} \xdef\consVI{33} \xdef\consVL{33} \xdef\consVV{100} \xdef\consVF{67} \xdef\consVY{50} \xdef\consVW{50} +\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\consFC{50} \xdef\consFS{50} \xdef\consFT{33} \xdef\consFP{50} \xdef\consFA{50} \xdef\consFG{33} \xdef\consFN{33} \xdef\consFD{17} \xdef\consFE{33} \xdef\consFQ{17} \xdef\consFH{33} \xdef\consFR{17} \xdef\consFK{17} \xdef\consFM{50} \xdef\consFI{67} \xdef\consFL{67} \xdef\consFV{67} \xdef\consFF{100} \xdef\consFY{83} \xdef\consFW{50} +\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\consYC{50} \xdef\consYS{50} \xdef\consYT{33} \xdef\consYP{33} \xdef\consYA{33} \xdef\consYG{33} \xdef\consYN{50} \xdef\consYD{33} \xdef\consYE{17} \xdef\consYQ{33} \xdef\consYH{50} \xdef\consYR{17} \xdef\consYK{17} \xdef\consYM{33} \xdef\consYI{50} \xdef\consYL{50} \xdef\consYV{50} \xdef\consYF{83} \xdef\consYY{100} \xdef\consYW{50} +\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\consWC{50} \xdef\consWS{33} \xdef\consWT{17} \xdef\consWP{33} \xdef\consWA{33} \xdef\consWG{50} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{17} \xdef\consWQ{17} \xdef\consWH{17} \xdef\consWR{33} \xdef\consWK{17} \xdef\consWM{50} \xdef\consWI{50} \xdef\consWL{67} \xdef\consWV{50} \xdef\consWF{50} \xdef\consWY{50} \xdef\consWW{100} +\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{100} \xdef\consBJ{0} \xdef\consBO{0} \xdef\consBU{0} \xdef\consBX{0} \xdef\consBZ{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{100} \xdef\consJO{0} \xdef\consJU{0} \xdef\consJX{0} \xdef\consJZ{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{100} \xdef\consOU{0} \xdef\consOX{0} \xdef\consOZ{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{100} \xdef\consUX{0} \xdef\consUZ{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{100} \xdef\consXZ{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{100} +\expandafter\xdef\csname consZ.\endcsname{0} + + \expandafter\xdef\csname cons.C\endcsname{0} \expandafter\xdef\csname cons.S\endcsname{0} \expandafter\xdef\csname cons.T\endcsname{0} @@ -5618,6 +5801,12 @@ \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} \def\c@d@ns{% @@ -6136,6 +6325,126 @@ \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{% @@ -6252,6 +6561,8 @@ \csname stack@@reg#1\endcsname} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% \csname stack@@tintreg#1\endcsname} + \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{% + \csname stack@@hidereg#1\endcsname} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% \csname stack@@emphreg#1\endcsname} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% @@ -6295,6 +6606,8 @@ \csname stack@reg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{% \csname stack@tintreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@hidereg\the\loopcount\endcsname{% + \csname stack@hidereg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{% \csname stack@emphreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{% @@ -6572,6 +6885,8 @@ \csname stack@reg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% \csname stack@tintreg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{% + \csname stack@hidereg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% \csname stack@emphreg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% @@ -6851,6 +7166,36 @@ \sort@stack \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack} } +\def\getregion@fromhidestack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@hidereg\temp@\endcsname} + \expandafter\get@fromstack\first@ + \expandafter\xdef\csname hidestart\temp@\endcsname{\first@} + \expandafter\xdef\csname hidestop\temp@\endcsname{\second@} + \expandafter\xdef\csname hidestyle\temp@\endcsname{\third@} + \expandafter\xdef\csname hidetext\temp@\endcsname{\fourth@} + \expandafter\xdef\csname stack@hidereg\temp@\endcsname{\last@} +} +\def\sort@hidestack{% + \expandafter\get@fromstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;&;&;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;% + \first@;\second@;\third@;\fourth@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack + \fi\fi +} +\def\get@hideregions#1..#2,#3@{% + \xdef\hide@true{y} + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@hidereg\seq@\endcsname} + \xdef\tmpstack{} + \sort@hidestack + \expandafter\xdef\csname stack@hidereg\seq@\endcsname{\tmpstack} +} \def\get@fromemphstack#1;#2;#3;#4@{% \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\last@{#4@} @@ -6965,6 +7310,14 @@ \sort@fstack \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack} } +\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\getarrow@shape#1#2#3#4&{% \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3} \if\first@@ v @@ -8331,6 +8684,23 @@ \ifx\list@\ampers@nd\else\repeat \fi } +\def\hideblock#1#2#3#4{% + \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\hideblock>} + \else + \xdef\@ll{#3} \xdef\text@{#4} + \xdef\list@{#2,&} + \loop + \xdef\list@{\list@ @} + \expandafter\get@hideregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi +} \def\bargraphstretch#1{\def\b@r@stretch{#1}} \def\colorscalestretch#1{\def\sc@le@stretch{#1}} \def\rm@@measure#1#2@{% @@ -8871,7 +9241,8 @@ \ifnum\last@<1 \xdef\last@{1}\fi \simmodetrue \funcmodefalse \threshold{0} - \donotshade{\last@} \constosingleseq{\last@} + \xdef\divref@{\last@} + \constosingleseq{\last@} \nomatchresidues{Black}{White}{lower}{up} \similarresidues{Black}{White}{lower}{up} \conservedresidues{Black}{White}{{.}}{up} @@ -9286,6 +9657,9 @@ } \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{% @@ -9350,6 +9724,9 @@ \xdef\temp@{legend} \ifx\first@\temp@ \xdef\legend@family{\third@} \else + \xdef\temp@{hideblock} + \ifx\first@\temp@ \xdef\hideblock@family{\third@} + \else \xdef\temp@{labels} \ifx\first@\temp@ \xdef\label@family{\third@} \else @@ -9365,8 +9742,9 @@ \xdef\residues@family{\third@} \xdef\legend@family{\third@} \xdef\label@family{\third@} + \xdef\hideblock@family{\third@} \xdef\ruler@family{\second@} - \fi\fi\fi\fi\fi\fi\fi\fi\fi + \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi \fi } \def\setseries#1#2{% @@ -9403,6 +9781,9 @@ \xdef\temp@{legend} \ifx\first@\temp@ \xdef\legend@series{\third@} \else + \xdef\temp@{hideblock} + \ifx\first@\temp@ \xdef\hideblock@series{\third@} + \else \xdef\temp@{labels} \ifx\first@\temp@ \xdef\label@series{\third@} \else @@ -9414,8 +9795,9 @@ \xdef\namestext@series{\third@} \xdef\residues@series{\third@} \xdef\legend@series{\third@} + \xdef\hideblock@series{\third@} \xdef\label@series{\third@} - \fi\fi\fi\fi\fi\fi\fi\fi + \fi\fi\fi\fi\fi\fi\fi\fi\fi \fi } \def\setshape#1#2{% @@ -9460,6 +9842,9 @@ \xdef\temp@{legend} \ifx\first@\temp@ \xdef\legend@shape{\third@} \else + \xdef\temp@{hideblock} + \ifx\first@\temp@ \xdef\hideblock@shape{\third@} + \else \xdef\temp@{labels} \ifx\first@\temp@ \xdef\label@shape{\third@} \else @@ -9471,8 +9856,9 @@ \xdef\namestext@shape{\third@} \xdef\residues@shape{\third@} \xdef\legend@shape{\third@} + \xdef\hideblock@shape{\third@} \xdef\label@shape{\third@} - \fi\fi\fi\fi\fi\fi\fi\fi + \fi\fi\fi\fi\fi\fi\fi\fi\fi \fi } \def\setsize#1#2{% @@ -9500,6 +9886,20 @@ \ifx\first@\temp@ \def\legend@size{\csname #2\endcsname} \else + \xdef\temp@{hideblock} + \ifx\first@\temp@ + \xdef\temp@@{#2} + \xdef\temp@{huge} + \ifx\temp@\temp@@ + \def\hideblock@size{\csname LARGE\endcsname} + \else + \xdef\temp@{Huge} + \ifx\temp@\temp@@ + \def\hideblock@size{\csname LARGE\endcsname} + \else + \def\hideblock@size{\csname #2\endcsname} + \fi\fi + \else \xdef\temp@{labels} \ifx\first@\temp@ \def\label@size{\csname #2\endcsname} @@ -9516,10 +9916,11 @@ \def\numbertext@size{\csname #2\endcsname} \def\namestext@size{\csname #2\endcsname} \def\legend@size{\csname #2\endcsname} + \def\hideblock@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\fi\fi\fi\fi\fi\fi\fi \xdef\temp@{Huge} \ifx\temp@\res@size \def\bottomruler@size{\csname Large\endcsname} @@ -9665,6 +10066,25 @@ \def\legendLARGE {\setsize{legend}{LARGE}} \def\legendhuge {\setsize{legend}{huge}} \def\legendHuge {\setsize{legend}{Huge}} +\def\hideblockrm{\setfamily{hideblock}{rm}} +\def\hideblocksf{\setfamily{hideblock}{sf}} +\def\hideblocktt{\setfamily{hideblock}{tt}} +\def\hideblockmd{\setseries{hideblock}{md}} +\def\hideblockbf{\setseries{hideblock}{bf}} +\def\hideblockup{\setshape {hideblock}{up}} +\def\hideblockit{\setshape {hideblock}{it}} +\def\hideblocksl{\setshape {hideblock}{sl}} +\def\hideblocksc{\setshape {hideblock}{sc}} +\def\hideblocktiny {\setsize{hideblock}{tiny}} +\def\hideblockscriptsize {\setsize{hideblock}{scriptsize}} +\def\hideblockfootnotesize{\setsize{hideblock}{footnotesize}} +\def\hideblocksmall {\setsize{hideblock}{small}} +\def\hideblocknormalsize {\setsize{hideblock}{normalsize}} +\def\hideblocklarge {\setsize{hideblock}{large}} +\def\hideblockLarge {\setsize{hideblock}{Large}} +\def\hideblockLARGE {\setsize{hideblock}{LARGE}} +\def\hideblockhuge {\setsize{hideblock}{LARGE}} +\def\hideblockHuge {\setsize{hideblock}{LARGE}} \def\rulerrm{\setfamily{ruler}{rm}} \def\rulersf{\setfamily{ruler}{sf}} \def\rulertt{\setfamily{ruler}{tt}} @@ -10186,6 +10606,16 @@ \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 +} + %%%%% Calculate consensus \def\check@sim{% @@ -10376,9 +10806,10 @@ \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 + \else \xdef\first@{\resn@m@tch} \fi\fi\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi @@ -10431,9 +10862,10 @@ \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 + \else \xdef\first@{\ressimm@tch} \fi\fi\fi \else \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% @@ -10457,9 +10889,10 @@ \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 + \else \xdef\first@{\resn@m@tch} \fi\fi\fi \fi \fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ @@ -10581,9 +11014,10 @@ \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 + \else \xdef\first@{\resn@m@tch} \fi\fi\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi @@ -10640,17 +11074,20 @@ \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 + \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 + \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 + \else \xdef\first@{\resn@m@tch} \fi\fi\fi \fi \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% @@ -10715,9 +11152,10 @@ 3\first@} \else \xdef\first@{\csname res\the\loopcount\endcsname} + \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 + \else \xdef\first@{\res@llm@tch} \fi\fi\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi @@ -10904,6 +11342,7 @@ \fi \fi\fi \ifnum\loopcount<\seq@count \repeat + \ifx\hide@now\n@ \loopcount=0 \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@ \else @@ -10923,6 +11362,7 @@ &\csname shade@style\the\loopcount\endcsname)} \fi \ifnum\loopcount<\seq@count \repeat + \fi } \def\getregion@fromemphstack@first{% @@ -11081,7 +11521,7 @@ } \def\calc@frame{% - \advance\pos@count by -1 +% \advance\pos@count by -1 \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 @@ -11141,7 +11581,7 @@ \fi \fi\fi \ifnum\loopcount<\seq@count \repeat - \advance\pos@count by 1 +% \advance\pos@count by 1 } \def\get@nextres#1#2:{% @@ -11870,7 +12310,7 @@ \def\calc@feature{% - \advance\pos@count by -1 +% \advance\pos@count by -1 \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 @@ -12175,12 +12615,32 @@ \fi \fi \ifnum\loopcount<\seq@count \repeat - \advance\pos@count by 1 +% \advance\pos@count by 1 } \def\c@nsensus{% \ifnum\pos@count>\res@perline \else + \global\advance\cons@count by 1\relax + \ifnum\cons@count=0\relax + \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi + \fi + \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} + \ifx\hide@true\y@ + \expandafter\ifx\csname hidestart0\endcsname\ampers@nd + \else + \expandafter\ifnum\csname hidestart0\endcsname>\cons@count + \else + \expandafter\ifnum\csname hidestop0\endcsname<\cons@count + \else + \xdef\hide@now{y} \xdef\eighth@{0} + \fi + \expandafter\ifnum\csname hidestop0\endcsname=\cons@count + \getregion@fromhidestack{0} + \fi + \fi + \fi + \fi \loopcount=0 \loop \advance\loopcount by 1 @@ -12198,74 +12658,112 @@ \ifx\allow@zero\n@ \advance\res@count by 1 \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 + \ifx\hide@true\y@ + \expandafter\ifx\csname hidestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname hidestart\the\loopcount\endcsname>\res@count + \else + \expandafter\ifnum\csname hidestop\the\loopcount\endcsname<\res@count + \else + \xdef\hide@now{y}\xdef\eighth@{\the\loopcount} + \fi + \expandafter\ifnum\csname hidestop\the\loopcount\endcsname=\res@count + \xdef\first@@{\first@} + \expandafter\getregion@fromhidestack{\the\loopcount} + \xdef\first@{\first@@} + \fi + \fi + \fi + \fi \ifnum\loopcount=\rule@num\relax \expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens - \xdef\ruler@{\ruler@ !<\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 + \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi \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@ -} + \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi \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@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@restop\yes - \ifnum\tr@nsseqtop=\loopcount - \xdef\last@restop{\last@@restop} - \xdef\tr@nslatetop{\tr@nslatetop\first@} - \xdef\last@@restop{\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\tr@nslatettop{\tr@nslatettop\first@} - \xdef\last@@resttop{\first@} - \innerloopcount=\triple@countttop - \advance\innerloopcount by 1 - \ifnum\innerloopcount>3 \innerloopcount=1 \fi - \xdef\triple@countttop{\the\innerloopcount} - \fi\fi - \ifx\collect@resbottom\yes - \ifnum\tr@nsseqbottom=\loopcount - \xdef\last@resbottom{\last@@resbottom} - \xdef\tr@nslatebottom{\tr@nslatebottom\first@} - \xdef\last@@resbottom{\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\tr@nslatebbottom{\tr@nslatebbottom\first@} - \xdef\last@@resbbottom{\first@} - \innerloopcount=\triple@countbbottom - \advance\innerloopcount by 1 - \ifnum\innerloopcount>3 \innerloopcount=1 \fi - \xdef\triple@countbbottom{\the\innerloopcount} - \fi\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\hide@now\n@ + \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@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 + \fi + \ifx\collect@restop\yes + \ifnum\tr@nsseqtop=\loopcount + \xdef\last@restop{\last@@restop} + \xdef\last@@restop{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatetop{\tr@nslatetop\first@} + \fi + \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@} + \ifx\hide@now\n@ + \xdef\tr@nslatettop{\tr@nslatettop\first@} + \fi + \innerloopcount=\triple@countttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resbottom\yes + \ifnum\tr@nsseqbottom=\loopcount + \xdef\last@resbottom{\last@@resbottom} + \xdef\last@@resbottom{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatebottom{\tr@nslatebottom\first@} + \fi + \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@} + \ifx\hide@now\n@ + \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@} + \fi + \innerloopcount=\triple@countbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbottom{\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{% @@ -12275,7 +12773,8 @@ \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{% \the\innerloopcount} \else - \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi + \ifnum\loopcount=\rule@num \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi\fi + \ifx\hide@now\n@ \ifx\collect@valtop\yes \ifnum\v@lseqtop=\loopcount \xdef\v@ltop{\v@ltop,N} @@ -12308,8 +12807,31 @@ \ifnum\tr@nsseqbbottom=\loopcount \xdef\tr@nslatebbottom{\tr@nslatebbottom -} \fi\fi + \fi \fi \ifnum\loopcount<\seq@count \repeat + \ifnum\rule@num=0 + \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 + \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi + \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 + \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi + \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 + \ifx\hide@now\n@ \ifx\collect@cons@graphtop\yes \outerloopcount=1\relax \temp@count=0\relax @@ -12345,34 +12867,48 @@ \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 + \fi - \global\advance\cons@count by 1\relax - \ifnum\cons@count=0\relax - \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi +%%%%%%%%%%%%% + \ifx\hide@now\y@ + \regionalshadenowtrue \regionaltintnowtrue + \regionalemphnowtrue \framenowtrue \fi - \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} - \ifnum\rule@num=0 - \ifnum\cons@count=\rule@tens - \xdef\ruler@{\ruler@ !<\rule@tens>} - \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 - \fi + \ifregionalshadenow \calc@regshade \fi + \ifregionaltintnow \calc@regtint \fi + \ifregionalemphnow \calc@regemph \fi + \ifframenow \calc@frame \fi + \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi + \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi + \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \ifx\hide@now\y@ + \xdef\hidebar@on{1} + \ifnum\pos@count=\bar@pos + \else + \loopcount=\pos@count + \advance\loopcount by -\bar@pos + \xdef\bar@pos{\the\pos@count} + \xdef\stylehidebar{\stylehidebar\the\loopcount;\csname hidestyle\eighth@\endcsname;\csname hidetext\eighth@\endcsname;} + \fi + \else +%%%%%%%%%%%%% \advance\pos@count by 1 - \ifshow@logo \calc@logo \fi - \ifregionalshadenow \calc@regshade \fi - \ifregionaltintnow \calc@regtint \fi - \ifregionalemphnow \calc@regemph \fi - \ifframenow \calc@frame \fi - \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi - \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi - \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi - \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \ifshow@logo \calc@logo \fi \ifall@fshade \all@funcshade \else \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi @@ -12383,6 +12919,10 @@ \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 + \xdef\hide@now{n} +%%%%%%%% \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax \c@nsensus \else @@ -12396,6 +12936,14 @@ \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 @@ -12434,8 +12982,10 @@ \csname sequence\the\loopcount\endcsname @} \ifnum\loopcount<\seq@count \repeat \end@count=0 \count@first \end@count=0 \xdef\start@number{0} - \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse - \framenowfalse + \ifx\hide@now\n@ + \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse + \framenowfalse + \fi \topfeaturenowfalse \bottomfeaturenowfalse \ttopfeaturenowfalse \bbottomfeaturenowfalse \innerloopcount=\cons@count @@ -12447,7 +12997,7 @@ \expandafter\ifnum\csname start\the\loopcount\endcsname>% \innerloopcount \else - \regionalshadenowtrue + \regionalshadenowtrue \fi \fi \fi @@ -12457,7 +13007,7 @@ \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% \innerloopcount \else - \regionaltintnowtrue + \regionaltintnowtrue \fi \fi \fi @@ -12467,7 +13017,8 @@ \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>% \innerloopcount \else - \regionalemphnowtrue + \else + \regionalemphnowtrue \fi \fi \fi @@ -12583,7 +13134,7 @@ \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% \innerloopcount \else - \regionaltintnowtrue + \regionaltintnowtrue \fi \fi \fi @@ -12969,66 +13520,69 @@ \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@{\ensuremath{\,\stackrel{\mathtt{#1}}{.}}}% + \def\third@{\ensuremath{\,\stackrel{\mathtt{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% \else \xdef\temp@{sf}% \ifx\ruler@family\temp@% - \def\third@{\ensuremath{\,\stackrel{\mathsf{#1}}{.}}}% + \def\third@{\ensuremath{\,\stackrel{\mathsf{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% \else \xdef\temp@{rm}% \ifx\ruler@family\temp@% - \def\third@{\ensuremath{\,\stackrel{\mathrm{#1}}{.}}}% + \def\third@{\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{\,\ensuremath{\cdot}\,#1\hss}\end{rotopo}}% + \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{\,\ensuremath{\cdot}\,#1\hss}\end{rotopo}}% + \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{\,\ensuremath{\cdot}\,#1\hss}\end{rotopo}}% + \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{.}{\mathtt{#1}}}}% + \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{.}{\mathsf{#1}}}}% + \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{.}{\mathrm{#1}}}}% + \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#1\,\ensuremath{\cdot}}\end{rotopo}}% + \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#1\,\ensuremath{\cdot}}\end{rotopo}}% + \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#1\,\ensuremath{\cdot}}\end{rotopo}}% + \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}% \fi\fi\fi \fi \fi} @@ -13038,8 +13592,8 @@ \xdef\first@{#2@}% \xdef\second@{!}% \ifx\third@\second@ \expandafter\get@rulenum\first@% - \else \xdef\third@{}\fi - \hbox to \box@width{\hss\third@\hss}% + \else \xdef\third@{}\xdef\f@color{Black}\fi + \textcolor{\f@color}{\hbox to \box@width{\hss\third@\hss}}% } \def\put@rulechar{% @@ -13080,7 +13634,7 @@ \fontseries{m}% \fontshape{n}% \selectfont% - \innerloopcount=1\relax\textcolor{\ruler@fg}{\put@rulechar}% + \innerloopcount=1\relax\put@rulechar% \newline\hbox{}% } \def\get@firstfill#1#2&{\xdef\second@@{#1}\xdef\fill@char{#2&}} @@ -13743,6 +14297,124 @@ \fi% \fi% } +\def\next@hidebar#1;#2;#3;#4@{% + \xdef\first@{#1}% + \ifx\first@\ampers@nd% + \else% + \fontfamily{\hideblock@family}\fontseries{\hideblock@series}% + \fontshape{\hideblock@shape}% + \selectfont% + \newline\hbox{}% + \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \hbox to -\box@width{\hss}% + \kern-0.1\box@width% + \xdef\last@{#3[,]&}\expandafter\opt@color\last@% + \ifx\f@color\comm@\xdef\f@color{Black}\fi% + \textcolor{\f@color}{% + \hbox to \first@\box@width{}% + \hbox to 0pt{\hss\strut\hideblock@size{\,\fourth@}\hss}}% + \xdef\last@{#2[,]&}\expandafter\opt@color\last@% + \ifx\f@color\comm@\xdef\f@color{Black}\fi% + \vspace{-0.23\box@height}% + \xdef\temp@{triangle}% + \ifx\fourth@\temp@% + \else + \xdef\temp@{square}% + \ifx\fourth@\temp@% + \else + \xdef\temp@{none}% + \ifx\fourth@\temp@% + \else + \vspace{-0.06\box@height}% + \fi\fi\fi% + \newline\hbox{}% + \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \hbox to -\box@width{\hss}% + \hbox to \first@\box@width{}% + \kern-0.1\box@width% + \textcolor{\f@color}{% + \raisebox{0.47\box@height}{\rule{0.2\box@width}{\temp@@length}}% + \xdef\first@{triangle}% + \ifx\fourth@\first@% + \kern-0.582\box@width% + \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigtriangledown$\hss}}% + \kern-0.418\box@width% + \else + \xdef\first@{square}% + \ifx\fourth@\first@% + \kern-0.6\box@width% + \raisebox{-0.12\box@height}{% + \raisebox{\temp@@length}{\hbox to \box@width{\hss$\square$\hss}}}% + \raisebox{-0.19\box@height}{% + \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}% + \kern-1.4\box@width% + \else + \xdef\first@{none}% + \ifx\fourth@\first@% + \kern-0.6\box@width% + \raisebox{-0.19\box@height}{% + \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}% + \kern-0.4\box@width% + \else + \kern-0.6\box@width% + \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigodot$\hss}}% + \kern-0.4\box@width% + \fi% + \fi% + \fi% + \kern-0.58\box@width% + \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bullet$\hss}}% + \xdef\first@{#4@}}% + \fi +} +\def\put@@hidebar{% + \if\first@ @% + \else + \hbox to -\box@width{\hss}% + \expandafter\next@hidebar\first@% + \put@@hidebar% + \fi% +} +\def\put@hidebar{% + \ifx\hide@seqs\n@% + \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi% + \temp@count=\seq@count% + \advance\temp@count by 1% + \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% + \advance\temp@@length by -0.75\box@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{-2.56\baselineskip}% + \xdef\first@{\stylehidebar @}% + \put@@hidebar% + \vspace{-\arrow@height}% + \vspace{-0.47\box@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}% @@ -14180,7 +14852,7 @@ \def\set@lines{% \pos@count=1 - \xdef\frame@pos{1}% + \xdef\frame@pos{1}\xdef\bar@pos{0}\xdef\hidebar@on{0}% \xdef\featurepostop{1}\xdef\featureposbottom{1}% \xdef\featureposttop{1}\xdef\featureposbbottom{1}% \findc@nsensus% @@ -14280,6 +14952,9 @@ \ifnum\frame@on=0 \xdef\frame@{0}\fi% \put@frame% \fi% + \ifnum\hidebar@on=1 % + \put@hidebar% + \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 @@ -14345,7 +15020,7 @@ \fi \fi \xdef\consensus{} \xdef\ruler@{} - \xdef\styleframe{} + \xdef\styleframe{} \xdef\stylehidebar{} \xdef\textfeaturetop{} \xdef\textfeaturebottom{} \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} @@ -14457,7 +15132,7 @@ \xdef\textfeaturettop{} \xdef\featureonttop{0} \xdef\textfeaturebottom{} \xdef\featureonbottom{0} \xdef\textfeaturebbottom{}\xdef\featureonbbottom{0} - \xdef\styleframe{} + \xdef\styleframe{} \xdef\stylehidebar{} \xdef\stylefeaturetop{} \xdef\stylefeaturettop{} \xdef\stylefeaturebottom{} @@ -14550,6 +15225,7 @@ \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} \ifnum\end@num>\end@count\relax\xdef\end@num{\the\end@count}\fi @@ -14593,6 +15269,7 @@ \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} \ifnum\end@num>\end@count\relax\xdef\end@num{\the\end@count}\fi @@ -14614,6 +15291,7 @@ \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 @@ -14621,7 +15299,6 @@ \loopcount=1 \read@loop \fi - \if\seq@type A \guess@DNA \fi \ifnum\seq@pointer>0 \ifstop@ \else @@ -14631,6 +15308,7 @@ \fi \fi \ifshow@sublogo \closein\sublogofile \fi + \ifx\exp@rt\y@ \closeout\exp@rtfile \fi \closein\alignfile \message{)} } @@ -14730,6 +15408,7 @@ \loopcount=0 \xdef\seq@order{} \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} @@ -14753,6 +15432,7 @@ \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@hidereg\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} @@ -14796,6 +15476,7 @@ \ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi \loopcount=0 \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\getregion@fromhidestack{\the\loopcount} \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} @@ -14842,6 +15523,7 @@ \baselineskip=\box@height \advance\baselineskip by \box@depth \fi \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\getregion@fromhidestack{\the\loopcount} \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} @@ -15150,6 +15832,10 @@ \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\hide@true{n} \xdef\hide@now{n} +\xdef\hide@label{circ} +\xdef\divref@{0} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% @@ -15233,6 +15919,10 @@ \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{hideblock}{rm} % Use roman family for hidden block labels +\setseries{hideblock}{md} % Use normal series for hidden block labels +\setshape {hideblock}{it} % Use italics shape for hidden block labels +\setsize {hideblock}{normalsize} % Use normal size for hidden block labels \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 @@ -15416,6 +16106,10 @@ \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{hideblock}{rm} % Use roman family for hidden block labels +\setseries{hideblock}{md} % Use normal series for hidden block labels +\setshape {hideblock}{it} % Use italics shape for hidden block labels +\setsize {hideblock}{normalsize} % Use normal size for hidden block labels \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 diff --git a/Master/texmf-dist/source/latex/texshade/texshade.ins b/Master/texmf-dist/source/latex/texshade/texshade.ins index be0114678f9..26560329661 100644 --- a/Master/texmf-dist/source/latex/texshade/texshade.ins +++ b/Master/texmf-dist/source/latex/texshade/texshade.ins @@ -1,7 +1,7 @@ %% %% docstrip install file for texshade.sty %% -%% Copyright 1999-2006 Eric Beitz +%% Copyright 1999-2007 Eric Beitz %% \def\batchfile{texshade.ins} @@ -14,7 +14,7 @@ LaTeX package for typesetting nucleotide and peptide alignments -Copyright (C) 1999-2006 Eric Beitz +Copyright (C) 1999-2007 Eric Beitz See the file texshade.txt \endpreamble diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.def b/Master/texmf-dist/tex/latex/texshade/texshade.def index a2ab60fb1a6..b9c55582a77 100644 --- a/Master/texmf-dist/tex/latex/texshade/texshade.def +++ b/Master/texmf-dist/tex/latex/texshade/texshade.def @@ -79,6 +79,10 @@ \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{hideblock}{rm} % Use roman family for hidden block labels +\setseries{hideblock}{md} % Use normal series for hidden block labels +\setshape {hideblock}{it} % Use italics shape for hidden block labels +\setsize {hideblock}{normalsize} % Use normal size for hidden block labels \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 diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty index 729d15deb04..792807ef473 100644 --- a/Master/texmf-dist/tex/latex/texshade/texshade.sty +++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty @@ -8,13 +8,13 @@ %% %% LaTeX package for typesetting nucleotide and peptide alignments %% -%% Copyright (C) 1999-2006 Eric Beitz +%% Copyright (C) 1999-2007 Eric Beitz %% See the file texshade.txt %% \NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{texshade}[2006/06/27 LaTeX TeXshade (v1.15)] -\message{Package `texshade', Version 1.15 of 2006/06/27.} +\ProvidesPackage{texshade}[2007/02/18 LaTeX TeXshade (v1.16)] +\message{Package `texshade', Version 1.16 of 2007/02/18.} \PassOptionsToPackage{dvips}{color} \PassOptionsToPackage{dvips}{graphicx} @@ -55,6 +55,7 @@ \newread\structurefile \newwrite\featurefile \newread\alignfile \newread\sublogofile +\newwrite\exp@rtfile \expandafter\ifx\csname blacktriangleright\endcsname\relax \openin\structurefile = amssymb.sty @@ -487,122 +488,184 @@ \xdef\consCG{50} \xdef\consCN{33} \xdef\consCD{17} \xdef\consCE{0} \xdef\consCQ{17} \xdef\consCH{33} \xdef\consCR{33} \xdef\consCK{0} \xdef\consCM{33} \xdef\consCI{33} \xdef\consCL{33} \xdef\consCV{33} \xdef\consCF{50} \xdef\consCY{50} \xdef\consCW{50} +\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\consSC{67} \xdef\consSS{100} \xdef\consST{83} \xdef\consSP{67} \xdef\consSA{83} \xdef\consSG{83} \xdef\consSN{83} \xdef\consSD{67} \xdef\consSE{50} \xdef\consSQ{50} \xdef\consSH{50} \xdef\consSR{50} \xdef\consSK{50} \xdef\consSM{33} \xdef\consSI{33} \xdef\consSL{33} \xdef\consSV{67} \xdef\consSF{50} \xdef\consSY{50} \xdef\consSW{33} +\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\consTC{33} \xdef\consTS{83} \xdef\consTT{100} \xdef\consTP{67} \xdef\consTA{83} \xdef\consTG{67} \xdef\consTN{67} \xdef\consTD{50} \xdef\consTE{50} \xdef\consTQ{50} \xdef\consTH{33} \xdef\consTR{50} \xdef\consTK{67} \xdef\consTM{50} \xdef\consTI{50} \xdef\consTL{33} \xdef\consTV{67} \xdef\consTF{33} \xdef\consTY{33} \xdef\consTW{17} +\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\consPC{33} \xdef\consPS{67} \xdef\consPT{67} \xdef\consPP{100} \xdef\consPA{83} \xdef\consPG{67} \xdef\consPN{33} \xdef\consPD{50} \xdef\consPE{50} \xdef\consPQ{50} \xdef\consPH{50} \xdef\consPR{50} \xdef\consPK{33} \xdef\consPM{33} \xdef\consPI{33} \xdef\consPL{50} \xdef\consPV{67} \xdef\consPF{50} \xdef\consPY{33} \xdef\consPW{33} +\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\consAC{33} \xdef\consAS{83} \xdef\consAT{83} \xdef\consAP{83} \xdef\consAA{100} \xdef\consAG{83} \xdef\consAN{50} \xdef\consAD{67} \xdef\consAE{67} \xdef\consAQ{50} \xdef\consAH{33} \xdef\consAR{33} \xdef\consAK{50} \xdef\consAM{50} \xdef\consAI{33} \xdef\consAL{33} \xdef\consAV{83} \xdef\consAF{50} \xdef\consAY{33} \xdef\consAW{33} +\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\consGC{50} \xdef\consGS{83} \xdef\consGT{67} \xdef\consGP{67} \xdef\consGA{83} \xdef\consGG{100} \xdef\consGN{50} \xdef\consGD{67} \xdef\consGE{67} \xdef\consGQ{33} \xdef\consGH{17} \xdef\consGR{50} \xdef\consGK{33} \xdef\consGM{17} \xdef\consGI{33} \xdef\consGL{33} \xdef\consGV{67} \xdef\consGF{33} \xdef\consGY{33} \xdef\consGW{50} +\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\consNC{33} \xdef\consNS{83} \xdef\consNT{67} \xdef\consNP{33} \xdef\consNA{50} \xdef\consNG{50} \xdef\consNN{100} \xdef\consND{83} \xdef\consNE{67} \xdef\consNQ{50} \xdef\consNH{67} \xdef\consNR{50} \xdef\consNK{67} \xdef\consNM{17} \xdef\consNI{33} \xdef\consNL{17} \xdef\consNV{33} \xdef\consNF{33} \xdef\consNY{50} \xdef\consNW{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\consDC{17} \xdef\consDS{67} \xdef\consDT{50} \xdef\consDP{50} \xdef\consDA{67} \xdef\consDG{67} \xdef\consDN{83} \xdef\consDD{100} \xdef\consDE{83} \xdef\consDQ{67} \xdef\consDH{50} \xdef\consDR{33} \xdef\consDK{50} \xdef\consDM{33} \xdef\consDI{17} \xdef\consDL{17} \xdef\consDV{50} \xdef\consDF{17} \xdef\consDY{33} \xdef\consDW{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\consEC{0} \xdef\consES{50} \xdef\consET{50} \xdef\consEP{50} \xdef\consEA{67} \xdef\consEG{67} \xdef\consEN{67} \xdef\consED{83} \xdef\consEE{100} \xdef\consEQ{67} \xdef\consEH{33} \xdef\consER{50} \xdef\consEK{67} \xdef\consEM{33} \xdef\consEI{17} \xdef\consEL{17} \xdef\consEV{67} \xdef\consEF{33} \xdef\consEY{17} \xdef\consEW{17} +\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\consQC{17} \xdef\consQS{50} \xdef\consQT{50} \xdef\consQP{50} \xdef\consQA{50} \xdef\consQG{33} \xdef\consQN{50} \xdef\consQD{67} \xdef\consQE{67} \xdef\consQQ{100} \xdef\consQH{67} \xdef\consQR{50} \xdef\consQK{67} \xdef\consQM{33} \xdef\consQI{17} \xdef\consQL{33} \xdef\consQV{33} \xdef\consQF{17} \xdef\consQY{33} \xdef\consQW{17} +\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\consHC{33} \xdef\consHS{50} \xdef\consHT{33} \xdef\consHP{50} \xdef\consHA{33} \xdef\consHG{17} \xdef\consHN{67} \xdef\consHD{50} \xdef\consHE{33} \xdef\consHQ{67} \xdef\consHH{100} \xdef\consHR{67} \xdef\consHK{50} \xdef\consHM{33} \xdef\consHI{33} \xdef\consHL{50} \xdef\consHV{17} \xdef\consHF{33} \xdef\consHY{50} \xdef\consHW{17} +\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\consRC{33} \xdef\consRS{50} \xdef\consRT{50} \xdef\consRP{50} \xdef\consRA{33} \xdef\consRG{50} \xdef\consRN{50} \xdef\consRD{33} \xdef\consRE{50} \xdef\consRQ{50} \xdef\consRH{67} \xdef\consRR{100} \xdef\consRK{83} \xdef\consRM{33} \xdef\consRI{33} \xdef\consRL{33} \xdef\consRV{33} \xdef\consRF{17} \xdef\consRY{17} \xdef\consRW{33} +\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\consKC{0} \xdef\consKS{50} \xdef\consKT{67} \xdef\consKP{33} \xdef\consKA{50} \xdef\consKG{33} \xdef\consKN{67} \xdef\consKD{50} \xdef\consKE{67} \xdef\consKQ{67} \xdef\consKH{50} \xdef\consKR{83} \xdef\consKK{100} \xdef\consKM{33} \xdef\consKI{33} \xdef\consKL{33} \xdef\consKV{50} \xdef\consKF{17} \xdef\consKY{17} \xdef\consKW{17} +\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\consMC{33} \xdef\consMS{50} \xdef\consMT{50} \xdef\consMP{33} \xdef\consMA{50} \xdef\consMG{17} \xdef\consMN{17} \xdef\consMD{33} \xdef\consME{33} \xdef\consMQ{33} \xdef\consMH{33} \xdef\consMR{33} \xdef\consMK{33} \xdef\consMM{100} \xdef\consMI{67} \xdef\consML{83} \xdef\consMV{67} \xdef\consMF{50} \xdef\consMY{33} \xdef\consMW{50} +\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\consIC{33} \xdef\consIS{33} \xdef\consIT{50} \xdef\consIP{33} \xdef\consIA{33} \xdef\consIG{33} \xdef\consIN{33} \xdef\consID{17} \xdef\consIE{17} \xdef\consIQ{17} \xdef\consIH{33} \xdef\consIR{33} \xdef\consIK{33} \xdef\consIM{67} \xdef\consII{100} \xdef\consIL{83} \xdef\consIV{33} \xdef\consIF{67} \xdef\consIY{50} \xdef\consIW{50} +\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\consLC{33} \xdef\consLS{33} \xdef\consLT{33} \xdef\consLP{50} \xdef\consLA{33} \xdef\consLG{33} \xdef\consLN{17} \xdef\consLD{17} \xdef\consLE{17} \xdef\consLQ{33} \xdef\consLH{50} \xdef\consLR{33} \xdef\consLK{33} \xdef\consLM{83} \xdef\consLI{83} \xdef\consLL{100} \xdef\consLV{33} \xdef\consLF{67} \xdef\consLY{50} \xdef\consLW{67} +\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\consVC{33} \xdef\consVS{67} \xdef\consVT{67} \xdef\consVP{67} \xdef\consVA{83} \xdef\consVG{67} \xdef\consVN{33} \xdef\consVD{50} \xdef\consVE{67} \xdef\consVQ{33} \xdef\consVH{17} \xdef\consVR{33} \xdef\consVK{50} \xdef\consVM{67} \xdef\consVI{33} \xdef\consVL{33} \xdef\consVV{100} \xdef\consVF{67} \xdef\consVY{50} \xdef\consVW{50} +\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\consFC{50} \xdef\consFS{50} \xdef\consFT{33} \xdef\consFP{50} \xdef\consFA{50} \xdef\consFG{33} \xdef\consFN{33} \xdef\consFD{17} \xdef\consFE{33} \xdef\consFQ{17} \xdef\consFH{33} \xdef\consFR{17} \xdef\consFK{17} \xdef\consFM{50} \xdef\consFI{67} \xdef\consFL{67} \xdef\consFV{67} \xdef\consFF{100} \xdef\consFY{83} \xdef\consFW{50} +\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\consYC{50} \xdef\consYS{50} \xdef\consYT{33} \xdef\consYP{33} \xdef\consYA{33} \xdef\consYG{33} \xdef\consYN{50} \xdef\consYD{33} \xdef\consYE{17} \xdef\consYQ{33} \xdef\consYH{50} \xdef\consYR{17} \xdef\consYK{17} \xdef\consYM{33} \xdef\consYI{50} \xdef\consYL{50} \xdef\consYV{50} \xdef\consYF{83} \xdef\consYY{100} \xdef\consYW{50} +\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\consWC{50} \xdef\consWS{33} \xdef\consWT{17} \xdef\consWP{33} \xdef\consWA{33} \xdef\consWG{50} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{17} \xdef\consWQ{17} \xdef\consWH{17} \xdef\consWR{33} \xdef\consWK{17} \xdef\consWM{50} \xdef\consWI{50} \xdef\consWL{67} \xdef\consWV{50} \xdef\consWF{50} \xdef\consWY{50} \xdef\consWW{100} +\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{100} \xdef\consBJ{0} \xdef\consBO{0} \xdef\consBU{0} \xdef\consBX{0} \xdef\consBZ{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{100} \xdef\consJO{0} \xdef\consJU{0} \xdef\consJX{0} \xdef\consJZ{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{100} \xdef\consOU{0} \xdef\consOX{0} \xdef\consOZ{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{100} \xdef\consUX{0} \xdef\consUZ{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{100} \xdef\consXZ{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{100} +\expandafter\xdef\csname consZ.\endcsname{0} + \expandafter\xdef\csname cons.C\endcsname{0} \expandafter\xdef\csname cons.S\endcsname{0} \expandafter\xdef\csname cons.T\endcsname{0} @@ -623,6 +686,12 @@ \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} \def\c@d@ns{% @@ -1141,6 +1210,126 @@ \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 @@ -1256,6 +1445,8 @@ \csname stack@@reg#1\endcsname} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% \csname stack@@tintreg#1\endcsname} + \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{% + \csname stack@@hidereg#1\endcsname} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% \csname stack@@emphreg#1\endcsname} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% @@ -1299,6 +1490,8 @@ \csname stack@reg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{% \csname stack@tintreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@hidereg\the\loopcount\endcsname{% + \csname stack@hidereg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{% \csname stack@emphreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{% @@ -1576,6 +1769,8 @@ \csname stack@reg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% \csname stack@tintreg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{% + \csname stack@hidereg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% \csname stack@emphreg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% @@ -1855,6 +2050,36 @@ \sort@stack \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack} } +\def\getregion@fromhidestack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@hidereg\temp@\endcsname} + \expandafter\get@fromstack\first@ + \expandafter\xdef\csname hidestart\temp@\endcsname{\first@} + \expandafter\xdef\csname hidestop\temp@\endcsname{\second@} + \expandafter\xdef\csname hidestyle\temp@\endcsname{\third@} + \expandafter\xdef\csname hidetext\temp@\endcsname{\fourth@} + \expandafter\xdef\csname stack@hidereg\temp@\endcsname{\last@} +} +\def\sort@hidestack{% + \expandafter\get@fromstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;&;&;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\text@;% + \first@;\second@;\third@;\fourth@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@hidestack + \fi\fi +} +\def\get@hideregions#1..#2,#3@{% + \xdef\hide@true{y} + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@hidereg\seq@\endcsname} + \xdef\tmpstack{} + \sort@hidestack + \expandafter\xdef\csname stack@hidereg\seq@\endcsname{\tmpstack} +} \def\get@fromemphstack#1;#2;#3;#4@{% \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\last@{#4@} @@ -1969,6 +2194,14 @@ \sort@fstack \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack} } +\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\getarrow@shape#1#2#3#4&{% \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3} \if\first@@ v @@ -3334,6 +3567,23 @@ \ifx\list@\ampers@nd\else\repeat \fi } +\def\hideblock#1#2#3#4{% + \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\hideblock>} + \else + \xdef\@ll{#3} \xdef\text@{#4} + \xdef\list@{#2,&} + \loop + \xdef\list@{\list@ @} + \expandafter\get@hideregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi +} \def\bargraphstretch#1{\def\b@r@stretch{#1}} \def\colorscalestretch#1{\def\sc@le@stretch{#1}} \def\rm@@measure#1#2@{% @@ -3874,7 +4124,8 @@ \ifnum\last@<1 \xdef\last@{1}\fi \simmodetrue \funcmodefalse \threshold{0} - \donotshade{\last@} \constosingleseq{\last@} + \xdef\divref@{\last@} + \constosingleseq{\last@} \nomatchresidues{Black}{White}{lower}{up} \similarresidues{Black}{White}{lower}{up} \conservedresidues{Black}{White}{{.}}{up} @@ -4289,6 +4540,9 @@ } \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{% @@ -4353,6 +4607,9 @@ \xdef\temp@{legend} \ifx\first@\temp@ \xdef\legend@family{\third@} \else + \xdef\temp@{hideblock} + \ifx\first@\temp@ \xdef\hideblock@family{\third@} + \else \xdef\temp@{labels} \ifx\first@\temp@ \xdef\label@family{\third@} \else @@ -4368,8 +4625,9 @@ \xdef\residues@family{\third@} \xdef\legend@family{\third@} \xdef\label@family{\third@} + \xdef\hideblock@family{\third@} \xdef\ruler@family{\second@} - \fi\fi\fi\fi\fi\fi\fi\fi\fi + \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi \fi } \def\setseries#1#2{% @@ -4406,6 +4664,9 @@ \xdef\temp@{legend} \ifx\first@\temp@ \xdef\legend@series{\third@} \else + \xdef\temp@{hideblock} + \ifx\first@\temp@ \xdef\hideblock@series{\third@} + \else \xdef\temp@{labels} \ifx\first@\temp@ \xdef\label@series{\third@} \else @@ -4417,8 +4678,9 @@ \xdef\namestext@series{\third@} \xdef\residues@series{\third@} \xdef\legend@series{\third@} + \xdef\hideblock@series{\third@} \xdef\label@series{\third@} - \fi\fi\fi\fi\fi\fi\fi\fi + \fi\fi\fi\fi\fi\fi\fi\fi\fi \fi } \def\setshape#1#2{% @@ -4463,6 +4725,9 @@ \xdef\temp@{legend} \ifx\first@\temp@ \xdef\legend@shape{\third@} \else + \xdef\temp@{hideblock} + \ifx\first@\temp@ \xdef\hideblock@shape{\third@} + \else \xdef\temp@{labels} \ifx\first@\temp@ \xdef\label@shape{\third@} \else @@ -4474,8 +4739,9 @@ \xdef\namestext@shape{\third@} \xdef\residues@shape{\third@} \xdef\legend@shape{\third@} + \xdef\hideblock@shape{\third@} \xdef\label@shape{\third@} - \fi\fi\fi\fi\fi\fi\fi\fi + \fi\fi\fi\fi\fi\fi\fi\fi\fi \fi } \def\setsize#1#2{% @@ -4503,6 +4769,20 @@ \ifx\first@\temp@ \def\legend@size{\csname #2\endcsname} \else + \xdef\temp@{hideblock} + \ifx\first@\temp@ + \xdef\temp@@{#2} + \xdef\temp@{huge} + \ifx\temp@\temp@@ + \def\hideblock@size{\csname LARGE\endcsname} + \else + \xdef\temp@{Huge} + \ifx\temp@\temp@@ + \def\hideblock@size{\csname LARGE\endcsname} + \else + \def\hideblock@size{\csname #2\endcsname} + \fi\fi + \else \xdef\temp@{labels} \ifx\first@\temp@ \def\label@size{\csname #2\endcsname} @@ -4519,10 +4799,11 @@ \def\numbertext@size{\csname #2\endcsname} \def\namestext@size{\csname #2\endcsname} \def\legend@size{\csname #2\endcsname} + \def\hideblock@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\fi\fi\fi\fi\fi\fi\fi \xdef\temp@{Huge} \ifx\temp@\res@size \def\bottomruler@size{\csname Large\endcsname} @@ -4668,6 +4949,25 @@ \def\legendLARGE {\setsize{legend}{LARGE}} \def\legendhuge {\setsize{legend}{huge}} \def\legendHuge {\setsize{legend}{Huge}} +\def\hideblockrm{\setfamily{hideblock}{rm}} +\def\hideblocksf{\setfamily{hideblock}{sf}} +\def\hideblocktt{\setfamily{hideblock}{tt}} +\def\hideblockmd{\setseries{hideblock}{md}} +\def\hideblockbf{\setseries{hideblock}{bf}} +\def\hideblockup{\setshape {hideblock}{up}} +\def\hideblockit{\setshape {hideblock}{it}} +\def\hideblocksl{\setshape {hideblock}{sl}} +\def\hideblocksc{\setshape {hideblock}{sc}} +\def\hideblocktiny {\setsize{hideblock}{tiny}} +\def\hideblockscriptsize {\setsize{hideblock}{scriptsize}} +\def\hideblockfootnotesize{\setsize{hideblock}{footnotesize}} +\def\hideblocksmall {\setsize{hideblock}{small}} +\def\hideblocknormalsize {\setsize{hideblock}{normalsize}} +\def\hideblocklarge {\setsize{hideblock}{large}} +\def\hideblockLarge {\setsize{hideblock}{Large}} +\def\hideblockLARGE {\setsize{hideblock}{LARGE}} +\def\hideblockhuge {\setsize{hideblock}{LARGE}} +\def\hideblockHuge {\setsize{hideblock}{LARGE}} \def\rulerrm{\setfamily{ruler}{rm}} \def\rulersf{\setfamily{ruler}{sf}} \def\rulertt{\setfamily{ruler}{tt}} @@ -5189,6 +5489,16 @@ \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 +} + %%%%% Calculate consensus \def\check@sim{% @@ -5379,9 +5689,10 @@ \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 + \else \xdef\first@{\resn@m@tch} \fi\fi\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi @@ -5434,9 +5745,10 @@ \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 + \else \xdef\first@{\ressimm@tch} \fi\fi\fi \else \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% @@ -5460,9 +5772,10 @@ \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 + \else \xdef\first@{\resn@m@tch} \fi\fi\fi \fi \fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ @@ -5584,9 +5897,10 @@ \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 + \else \xdef\first@{\resn@m@tch} \fi\fi\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi @@ -5643,17 +5957,20 @@ \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 + \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 + \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 + \else \xdef\first@{\resn@m@tch} \fi\fi\fi \fi \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% @@ -5718,9 +6035,10 @@ 3\first@} \else \xdef\first@{\csname res\the\loopcount\endcsname} + \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 + \else \xdef\first@{\res@llm@tch} \fi\fi\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi @@ -5907,6 +6225,7 @@ \fi \fi\fi \ifnum\loopcount<\seq@count \repeat + \ifx\hide@now\n@ \loopcount=0 \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@ \else @@ -5926,6 +6245,7 @@ &\csname shade@style\the\loopcount\endcsname)} \fi \ifnum\loopcount<\seq@count \repeat + \fi } \def\getregion@fromemphstack@first{% @@ -6084,7 +6404,6 @@ } \def\calc@frame{% - \advance\pos@count by -1 \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 @@ -6144,7 +6463,6 @@ \fi \fi\fi \ifnum\loopcount<\seq@count \repeat - \advance\pos@count by 1 } \def\get@nextres#1#2:{% @@ -6871,7 +7189,6 @@ } \def\calc@feature{% - \advance\pos@count by -1 \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 @@ -7176,12 +7493,31 @@ \fi \fi \ifnum\loopcount<\seq@count \repeat - \advance\pos@count by 1 } \def\c@nsensus{% \ifnum\pos@count>\res@perline \else + \global\advance\cons@count by 1\relax + \ifnum\cons@count=0\relax + \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi + \fi + \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} + \ifx\hide@true\y@ + \expandafter\ifx\csname hidestart0\endcsname\ampers@nd + \else + \expandafter\ifnum\csname hidestart0\endcsname>\cons@count + \else + \expandafter\ifnum\csname hidestop0\endcsname<\cons@count + \else + \xdef\hide@now{y} \xdef\eighth@{0} + \fi + \expandafter\ifnum\csname hidestop0\endcsname=\cons@count + \getregion@fromhidestack{0} + \fi + \fi + \fi + \fi \loopcount=0 \loop \advance\loopcount by 1 @@ -7199,74 +7535,112 @@ \ifx\allow@zero\n@ \advance\res@count by 1 \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 + \ifx\hide@true\y@ + \expandafter\ifx\csname hidestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname hidestart\the\loopcount\endcsname>\res@count + \else + \expandafter\ifnum\csname hidestop\the\loopcount\endcsname<\res@count + \else + \xdef\hide@now{y}\xdef\eighth@{\the\loopcount} + \fi + \expandafter\ifnum\csname hidestop\the\loopcount\endcsname=\res@count + \xdef\first@@{\first@} + \expandafter\getregion@fromhidestack{\the\loopcount} + \xdef\first@{\first@@} + \fi + \fi + \fi + \fi \ifnum\loopcount=\rule@num\relax \expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens - \xdef\ruler@{\ruler@ !<\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 + \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi \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@ -} + \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi + \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@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@restop\yes - \ifnum\tr@nsseqtop=\loopcount - \xdef\last@restop{\last@@restop} - \xdef\tr@nslatetop{\tr@nslatetop\first@} - \xdef\last@@restop{\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\tr@nslatettop{\tr@nslatettop\first@} - \xdef\last@@resttop{\first@} - \innerloopcount=\triple@countttop - \advance\innerloopcount by 1 - \ifnum\innerloopcount>3 \innerloopcount=1 \fi - \xdef\triple@countttop{\the\innerloopcount} - \fi\fi - \ifx\collect@resbottom\yes - \ifnum\tr@nsseqbottom=\loopcount - \xdef\last@resbottom{\last@@resbottom} - \xdef\tr@nslatebottom{\tr@nslatebottom\first@} - \xdef\last@@resbottom{\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\tr@nslatebbottom{\tr@nslatebbottom\first@} - \xdef\last@@resbbottom{\first@} - \innerloopcount=\triple@countbbottom - \advance\innerloopcount by 1 - \ifnum\innerloopcount>3 \innerloopcount=1 \fi - \xdef\triple@countbbottom{\the\innerloopcount} - \fi\fi + \ifx\hide@now\n@ + \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@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 + \fi + \ifx\collect@restop\yes + \ifnum\tr@nsseqtop=\loopcount + \xdef\last@restop{\last@@restop} + \xdef\last@@restop{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatetop{\tr@nslatetop\first@} + \fi + \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@} + \ifx\hide@now\n@ + \xdef\tr@nslatettop{\tr@nslatettop\first@} + \fi + \innerloopcount=\triple@countttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resbottom\yes + \ifnum\tr@nsseqbottom=\loopcount + \xdef\last@resbottom{\last@@resbottom} + \xdef\last@@resbottom{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatebottom{\tr@nslatebottom\first@} + \fi + \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@} + \ifx\hide@now\n@ + \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@} + \fi + \innerloopcount=\triple@countbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbottom{\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{% @@ -7276,7 +7650,8 @@ \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{% \the\innerloopcount} \else - \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi + \ifnum\loopcount=\rule@num \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi\fi + \ifx\hide@now\n@ \ifx\collect@valtop\yes \ifnum\v@lseqtop=\loopcount \xdef\v@ltop{\v@ltop,N} @@ -7309,8 +7684,31 @@ \ifnum\tr@nsseqbbottom=\loopcount \xdef\tr@nslatebbottom{\tr@nslatebbottom -} \fi\fi + \fi \fi \ifnum\loopcount<\seq@count \repeat + \ifnum\rule@num=0 + \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 + \ifx\hide@now\n@ \xdef\ruler@{\ruler@ !<\temp@>} \fi + \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 + \ifx\hide@now\n@ \xdef\ruler@{\ruler@ -} \fi + \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 + \ifx\hide@now\n@ \ifx\collect@cons@graphtop\yes \outerloopcount=1\relax \temp@count=0\relax @@ -7346,34 +7744,48 @@ \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 + \fi - \global\advance\cons@count by 1\relax - \ifnum\cons@count=0\relax - \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi - \fi - \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} - \ifnum\rule@num=0 - \ifnum\cons@count=\rule@tens - \xdef\ruler@{\ruler@ !<\rule@tens>} - \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 +%%%%%%%%%%%%% + \ifx\hide@now\y@ + \regionalshadenowtrue \regionaltintnowtrue + \regionalemphnowtrue \framenowtrue \fi + \ifregionalshadenow \calc@regshade \fi + \ifregionaltintnow \calc@regtint \fi + \ifregionalemphnow \calc@regemph \fi + \ifframenow \calc@frame \fi + \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi + \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi + \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \ifx\hide@now\y@ + \xdef\hidebar@on{1} + \ifnum\pos@count=\bar@pos + \else + \loopcount=\pos@count + \advance\loopcount by -\bar@pos + \xdef\bar@pos{\the\pos@count} + \xdef\stylehidebar{\stylehidebar\the\loopcount;\csname hidestyle\eighth@\endcsname;\csname hidetext\eighth@\endcsname;} + \fi + \else +%%%%%%%%%%%%% \advance\pos@count by 1 - \ifshow@logo \calc@logo \fi - \ifregionalshadenow \calc@regshade \fi - \ifregionaltintnow \calc@regtint \fi - \ifregionalemphnow \calc@regemph \fi - \ifframenow \calc@frame \fi - \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi - \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi - \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi - \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \ifshow@logo \calc@logo \fi \ifall@fshade \all@funcshade \else \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi @@ -7384,6 +7796,10 @@ \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 + \xdef\hide@now{n} +%%%%%%%% \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax \c@nsensus \else @@ -7398,6 +7814,14 @@ \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 \xdef\seq@line{\csname sequence\the\loopcount\endcsname} @@ -7435,8 +7859,10 @@ \csname sequence\the\loopcount\endcsname @} \ifnum\loopcount<\seq@count \repeat \end@count=0 \count@first \end@count=0 \xdef\start@number{0} - \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse - \framenowfalse + \ifx\hide@now\n@ + \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse + \framenowfalse + \fi \topfeaturenowfalse \bottomfeaturenowfalse \ttopfeaturenowfalse \bbottomfeaturenowfalse \innerloopcount=\cons@count @@ -7448,7 +7874,7 @@ \expandafter\ifnum\csname start\the\loopcount\endcsname>% \innerloopcount \else - \regionalshadenowtrue + \regionalshadenowtrue \fi \fi \fi @@ -7458,7 +7884,7 @@ \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% \innerloopcount \else - \regionaltintnowtrue + \regionaltintnowtrue \fi \fi \fi @@ -7468,7 +7894,8 @@ \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>% \innerloopcount \else - \regionalemphnowtrue + \else + \regionalemphnowtrue \fi \fi \fi @@ -7584,7 +8011,7 @@ \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% \innerloopcount \else - \regionaltintnowtrue + \regionaltintnowtrue \fi \fi \fi @@ -7970,66 +8397,69 @@ \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@{\ensuremath{\,\stackrel{\mathtt{#1}}{.}}}% + \def\third@{\ensuremath{\,\stackrel{\mathtt{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% \else \xdef\temp@{sf}% \ifx\ruler@family\temp@% - \def\third@{\ensuremath{\,\stackrel{\mathsf{#1}}{.}}}% + \def\third@{\ensuremath{\,\stackrel{\mathsf{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% \else \xdef\temp@{rm}% \ifx\ruler@family\temp@% - \def\third@{\ensuremath{\,\stackrel{\mathrm{#1}}{.}}}% + \def\third@{\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{\,\ensuremath{\cdot}\,#1\hss}\end{rotopo}}% + \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{\,\ensuremath{\cdot}\,#1\hss}\end{rotopo}}% + \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{\,\ensuremath{\cdot}\,#1\hss}\end{rotopo}}% + \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{.}{\mathtt{#1}}}}% + \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{.}{\mathsf{#1}}}}% + \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{.}{\mathrm{#1}}}}% + \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#1\,\ensuremath{\cdot}}\end{rotopo}}% + \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#1\,\ensuremath{\cdot}}\end{rotopo}}% + \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#1\,\ensuremath{\cdot}}\end{rotopo}}% + \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}% \fi\fi\fi \fi \fi} @@ -8039,8 +8469,8 @@ \xdef\first@{#2@}% \xdef\second@{!}% \ifx\third@\second@ \expandafter\get@rulenum\first@% - \else \xdef\third@{}\fi - \hbox to \box@width{\hss\third@\hss}% + \else \xdef\third@{}\xdef\f@color{Black}\fi + \textcolor{\f@color}{\hbox to \box@width{\hss\third@\hss}}% } \def\put@rulechar{% @@ -8081,7 +8511,7 @@ \fontseries{m}% \fontshape{n}% \selectfont% - \innerloopcount=1\relax\textcolor{\ruler@fg}{\put@rulechar}% + \innerloopcount=1\relax\put@rulechar% \newline\hbox{}% } \def\get@firstfill#1#2&{\xdef\second@@{#1}\xdef\fill@char{#2&}} @@ -8743,6 +9173,124 @@ \fi% \fi% } +\def\next@hidebar#1;#2;#3;#4@{% + \xdef\first@{#1}% + \ifx\first@\ampers@nd% + \else% + \fontfamily{\hideblock@family}\fontseries{\hideblock@series}% + \fontshape{\hideblock@shape}% + \selectfont% + \newline\hbox{}% + \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \hbox to -\box@width{\hss}% + \kern-0.1\box@width% + \xdef\last@{#3[,]&}\expandafter\opt@color\last@% + \ifx\f@color\comm@\xdef\f@color{Black}\fi% + \textcolor{\f@color}{% + \hbox to \first@\box@width{}% + \hbox to 0pt{\hss\strut\hideblock@size{\,\fourth@}\hss}}% + \xdef\last@{#2[,]&}\expandafter\opt@color\last@% + \ifx\f@color\comm@\xdef\f@color{Black}\fi% + \vspace{-0.23\box@height}% + \xdef\temp@{triangle}% + \ifx\fourth@\temp@% + \else + \xdef\temp@{square}% + \ifx\fourth@\temp@% + \else + \xdef\temp@{none}% + \ifx\fourth@\temp@% + \else + \vspace{-0.06\box@height}% + \fi\fi\fi% + \newline\hbox{}% + \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \hbox to -\box@width{\hss}% + \hbox to \first@\box@width{}% + \kern-0.1\box@width% + \textcolor{\f@color}{% + \raisebox{0.47\box@height}{\rule{0.2\box@width}{\temp@@length}}% + \xdef\first@{triangle}% + \ifx\fourth@\first@% + \kern-0.582\box@width% + \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigtriangledown$\hss}}% + \kern-0.418\box@width% + \else + \xdef\first@{square}% + \ifx\fourth@\first@% + \kern-0.6\box@width% + \raisebox{-0.12\box@height}{% + \raisebox{\temp@@length}{\hbox to \box@width{\hss$\square$\hss}}}% + \raisebox{-0.19\box@height}{% + \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}% + \kern-1.4\box@width% + \else + \xdef\first@{none}% + \ifx\fourth@\first@% + \kern-0.6\box@width% + \raisebox{-0.19\box@height}{% + \raisebox{\temp@@length}{\hbox to \box@width{\hss\strut}}}% + \kern-0.4\box@width% + \else + \kern-0.6\box@width% + \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bigodot$\hss}}% + \kern-0.4\box@width% + \fi% + \fi% + \fi% + \kern-0.58\box@width% + \raisebox{\temp@@length}{\hbox to \box@width{\hss$\bullet$\hss}}% + \xdef\first@{#4@}}% + \fi +} +\def\put@@hidebar{% + \if\first@ @% + \else + \hbox to -\box@width{\hss}% + \expandafter\next@hidebar\first@% + \put@@hidebar% + \fi% +} +\def\put@hidebar{% + \ifx\hide@seqs\n@% + \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi% + \temp@count=\seq@count% + \advance\temp@count by 1% + \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% + \advance\temp@@length by -0.75\box@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{-2.56\baselineskip}% + \xdef\first@{\stylehidebar @}% + \put@@hidebar% + \vspace{-\arrow@height}% + \vspace{-0.47\box@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}% @@ -9180,7 +9728,7 @@ \def\set@lines{% \pos@count=1 - \xdef\frame@pos{1}% + \xdef\frame@pos{1}\xdef\bar@pos{0}\xdef\hidebar@on{0}% \xdef\featurepostop{1}\xdef\featureposbottom{1}% \xdef\featureposttop{1}\xdef\featureposbbottom{1}% \findc@nsensus% @@ -9280,6 +9828,9 @@ \ifnum\frame@on=0 \xdef\frame@{0}\fi% \put@frame% \fi% + \ifnum\hidebar@on=1 % + \put@hidebar% + \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 @@ -9345,7 +9896,7 @@ \fi \fi \xdef\consensus{} \xdef\ruler@{} - \xdef\styleframe{} + \xdef\styleframe{} \xdef\stylehidebar{} \xdef\textfeaturetop{} \xdef\textfeaturebottom{} \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} @@ -9457,7 +10008,7 @@ \xdef\textfeaturettop{} \xdef\featureonttop{0} \xdef\textfeaturebottom{} \xdef\featureonbottom{0} \xdef\textfeaturebbottom{}\xdef\featureonbbottom{0} - \xdef\styleframe{} + \xdef\styleframe{} \xdef\stylehidebar{} \xdef\stylefeaturetop{} \xdef\stylefeaturettop{} \xdef\stylefeaturebottom{} @@ -9550,6 +10101,7 @@ \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} \ifnum\end@num>\end@count\relax\xdef\end@num{\the\end@count}\fi @@ -9593,6 +10145,7 @@ \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} \ifnum\end@num>\end@count\relax\xdef\end@num{\the\end@count}\fi @@ -9614,6 +10167,7 @@ \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 @@ -9621,7 +10175,6 @@ \loopcount=1 \read@loop \fi - \if\seq@type A \guess@DNA \fi \ifnum\seq@pointer>0 \ifstop@ \else @@ -9631,6 +10184,7 @@ \fi \fi \ifshow@sublogo \closein\sublogofile \fi + \ifx\exp@rt\y@ \closeout\exp@rtfile \fi \closein\alignfile \message{)} } @@ -9729,6 +10283,7 @@ \loopcount=0 \xdef\seq@order{} \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@hidereg\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} @@ -9752,6 +10307,7 @@ \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@hidereg\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} @@ -9795,6 +10351,7 @@ \ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi \loopcount=0 \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\getregion@fromhidestack{\the\loopcount} \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} @@ -9841,6 +10398,7 @@ \baselineskip=\box@height \advance\baselineskip by \box@depth \fi \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\getregion@fromhidestack{\the\loopcount} \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} @@ -10149,6 +10707,10 @@ \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\hide@true{n} \xdef\hide@now{n} +\xdef\hide@label{circ} +\xdef\divref@{0} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% @@ -10232,6 +10794,10 @@ \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{hideblock}{rm} % Use roman family for hidden block labels +\setseries{hideblock}{md} % Use normal series for hidden block labels +\setshape {hideblock}{it} % Use italics shape for hidden block labels +\setsize {hideblock}{normalsize} % Use normal size for hidden block labels \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 diff --git a/Master/texmf-dist/tpm/texshade.tpm b/Master/texmf-dist/tpm/texshade.tpm index 7580e923c30..9e76e01c9e0 100644 --- a/Master/texmf-dist/tpm/texshade.tpm +++ b/Master/texmf-dist/tpm/texshade.tpm @@ -3,7 +3,7 @@ <rdf:Description about="http://texlive.dante.de/texlive/Package/texshade.zip"> <TPM:Name>texshade</TPM:Name> <TPM:Type>Package</TPM:Type> - <TPM:Date>2006/06/30 13:15:37</TPM:Date> + <TPM:Date>2007/02/22 19:55:31</TPM:Date> <TPM:Version></TPM:Version> <TPM:Creator>rahtz</TPM:Creator> <TPM:Title> @@ -25,12 +25,12 @@ habitual TeX output quality--with reasonable time expenditure. <TPM:Size>1964025</TPM:Size> <TPM:License></TPM:License> <TPM:Build/> - <TPM:RunFiles size="418343"> + <TPM:RunFiles size="445246"> texmf-dist/tex/latex/texshade/texshade.def texmf-dist/tex/latex/texshade/texshade.sty texmf-dist/tpm/texshade.tpm </TPM:RunFiles> - <TPM:DocFiles size="807085"> + <TPM:DocFiles size="815347"> texmf-dist/doc/latex/texshade/AQP1.phd texmf-dist/doc/latex/texshade/AQP1.top texmf-dist/doc/latex/texshade/AQP2spec.ALN @@ -45,7 +45,7 @@ texmf-dist/doc/latex/texshade/texshade.pdf texmf-dist/doc/latex/texshade/tsfaq.pdf texmf-dist/doc/latex/texshade/tsfaq.tex </TPM:DocFiles> - <TPM:SourceFiles size="738597"> + <TPM:SourceFiles size="771125"> texmf-dist/source/latex/texshade/texshade.dtx texmf-dist/source/latex/texshade/texshade.ins </TPM:SourceFiles> |