From 679b379df816aa8af46fd18bd199c5ade5cb9662 Mon Sep 17 00:00:00 2001 From: Karl Berry Date: Thu, 17 Apr 2008 15:21:19 +0000 Subject: texshade 1.18 git-svn-id: svn://tug.org/texlive/trunk@7474 c570f23f-e606-0410-a88d-b1316a301751 --- Master/texmf-dist/doc/latex/texshade/AQP_TC.asc | 56 + Master/texmf-dist/doc/latex/texshade/AQPpro.MSF | 2 +- Master/texmf-dist/doc/latex/texshade/README | 6 +- Master/texmf-dist/doc/latex/texshade/texshade.pdf | Bin 628139 -> 640261 bytes .../texmf-dist/source/latex/texshade/texshade.dtx | 1406 +++++++++++++++++--- .../texmf-dist/source/latex/texshade/texshade.ins | 3 +- Master/texmf-dist/tex/latex/texshade/texshade.sty | 1106 +++++++++++++-- 7 files changed, 2311 insertions(+), 268 deletions(-) create mode 100644 Master/texmf-dist/doc/latex/texshade/AQP_TC.asc (limited to 'Master/texmf-dist') diff --git a/Master/texmf-dist/doc/latex/texshade/AQP_TC.asc b/Master/texmf-dist/doc/latex/texshade/AQP_TC.asc new file mode 100644 index 00000000000..aed297dac4a --- /dev/null +++ b/Master/texmf-dist/doc/latex/texshade/AQP_TC.asc @@ -0,0 +1,56 @@ + +T-COFFEE, Version_5.31(Fri Oct 26 17:01:36 2007) +Cedric Notredame +CPU TIME:1 sec. +SCORE=54 +* + BAD AVG GOOD +* +AQP1.PRO : 55 +AQP2.PRO : 58 +AQP3.PRO : 46 +AQP4.PRO : 55 +AQP5.PRO : 58 +cons : 54 + +AQP1.PRO 1 65------------------------3777666677777766666666556666666554 36 +AQP2.PRO 1 -2------------------------2776667777777777777667666666666654 35 +AQP3.PRO 1 5---------9644-----33322111------457777665555556555657555544 40 +AQP4.PRO 1 63DGAAARRW9644PPCSR33322113667667677777666666666666767666665 60 +AQP5.PRO 1 65------------------------4877667667777777776666666667666665 36 +cons 1 54--------9644-----33322113777667667777766666666666666666554 60 + +AQP1.PRO 37 111221111223454555555555444444444554455555555544544445555444 96 +AQP2.PRO 36 ---33----323444444444444444454444455556666555555555455565555 88 +AQP3.PRO 41 111211----11444444444433333232333344455565555544444445555444 96 +AQP4.PRO 61 ---331111223554555555544444454455555666666666555555455555555 117 +AQP5.PRO 37 ---43----323555555555554444454455555555666555555555555565555 89 +cons 61 111331111323454545444444444444444455555665555555555455555555 120 + +AQP1.PRO 97 5555555556555655555----------4444445555555555555555-----5555 141 +AQP2.PRO 89 6556666666666665555----------5555555566666666666666-----5556 133 +AQP3.PRO 97 4445555555555554443YYDAIWAFAG2322222333333344443454LDMVN4445 156 +AQP4.PRO 118 5556666666666665544----------4445545555555555665666-----6666 162 +AQP5.PRO 90 5555555556666665554----------4455555666666666666677-----6676 134 +cons 121 5555556666666655554----------4444444555555555555566-----5566 180 + +AQP1.PRO 142 6677777777777766666666-5666656666666555666556677777778777766 200 +AQP2.PRO 134 5566777777777766666555-5565556666666555556556788888888888777 192 +AQP3.PRO 157 7666777777777777765444V3454455554444322222224577777777777665 216 +AQP4.PRO 163 7777777777777777776666-5555555555666555555555677777777777766 221 +AQP5.PRO 135 7777888788887777776666-5666666666666555555556677777777777776 193 +cons 181 7677777777777777666555-5565555565556544555555677777777777766 240 + +AQP1.PRO 201 7766--666---------66666666665555666666555566544455555220111- 248 +AQP2.PRO 193 7766--666---------6666666665555555555555556664456666633-222- 239 +AQP3.PRO 217 5544LA2220EVFTTGQN223333434333334433332322------------------ 258 +AQP4.PRO 222 6555--555---------55655666656666655555555454-33345544100111- 268 +AQP5.PRO 194 6666--5440--------5555556655555555555544445664444555533-222T 242 +cons 241 6665--5550--------55555555555555555555444455544455555220221- 300 + +AQP1.PRO 249 22222--2111111111----11000----------------------------3 269 +AQP2.PRO 240 33333--42222222223--3333333233322-------------------223 271 +AQP3.PRO 259 --------------------2111222122211122-111112221-------12 285 +AQP4.PRO 269 11111KG22111111123VE3222333233322122D111112221SSGEVL224 323 +AQP5.PRO 243 23333--33222223334--3333333---------------------------- 265 +cons 301 23322--32222222223--3222223233322122-111112221------223 355 diff --git a/Master/texmf-dist/doc/latex/texshade/AQPpro.MSF b/Master/texmf-dist/doc/latex/texshade/AQPpro.MSF index aef0f2b0e06..e8a39be7f01 100644 --- a/Master/texmf-dist/doc/latex/texshade/AQPpro.MSF +++ b/Master/texmf-dist/doc/latex/texshade/AQPpro.MSF @@ -16,7 +16,7 @@ AQP5.PRO MK........................KEVCSLAFFKAVFAEFLATLIFVFFGLGSALKWP 61 120 AQP1.PRO YPLERNQTLVQDNVKVSLAFGLSIATLAQSVGHISGAHSNPAVTLGLLLSCQISILRAVM AQP2.PRO ...SS....PPSVLQIAVAFGLGIGILVQALGHVSGAHINPAVTVACLVGCHVSFLRAAF -AQP3.PRO LSRGTHGGF....LTINLAFGFAVTLAILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPI +AQP3.PRO LSRGTH....GGFLTINLAFGFAVTLAILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPI AQP4.PRO ...GSENPLPVDMVLISLCFGLSIATMVQCFGHISGGHINPAVTVAMVCTRKISIAKSVF AQP5.PRO ...SA....LPTILQISIAFGLAIGTLAQALGPVSGGHINPAITLALLIGNQISLLRAVF diff --git a/Master/texmf-dist/doc/latex/texshade/README b/Master/texmf-dist/doc/latex/texshade/README index 7f5f24c0a1c..bb80eed3bd1 100644 --- a/Master/texmf-dist/doc/latex/texshade/README +++ b/Master/texmf-dist/doc/latex/texshade/README @@ -1,4 +1,4 @@ - TeXshade v1.17 + TeXshade v1.18 >> >> 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 - 2007 Eric Beitz + Copyright (C) 1999 - 2008 Eric Beitz @@ -125,7 +125,7 @@ 3 - CONTACT E-Mail: ebeitz@pharmazie.uni-kiel.de - WWW: http://www.pharmazie.uni-kiel.de/chem/ + WWW: http://www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html (On-line documentation and updates) 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 index 377a84ff478..1b47c480cdc 100644 Binary files a/Master/texmf-dist/doc/latex/texshade/texshade.pdf and b/Master/texmf-dist/doc/latex/texshade/texshade.pdf differ diff --git a/Master/texmf-dist/source/latex/texshade/texshade.dtx b/Master/texmf-dist/source/latex/texshade/texshade.dtx index 67f26d001a0..61e88ddf8d0 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) 1999-2007 Eric Beitz +% Copyright (C) 1999-2008 Eric Beitz % See the file texshade.txt % % \fi @@ -280,10 +280,11 @@ % `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' +% `www.pharmazie.uni-kiel.de/chem/Prof_Beitz/biotex.html' % } % % \changes{1.17}{2007-06-19}{% +% Corrections: . % Introduction: `allmatchspecial' now accepts an optional threshold % percentage allowing one to set two levels off % conservation; @@ -306,6 +307,23 @@ % } % % +% \changes{1.18}{2008-04-15}{% +% Corrections: bug fixes concerning: +% featurenames, ordering, numbering, setends. +% Introduction: T-Coffee shading can be imported and displayed +% in the alignment, in the consensus, +% in feature color scales and bar graphs by +% `shadingmode[ASCII-file]{T-Coffee}' and +% `includeTCoffee'; +% two more feature lines on top and at bottom: +% `ttttop', `tttop', `bbbottom', and `bbbbottom'; +% fusion of the `startnumber' and `setends' commands +% via optional parameters. +% } +% +% +% +% % \CharacterTable % {Upper-case \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z % Lower-case \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z @@ -342,8 +360,8 @@ % send electronic mail to \texttt{ebeitz@pharmazie.uni-kiel.de}; % for further information, updates and on-line documentation % see my homepage at -% \texttt{www.pharmazie.uni-kiel.de/chem/} -- click on `Beitz'}} -% \date{v1.17; 2007/06/19\\} +% \texttt{www.pharmazie.uni-kiel.de/chem/Prof\_Beitz/biotex.html} }} +% \date{v1.18; 2008/04/15\\} % \maketitle % \begin{abstract} % Setting alignments of nucleotides and peptides for publication @@ -395,6 +413,8 @@ % (MSF-format)\\ % \quad|AQPpro.MSF| \> an example protein alignment % (MSF-format)\\ +% \quad|AQP_TC.asc| \> an example T-Coffee shading file +% (|score_ascii|-format)\\ % \quad|AQP2spec.ALN|\> a further protein alignment % (minimal ALN-file)\\ % \quad|AQP1.phd|\> secondary structure information @@ -420,6 +440,26 @@ % % \subsection{Version History} % +% \textbf{v1.18 2008/04/15} +% \medskip +% +% \emph{Correction:} several bug fixed concerning featurename +% display, sequence ordering and numbering. +% +% \emph{Introduction:} +% (a) T-Coffee shading information can be loaded and put on the +% alignment.\footnote{Suggestion by Florian Mertes.} +% The conservation data can also be displayed in the +% consensus as well as feature color scales and bar plots. +% (b) Two more feature lines were added on the top and at the +% bottom (|ttttop|, |tttop|, |bbbottom|, |bbbbottom|). +% (c) The |startnumber| and |setends| commands have been fused; +% either command can set both, a new start number as well as +% end definitions of the sequence section to be displayed. +% \bigskip +% +% \newpage +% % \textbf{v1.17 2007/06/19} % \medskip % @@ -438,7 +478,7 @@ % |\featurenamescolor|, |\featurestylenamescolor|, % Font styles in feature names can be set as usual, e.g. % |\setsize{featurenames}{large}| or -% |\featurestylenamesrm|, etc. +% |\featurestylenamesrm|. % \bigskip % % @@ -593,6 +633,7 @@ % alignment\footnote{Inspired by Christoph Gille's {\tt STRAP}}. % \bigskip % +% % \textbf{v1.7 2004/01/05} % \medskip % @@ -650,6 +691,7 @@ % breaks of the gaps after the sequences. % \bigskip % +% % \textbf{v1.4\&4a 2000/9/12 \& 2000/10/3} % \medskip % @@ -774,7 +816,7 @@ % as \textsc{PostScript} and on-line viewable PDF. % I also put a link from the \BioTeX{} (\TeXshade/\TeXtopo) homepage % to the document collection -% (|http://homepages.uni-tuebingen.de/beitz/biotex.html|). +% (|http://pharmazie.uni-kiel.de/chem/Prof_Beitz/BioTeX|). % % % \subsubsection{Memory shortness when using \TeX{}shade} @@ -1052,12 +1094,53 @@ % \end{verbatim}} % % Probably you know -% this kind of shading from the VMS/Unix and DOS public domain program +% this kind of shading from the public domain program % |BoxShade| % by \textsc{Kay Hofmann} or from the Macintosh version % |MacBoxShade| by \textsc{Michael D. Barron}. \TeXshade{} % provides the same functionality---and goes truly beyond---for the % \TeX{} community. +% +% +% \subsubsection{T-Coffee shading} +% +% \label{TCoffee} +% +% \TeXshade{}'s capabilities of calculating alignment shadings are +% limited. |T-Coffee| (|www.tcoffee.org|) is a sophisticated alignment/shading +% software. You can apply shading from |T-Coffee| in \TeXshade{} +% by loading the shading information file (|score_ascii|) generated by +% |T-Coffee|. +% \medskip +% +% +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[AQP_TC.asc]{T-Coffee} +% \setends{1}{30..63} +% \hideconsensus +% \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{} +% \showfeaturestylename{top}{feat-cons} +% \showconsensus{bottom} +% \end{texshade} +% +% Code:\medskip +% +% \vbox{% +% \begin{verbatim} +% \begin{texshade}{AQPpro.MSF} +% \shadingmode[AQP_TC.asc]{T-Coffee} +% \setends{1}{30..63} +% \hideconsensus +% \feature{top}{1}{30..63}{color:conservation[T-Coffee]}{} +% \showfeaturestylename{top}{feat-cons} +% \showconsensus{bottom} +% \end{texshade} +% \end{verbatim}} +% +% +% +% +% % % % \subsubsection{Diversity mode} @@ -1952,7 +2035,7 @@ % modes or new color schemes (i.\,e.\ for a satisfying grayscale output) % with other users. If you have created a % parameter file, which you think is of interest for others, please -% submit it to me\footnote{|eric.beitz@uni-tuebingen.de|} as an e-mail +% submit it to me\footnote{|ebeitz@pharmazie.uni-kiel.de|} as an e-mail % attachment together with a short % description. I will take care of those files and post them---with % a reference to the author---together with the next \TeXshade{} @@ -2195,6 +2278,23 @@ % \end{verbatim} % % +% \item |\shadingmode[|\meta{filename}|]{T-Coffee}| +% +% Enter a \meta{filename} to load the shading +% information from a |T-Coffee| |score_ascii| file (|www.tcoffee.org|); +% see example in \ref{TCoffee}. Make sure +% that the alignment file specified in the |\texshade| command +% and this shading file correspond to each other. +% +% If you do not enter a \meta{filename} here, a separate +% command |\includeTCoffee{|\meta{filename}|}| must be used. +% +% |T-Coffee| shading can also be used in the consensus +% p.\,\pageref{Lshowconsensus} and in the feature lines, +% in particular color scales and bar plots p.\,\pageref{Lgraphs}, +% for the display of shading information. +% +% % \item |\shadingmode[|\meta{seqref}|]{diverse}| % % \ref{diverse} depicts an example alignment. Choose the @@ -2413,7 +2513,7 @@ % % with % \meta{scale} |Gray|, |BlueRed|, |RedBlue|, |GreenRed|, |RedGreen|, -% |ColdHot| (recommended) or |HotCold| and \meta{position} |top| +% |ColdHot| (recommended), |HotCold|, or |T-Coffee| \ref{TCoffee}, and \meta{position} |top| % or |bottom|. % % The first color defines the foreground, i.e. the letters, the @@ -2735,13 +2835,15 @@ % displayed, one % may not want to have the residue numbering start out with number~1. % The command -% |\startnumber{|\meta{seqref}|}{|\meta{first residue number}|}| +% |\startnumber[|\meta{start..stop}|]{|\meta{seqref}|}{|\meta{startnumber}|}| % allows one to set the starting number of any sequence to any value % incl.\ negative values but except `0' which is not usually used in % sequence numbering (the transition from negative to positive % values is like this: \ldots\ $-2$, $-1$, 1, 2 \ldots). If, however, % the use of the number `0' is wanted as sometimes in sequence logos % this can be turned on by |\allowzero| and off with |\disallowzero|. +% The optional parameter can be used to truncate the sequence display +% to a certain section (see also |\setends| below). % % \label{Lseqlength} % \TeXshade{} needs to know the correct length of the sequences @@ -2783,7 +2885,7 @@ % is done by % \medskip % -% \quad|\setends{|\meta{seqref}|}{|\meta{startnumber}|..|\meta{stopnumber}|}|. +% \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}|. % \medskip % % Again, \meta{seqref} is the sequence number based on the @@ -2791,28 +2893,44 @@ % the consensus as a measure for the sequence section the % string `|consensus|' as \meta{seqref} is accepted. The % specified sequence is truncated at -% positions \meta{startnumber} and \meta{stopnumber}. All other +% positions \meta{start} and \meta{stop}. All other % sequences are cut accordingly. If the number of the first % residue in the sequence is set to a new value with the -% |\startnumber| command (s.\,a.) this is taken into account. Some examples: +% |\startnumber| command (s.\,a.) this is taken into account. The +% \meta{startnumber} can be set as an optional parameter directly +% in the |\setends| command as well. +% \medskip +% +% Some examples: % \medskip % -% \quad a) |\setends{1}{20..100}| +% \quad a) |\setends{1}{21..100}| % \medskip % -% \quad b) |\startnumber{1}{15} \setends{1}{35..115}| +% \quad b) |\startnumber{1}{101} \setends{1}{121..200}| % \medskip % -% Both commands select the same section from the alignment but the -% numbering for sequence 1 starts at position~20 in the first example and at -% position~35 in the latter. +% Both commands select the same sequence section from the alignment but +% numbering for sequence 1 starts at position~21 in the first example and at +% position~121 in the latter. % \medskip % -% \quad c) |\setends{consensus}{20..100}| +% \quad c) |\setends[101]{1}{121..200}| equals example b. % \medskip % -% This may describe a completely different section of the multiple -% sequence alignment. +% \medskip +% +% \quad d) |\startnumber[121..200]{1}{101}| also equals example b. +% \medskip +% +% \medskip +% +% \quad e) |\setends{consensus}{21..100}| +% \medskip +% +% This may describe a very different section of the multiple +% sequence alignment because the consensus counts every position +% including gaps. % % \label{Lshowruler}\label{Lhideruler} % \label{Lrulersteps}\label{Lrulercolor} @@ -3147,7 +3265,7 @@ % 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!)} +% \subsubsection{Hiding blocks of the alignment (experimental!)} % % \label{Lhideblock} % \textit{Be aware that this feature is still highly experimental. There are many instances @@ -3208,20 +3326,21 @@ % this rather complex but mighty command are discussed in detail. % The parameter \meta{position} tells \TeXshade{} where to display % the feature label, i.\,e. on the top of the alignment (|top|), -% or at the bottom (|bottom|). Further, there can be a feature line -% ontop of the top feature line (|ttop|) or below the bottom -% feature line (|bbottom|). Thus, up to four features -% overlapping in four different lines may be displayed. +% or at the bottom (|bottom|). Further, there can be three more feature lines +% ontop of the top feature line (|ttop|, |tttop|, and |ttttop|) or below the bottom +% feature line (|bbottom|, |bbbottom|, |bbbbottom|). Thus, up to eight features +% overlapping in eight different lines may be displayed. % Depending on the content of the feature lines the gaps between % them might be not satisfactory. % \label{Ltopspace}\label{Lttopspace} +% \label{Ltttopspace}\label{Lttttopspace} % \label{Lbottomspace}\label{Lbbottomspace} -% Therefore, four separate commands can be employed to change the -% space between |ttop| and |top| -% (|\ttopspace{|\meta{length}|}|), between |top| and the alignment -% (|\topspace{|\meta{length}|}|), between the alignment and -% |bottom| (|\bottomspace{|\meta{length}|}|) and between |bottom| -% and |bbottom| (|\bbottomspace{|\meta{length}|}|). Use positive +% \label{Lbbbottomspace}\label{Lbbbbottomspace} +% Therefore, eight separate commands can be employed to change the +% space below |ttttop|, |tttop|, |ttop|, or |top| +% (|\topspace{|\meta{length}|}| etc.), and above +% |bottom|, |bbottom|, |bbbottom|, or |bbbbottom| +% (|\bottomspace{|\meta{length}|}| etc.). Use positive % values to further separate the lines, e.\,g. % |\ttopspace{3mm}| or negative values to reduce the space, e.\,g. % |\bottomspace{-0.1in}|. @@ -3240,7 +3359,8 @@ % \textbf{Braces:}\\ % In order to display an over- or underbrace as % a label use the parameter |{brace}|. Depending on the -% \meta{position} (|ttop|, |top|, |bottom| or |bbottom|) the respective brace is +% \meta{position} (|ttttop|, |tttop|, |ttop|, |top|, |bottom|, +% |bbottom|, |bbbottom|, or |bbbbottom|) the respective brace is % displayed. The standard color of braces is % black. It can be changed by an optional parameter directly after % the definition of the symbol, e.\,g. |{brace[Red]}|. @@ -3491,7 +3611,11 @@ % color scales is a 5\% gray scale from very light gray to black (|Gray|). % More colorful scales have been implemented, i.e. |BlueRed|, |RedBlue|, |GreenRed|, % |RedGreen|, |ColdHot| and |HotCold|, the latter two being particularly -% useful for ranges from negative to positive values. +% useful for ranges from negative to positive values. Further, a scale called |T-Coffee| +% is available if |T-Coffee| shading information has been imported as the +% |\shadindmode| \ref{Lshadingmode}. +% +% % % The general format of this feature label definition for bar graphs is: % \medskip @@ -3511,6 +3635,9 @@ % \qquad |{bar:conservation}| % \medskip % +% \qquad |{bar:conservation[T-Coffee]}| +% \medskip +% % \qquad |{bar:hydrophobicity}| % \medskip % @@ -3535,6 +3662,9 @@ % \qquad |{color:conservation[BlueRed]}| % \medskip % +% \qquad |{color:conservation[T-Coffee]}| +% \medskip +% % \qquad |{color:hydrophobicity[GreenRed]}| % \medskip % @@ -3588,16 +3718,16 @@ % \label{Lshowfeaturename} \label{Lshowfeaturestylename} % \label{Lhidefeaturename} \label{Lhidefeaturestylename} % \label{Lhidefeaturenames} \label{Lhidefeaturestylenames} -% \quad |\showfeaturename{|\meta{ttop/top/bottom/bbottom}|}{|\meta{name}|}|, +% \quad |\showfeaturename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}|, % \medskip % -% \quad |\showfeaturestylename{|\meta{ttop/top/bottom/bbottom}|}{|\meta{name}|}| +% \quad |\showfeaturestylename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}| % \medskip % -% \quad |\hidefeaturename{|\meta{ttop/top/bottom/bbottom}|}| +% \quad |\hidefeaturename{|\meta{ttttop...bbbbottom}|}| % \medskip % -% \quad |\hidefeaturestylename{|\meta{ttop/top/bottom/bbottom}|}| +% \quad |\hidefeaturestylename{|\meta{ttttop...bbbbottom}|}| % \medskip % % \quad |\hidefeaturenames|, and |\hidefeaturestylenames|. @@ -3619,10 +3749,10 @@ % or individually with \label{Lfeaturenamecolor} % \medskip % -% \quad |\featurenamecolor{|\meta{ttop/top/bottom/bbottom}|}{|\meta{color}|}| and \label{Lfeaturestylenamecolor} +% \quad |\featurenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}| and \label{Lfeaturestylenamecolor} % \medskip % -% \quad |\featurestylenamecolor{|\meta{ttop/top/bottom/bbottom}|}{|\meta{color}|}| +% \quad |\featurestylenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}| % \medskip % % See section \ref{colors} for how to select colors in \TeX{}shade. @@ -3645,6 +3775,13 @@ % \quad|\feature{bottom}{1}{98..98}{fill:$\uparrow$}{second...}| % \medskip % +% \emph{T-Coffee mode} (\ref{TCoffee}): |T-Coffee| color scale +% +% \quad|\feature{top}{1}{30..63}{color:conservation[T-Coffee]}{}| +% +% \quad|\showfeaturestylename{bottom}{cons}| +% \medskip +% % \emph{diversity mode} (\ref{diverse}): frames, text only % % \quad|\feature{top}{1}{77..109}{}{AQP2 species variants}| @@ -4530,6 +4667,7 @@ % \meta{mode} & \meta{option} &\\ \hline % |identical| & |allmatchspecial/number| &\\ % |similar| & |allmatchspecial/number| &\\ +% |T-Coffee| & \meta{filename} &\\ % |diverse| & \meta{seqref} &\\ % |functional|& \meta{type} & |charge| \\ % & & |hydropathy| \\ @@ -4745,7 +4883,7 @@ % \quad|\showresidues| % \hfill[\pageref{Lshowresidues}] % -% \quad|\startnumber{|\meta{seqref}|}{|\meta{first residue number}|}| +% \quad|\startnumber[|\meta{start..stop}|]{|\meta{seqref}|}{|\meta{startnumber}|}| % \hfill[\pageref{Lstartnumber}] % % \quad|\allowzero| @@ -4757,7 +4895,7 @@ % \quad|\seqlength{|\meta{seqref}|}{|\meta{length}|}| % \hfill[\pageref{Lseqlength}] % -% \quad|\setends{|\meta{seqref}|}{|\meta{startnumber}|..|\meta{stopnumber}|}| +% \quad|\setends[|\meta{startnumber}|]{|\meta{seqref}|}{|\meta{start..stop}|}| % \hfill[\pageref{Lsetends}] % % \quad|\showruler[|\meta{color}|]{|\meta{top/bottom}|}{|\meta{seqref}|}| @@ -4995,16 +5133,16 @@ % \> = |{vertical}| % \end{tabbing} % -% \quad |\showfeaturename{|\meta{ttop/top/bottom/bbottom}|}{|\meta{name}|}| +% \quad |\showfeaturename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}| % \hfill[\pageref{Lshowfeaturename}] % -% \quad |\showfeaturestylename{|\meta{ttop/\ldots/bbottom}|}{|\meta{name}|}| +% \quad |\showfeaturestylename{|\meta{ttttop...bbbbottom}|}{|\meta{name}|}| % \hfill[\pageref{Lshowfeaturestylename}] % -% \quad |\hidefeaturename{|\meta{ttop/top/bottom/bbottom}|}| +% \quad |\hidefeaturename{|\meta{ttttop...bbbbottom}|}| % \hfill[\pageref{Lhidefeaturename}] % -% \quad |\hidefeaturestylename{|\meta{ttop/top/bottom/bbottom}|}| +% \quad |\hidefeaturestylename{|\meta{ttttop...bbbbottom}|}| % \hfill[\pageref{Lhidefeaturestylename}] % % \quad |\hidefeaturenames| @@ -5019,10 +5157,10 @@ % \quad |\featurestylenamescolor{|\meta{color}|}| % \hfill[\pageref{Lfeaturestylenamescolor}] % -% \quad |\featurenamecolor{|\meta{ttop/top/bottom/bbottom}|}{|\meta{color}|}| +% \quad |\featurenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}| % \hfill[\pageref{Lfeaturenamecolor}] % -% \quad |\featurestylenamecolor{|\meta{ttop/\ldots/bbottom}|}{|\meta{color}|}| +% \quad |\featurestylenamecolor{|\meta{ttttop...bbbbottom}|}{|\meta{color}|}| % \hfill[\pageref{Lfeaturestylenamecolor}] % % \vspace{1.5\baselineskip} @@ -5380,6 +5518,7 @@ \newif\ifnumbers@left \newif\ifnumbers@right \newif\ifhide@cons \newif\ifshow@cons \newif\iffuncmode \newif\iflegend@ +\newif\ifT@coffee \newif\ifnumbers@ \newif\ifnames@ \newif\ifgerm@n \newif\ifsp@nish \newif\ifrpl@fix @@ -5387,6 +5526,8 @@ \newif\ifstart@ \newif\ifstop@ \newif\iftopfeature \newif\ifbottomfeature \newif\ifttopfeature \newif\ifbbottomfeature +\newif\iftttopfeature \newif\ifbbbottomfeature +\newif\ifttttopfeature\newif\ifbbbbottomfeature \newif\ifall@fshade \newif\ifregionalemph \newif\ifframe@ \newif\ifregionaltint \newif\ifshow@logo \newif\ifshow@sublogo @@ -5397,8 +5538,12 @@ \newif\ifregionalshadenow \newif\iftopfeaturenow \newif\ifttopfeaturenow +\newif\iftttopfeaturenow +\newif\ifttttopfeaturenow \newif\ifbottomfeaturenow \newif\ifbbottomfeaturenow +\newif\ifbbbottomfeaturenow +\newif\ifbbbbottomfeaturenow \newif\ifframenow \newif\iffix@ @@ -6097,6 +6242,17 @@ \definecolor{Gray95} {cmyk}{0,0,0,0.95} \definecolor{Black} {cmyk}{0,0,0,1} \definecolor{Gray100} {cmyk}{0,0,0,1} +\definecolor{TC0} {cmyk}{0.4,0.4,0,0} +\definecolor{TC1} {cmyk}{0.6,0,0.7,0} +\definecolor{TC2} {cmyk}{0.4,0,0.7,0} +\definecolor{TC3} {cmyk}{0.2,0,1,0} +\definecolor{TC4} {cmyk}{0,0,1,0} +\definecolor{TC5} {cmyk}{0,0.2,1,0} +\definecolor{TC6} {cmyk}{0,0.4,1,0} +\definecolor{TC7} {cmyk}{0,0.6,1,0} +\definecolor{TC8} {cmyk}{0,0.8,1,0} +\definecolor{TC9} {cmyk}{0,0.875,1,0} +\definecolor{TC99} {cmyk}{0,0,0,0} \definecolor{LightGreenYellow} {cmyk}{0.08,0,0.35,0} \definecolor{LightYellow} {cmyk}{0,0,0.50,0} \definecolor{LightGoldenrod} {cmyk}{0,0.05,0.42,0} @@ -6188,6 +6344,16 @@ \definecolor{LightGray95} {cmyk}{0,0,0,0.47} \definecolor{LightBlack} {cmyk}{0,0,0,0.50} \definecolor{LightGray100} {cmyk}{0,0,0,0.50} +\definecolor{LightTC0} {cmyk}{0.2,0.2,0,0} +\definecolor{LightTC1} {cmyk}{0.3,0,0.35,0} +\definecolor{LightTC2} {cmyk}{0.2,0,0.35,0} +\definecolor{LightTC3} {cmyk}{0.1,0,0.5,0} +\definecolor{LightTC4} {cmyk}{0,0,0.5,0} +\definecolor{LightTC5} {cmyk}{0,0.1,0.5,0} +\definecolor{LightTC6} {cmyk}{0,0.2,0.5,0} +\definecolor{LightTC7} {cmyk}{0,0.3,0.5,0} +\definecolor{LightTC8} {cmyk}{0,0.4,0.5,0} +\definecolor{LightTC99} {cmyk}{0,0,0,0} \definecolor{LightLightGreenYellow} {cmyk}{0.04,0,0.17,0} \definecolor{LightLightYellow} {cmyk}{0,0,0.25,0} \definecolor{LightLightGoldenrod} {cmyk}{0,0.02,0.21,0} @@ -6279,6 +6445,16 @@ \definecolor{LightLightGray95} {cmyk}{0,0,0,0.23} \definecolor{LightLightBlack} {cmyk}{0,0,0,0.25} \definecolor{LightLightGray100} {cmyk}{0,0,0,0.25} +\definecolor{LightLightTC0} {cmyk}{0.1,0.1,0,0} +\definecolor{LightLightTC1} {cmyk}{0.15,0,0.175,0} +\definecolor{LightLightTC2} {cmyk}{0.1,0,0.175,0} +\definecolor{LightLightTC3} {cmyk}{0.05,0,0.25,0} +\definecolor{LightLightTC4} {cmyk}{0,0,0.25,0} +\definecolor{LightLightTC5} {cmyk}{0,0.05,0.25,0} +\definecolor{LightLightTC6} {cmyk}{0,0.1,0.25,0} +\definecolor{LightLightTC7} {cmyk}{0,0.15,0.25,0} +\definecolor{LightLightTC8} {cmyk}{0,0.2,0.25,0} +\definecolor{LightLightTC99} {cmyk}{0,0,0,0} \definecolor{LightLightLightGreenYellow} {cmyk}{0.02,0,0.08,0} \definecolor{LightLightLightYellow} {cmyk}{0,0,0.12,0} \definecolor{LightLightLightGoldenrod} {cmyk}{0,0.01,0.10,0} @@ -6371,6 +6547,16 @@ \definecolor{LightLightLightGray95} {cmyk}{0,0,0,0.115} \definecolor{LightLightLightBlack} {cmyk}{0,0,0,0.12} \definecolor{LightLightLightGray100} {cmyk}{0,0,0,0.125} +\definecolor{LightLightLightTC0} {cmyk}{0.05,0.05,0,0} +\definecolor{LightLightLightTC1} {cmyk}{0.075,0,0.086,0} +\definecolor{LightLightLightTC2} {cmyk}{0.05,0,0.086,0} +\definecolor{LightLightLightTC3} {cmyk}{0.025,0,0.125,0} +\definecolor{LightLightLightTC4} {cmyk}{0,0,0.125,0} +\definecolor{LightLightLightTC5} {cmyk}{0,0.025,0.125,0} +\definecolor{LightLightLightTC6} {cmyk}{0,0.05,0.125,0} +\definecolor{LightLightLightTC7} {cmyk}{0,0.0175,0.125,0} +\definecolor{LightLightLightTC8} {cmyk}{0,0.1,0.125,0} +\definecolor{LightLightLightTC99} {cmyk}{0,0,0,0} \definecolor{BlueRed5} {rgb} {0.15,0.17,0.55} \definecolor{BlueRed10} {rgb} {0.20,0.23,0.57} \definecolor{BlueRed15} {rgb} {0.24,0.29,0.60} @@ -6686,6 +6872,16 @@ \expandafter\xdef\csname res\the\loopcount\endcsname{\first@} \expandafter\xdef\csname sequence\the\loopcount\endcsname{#2@}} \def\remove@fromseq#1@{\expandafter\xdef\csname sequence\the\loopcount\endcsname{#1}} +\def\TC@get#1#2@{\xdef\char@num{`#1} + \ifnum\char@num=45 \xdef\TC@first@{*} + \else + \ifnum\char@num>57 \xdef\TC@first@{*} + \else + \xdef\TC@first@{#1} + \fi + \fi + \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\TC@first@} + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{#2@}} \def\sublogo@get#1 @{\xdef\first@{#1}} \def\re@write#1,#2@{% \xdef\third@{#2,@} @@ -6737,10 +6933,18 @@ \csname stack@@top#1\endcsname} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% \csname stack@@ttop#1\endcsname} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% + \csname stack@@tttop#1\endcsname} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% + \csname stack@@ttttop#1\endcsname} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% \csname stack@@bottom#1\endcsname} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% \csname stack@@bbottom#1\endcsname} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% + \csname stack@@bbbottom#1\endcsname} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% + \csname stack@@bbbbottom#1\endcsname} } \def\reorder@seqs#1{% \loopcount=0 @@ -6782,10 +6986,18 @@ \csname stack@top\the\loopcount\endcsname} \expandafter\xdef\csname stack@@ttop\the\loopcount\endcsname{% \csname stack@ttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@tttop\the\loopcount\endcsname{% + \csname stack@tttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@ttttop\the\loopcount\endcsname{% + \csname stack@ttttop\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bottom\the\loopcount\endcsname{% \csname stack@bottom\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bbottom\the\loopcount\endcsname{% \csname stack@bbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbbottom\the\loopcount\endcsname{% + \csname stack@bbbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbbbottom\the\loopcount\endcsname{% + \csname stack@bbbbottom\the\loopcount\endcsname} \ifnum\loopcount<\killseq@count \repeat \xdef\third@{#1} \loopcount=0 \innerloopcount=0 \xdef\last@{kill} \xdef\second@{e} @@ -7061,10 +7273,18 @@ \csname stack@top\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% \csname stack@ttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% + \csname stack@tttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% + \csname stack@ttttop\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% \csname stack@bottom\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% \csname stack@bbottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% + \csname stack@bbbottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% + \csname stack@bbbbottom\the\innerloopcount\endcsname} \expandafter\xdef\csname res@count\the\loopcount\endcsname{% \csname res@count\the\innerloopcount\endcsname} \expandafter\xdef\csname hide@seq\the\innerloopcount\endcsname{kill} @@ -7868,6 +8088,97 @@ \fi \ifx\sim@char\ampers@nd\else\write@PHDtopo\fi } +\def\include@T@coffee{% + \bgroup + \immediate\openin\structurefile = \TC@first@\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\TC@first@' not found} + {\MessageBreak + The file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No T-Coffee shading will be displayed (using "similar"). \MessageBreak + Type to proceed. \MessageBreak + Type X to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \simmodetrue \funcmodefalse \T@coffeefalse + \else + \message{} + \xdef\first@{} \xdef\temp@{*} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\temp@ \xdef\temp@{y} + \read\structurefile to \readline + \read\structurefile to \readline + \fi + \fi + \ifx\temp@\y@ \else\repeat + \loopcount=0 + \xdef\temp@{cons} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \if\second@ : + \advance\loopcount by 1\relax + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} + \fi + \fi + \ifx\first@\temp@\expandafter\xdef\csname T@coffee0\endcsname{} \else\repeat + \xdef\temp@{\the\loopcount} + \loopcount=0 + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \advance\loopcount by 1 + \ifnum\loopcount=\temp@ \loopcount=0 \fi + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname \third@} + \fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \loopcount=0 + \loop + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} + \advance\loopcount by 1 + \ifnum\loopcount=\temp@ \else\repeat + \egroup + \def\n@m@tch{{$\bullet$}} + \expandafter\def\csname fg@color0\endcsname{TC0} + \expandafter\def\csname fg@color1\endcsname{TC1} + \expandafter\def\csname fg@color2\endcsname{TC2} + \expandafter\def\csname fg@color3\endcsname{TC3} + \expandafter\def\csname fg@color4\endcsname{TC4} + \expandafter\def\csname fg@color5\endcsname{TC5} + \expandafter\def\csname fg@color6\endcsname{TC6} + \expandafter\def\csname fg@color7\endcsname{TC7} + \expandafter\def\csname fg@color8\endcsname{TC8} + \expandafter\def\csname fg@color9\endcsname{TC9} + \expandafter\def\csname fg@textcolor0\endcsname{Black} + \expandafter\def\csname fg@textcolor1\endcsname{Black} + \expandafter\def\csname fg@textcolor2\endcsname{Black} + \expandafter\def\csname fg@textcolor3\endcsname{Black} + \expandafter\def\csname fg@textcolor4\endcsname{Black} + \expandafter\def\csname fg@textcolor5\endcsname{Black} + \expandafter\def\csname fg@textcolor6\endcsname{Black} + \expandafter\def\csname fg@textcolor7\endcsname{Black} + \expandafter\def\csname fg@textcolor8\endcsname{Black} + \expandafter\def\csname fg@textcolor9\endcsname{Black} + \fi + } + \def\include@DSSP{% \xdef\first@{\csname optiondssp\the\loopcount\endcsname} \xdef\bottop@{\csname bottopdssp\the\loopcount\endcsname} @@ -9158,10 +9469,18 @@ \ifx\bottop@\temp@ \topfeaturetrue\fi \xdef\temp@{ttop} \ifx\bottop@\temp@ \ttopfeaturetrue\fi + \xdef\temp@{tttop} + \ifx\bottop@\temp@ \tttopfeaturetrue\fi + \xdef\temp@{ttttop} + \ifx\bottop@\temp@ \ttttopfeaturetrue\fi \xdef\temp@{bottom} \ifx\bottop@\temp@ \bottomfeaturetrue\fi \xdef\temp@{bbottom} \ifx\bottop@\temp@ \bbottomfeaturetrue\fi + \xdef\temp@{bbbottom} + \ifx\bottop@\temp@ \bbbottomfeaturetrue\fi + \xdef\temp@{bbbbottom} + \ifx\bottop@\temp@ \bbbbottomfeaturetrue\fi \xdef\seq@{#2} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ @@ -9226,6 +9545,10 @@ \ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi \xdef\temp@{bbottom} \ifx\bottop@\temp@ \xdef\bbottom@stretch{y}\fi + \xdef\temp@{bbbottom} + \ifx\bottop@\temp@ \xdef\bbbottom@stretch{y}\fi + \xdef\temp@{bbbbottom} + \ifx\bottop@\temp@ \xdef\bbbbottom@stretch{y}\fi \else \xdef\last@{color} \ifx\second@@\last@ @@ -9270,6 +9593,11 @@ \xdef\last@{bcons} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\last@{T-Coffee} + \ifx\f@color\last@ + \xdef\T@coffee@bcons{y} + \xdef\f@color{Gray50} + \fi \xdef\style@{cons[bar]:cons[\f@color][0]} \else \xdef\last@{ch} @@ -9290,6 +9618,11 @@ \xdef\last@{ccons} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{ColdHot}\fi + \xdef\last@{T-Coffee} + \ifx\f@color\last@ + \xdef\T@coffee@ccons{y} + \xdef\f@color{TC} + \fi \xdef\style@{cons[color]:cons[\f@color][0]} \else \xdef\style@{#4} \expandafter\getarrow@shape\temp@ @@ -9313,9 +9646,11 @@ \def\showfeaturename#1#2{\expandafter\xdef\csname featuretextn@me#1\endcsname{#2}} \def\showfeaturestylename#1#2{\expandafter\xdef\csname featurestylesn@me#1\endcsname{#2}} \def\hidefeaturename#1{\expandafter\xdef\csname featuretextn@me#1\endcsname{}} -\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{}} +\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{} + \xdef\featuretextn@metttop{}\xdef\featuretextn@mettttop{}\xdef\featuretextn@mebbbbottom{}\xdef\featuretextn@mebbbottom{}} \def\hidefeaturestylename#1{\expandafter\xdef\csname featurestylesn@me#1\endcsname{}} -\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{}} +\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{} + \xdef\featurestylesn@metttop{}\xdef\featurestylesn@mettttop{}\xdef\featurestylesn@mebbbbottom{}\xdef\featurestylesn@mebbbottom{}} \def\seqtype#1{\xdef\seq@type{#1} \if\seq@type P \xdef\prefix@{pep} \else \if\seq@type p \xdef\seq@type{P} \xdef\prefix@{pep} @@ -9375,8 +9710,12 @@ \def\vblockspace#1{\def\block@skip{\vspace{#1}}} \def\topspace#1{\def\t@sp@ce{#1}} \def\ttopspace#1{\def\tt@sp@ce{#1}} +\def\tttopspace#1{\def\ttt@sp@ce{#1}} +\def\ttttopspace#1{\def\tttt@sp@ce{#1}} \def\bottomspace#1{\def\b@sp@ce{#1}} \def\bbottomspace#1{\def\bb@sp@ce{#1}} +\def\bbbottomspace#1{\def\bbb@sp@ce{#1}} +\def\bbbbottomspace#1{\def\bbbb@sp@ce{#1}} \def\fixblockspace{\fix@true} \def\flexblockspace{\fix@false} \def\nosepline{\def\seq@skip{\relax}} @@ -9400,6 +9739,7 @@ \fi \fi} \newcommand{\shadingmode}[2][-1]{% + \T@coffeefalse \xdef\last@{#2} \xdef\first@{identical} \ifx\first@\last@ @@ -9445,6 +9785,12 @@ \else \simmodefalse \funcmodetrue \func@shading{#1} \xdef\seq@type{P} \xdef\prefix@{pep} \fi \else + \xdef\first@{T-Coffee} + \ifx\first@\last@ + \simmodefalse \funcmodefalse \T@coffeetrue + \xdef\second@{#1 @} \expandafter\check@letter\second@ + \ifletter \xdef\TC@first@{#1}\include@T@coffee\fi + \else \xdef\first@{diverse} \ifx\first@\last@ \xdef\last@{#1} @@ -9463,7 +9809,7 @@ \else \message{} \simmodetrue \funcmodefalse - \fi\fi\fi\fi} + \fi\fi\fi\fi\fi} \newcommand\allmatchspecial[1][100]{% \ifnum#1<0 \xdef\all@thresh@ld{0} @@ -9480,8 +9826,8 @@ \ifx\first@\second@\def\gap@char{o} \else\def\gap@char{#1}\fi} \def\gaprule#1{\def\gap@rulethick{#1}} -\def\setends#1#2{% - \xdef\start@seq{#1} +\newcommand{\setends}[3][&]{% + \xdef\start@seq{#2} \xdef\temp@{consensus} \ifx\start@seq\temp@ \message{<\noexpand\setends does not accept `consensus'>} @@ -9491,14 +9837,14 @@ \xdef\first@{\start@seq} \ifletter \get@name@number \xdef\start@seq{\first@} \fi \ifnum\start@seq>\seq@count - \message{<\noexpand\setends{} error: sequence `#1' not defined>} + \message{<\noexpand\setends{} error: sequence `#2' not defined>} \xdef\start@seq{0} \else \ifnum\start@seq<1 - \message{<\noexpand\setends{} error: sequence `#1' not defined>} + \message{<\noexpand\setends{} error: sequence `#2' not defined>} \xdef\start@seq{0} \else - \xdef\second@{#2@} \expandafter\get@nums\second@ + \xdef\second@{#3@} \expandafter\get@nums\second@ \xdef\start@num{\first@} \xdef\end@num{\second@} \ifnum\start@num=0 \xdef\allow@zero{y}\fi \ifnum\end@num=0 \xdef\allow@zero{y}\fi @@ -9506,20 +9852,21 @@ \fi \fi \fi + \xdef\first@{#1}\ifx\first@\ampers@nd\else\startnumber{#2}{#1}\fi } -\def\startnumber#1#2{% - \xdef\first@{#1} \xdef\second@{consensus} +\newcommand{\startnumber}[3][&]{% + \xdef\first@{#2} \xdef\second@{consensus} \ifx\first@\second@ - \ifnum#2=0 \xdef\allow@zero{y} \fi + \ifnum#3=0 \xdef\allow@zero{y} \fi \expandafter\xdef\csname seq@start0\endcsname{#2} - \cons@count=#2 \advance\cons@count by -1\relax + \cons@count=#3 \advance\cons@count by -1\relax \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} \else - \xdef\first@{#1 @} \expandafter\check@letter\first@ - \xdef\first@{#1} \ifletter \get@name@number \fi - \ifnum\first@>\seq@count \message{} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count \message{} \else - \xdef\second@{#2} + \xdef\second@{#3} \ifnum\second@=0 \xdef\allow@zero{y} \fi \expandafter\xdef\csname seq@start\first@\endcsname{\second@} \res@count=\second@ @@ -9527,6 +9874,7 @@ \expandafter\xdef\csname res@count\first@\endcsname{\the\res@count} \fi \fi + \xdef\first@{#1}\ifx\first@\ampers@nd\else\setends{#2}{#1}\fi } \def\seqlength#1#2{% \xdef\first@{#1 @} \expandafter\check@letter\first@ @@ -10491,16 +10839,24 @@ \ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi \fi\fi\fi\fi} \def\featurenamescolor#1{% + \expandafter\xdef\csname ftext@fg@ttttop\endcsname{#1} + \expandafter\xdef\csname ftext@fg@tttop\endcsname{#1} \expandafter\xdef\csname ftext@fg@ttop\endcsname{#1} \expandafter\xdef\csname ftext@fg@top\endcsname{#1} \expandafter\xdef\csname ftext@fg@bottom\endcsname{#1} \expandafter\xdef\csname ftext@fg@bbottom\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bbbottom\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bbbbottom\endcsname{#1} } \def\featurestylenamescolor#1{% + \expandafter\xdef\csname fstyles@fg@ttttop\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@tttop\endcsname{#1} \expandafter\xdef\csname fstyles@fg@ttop\endcsname{#1} \expandafter\xdef\csname fstyles@fg@top\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bottom\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bbottom\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bbbottom\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bbbbottom\endcsname{#1} } \def\featurenamecolor#1#2{\expandafter\xdef\csname ftext@fg@#1\endcsname{#2}} \def\featurestylenamecolor#1#2{\expandafter\xdef\csname fstyles@fg@#1\endcsname{#2}} @@ -10611,6 +10967,9 @@ \logo@rule\kern-\wd1\textcolor{White}{\texttt{d}}% \texttt{e}} +\def\includeTCoffee#1{% + \xdef\TC@first@{#1}\include@T@coffee} + \def\firstcolumnDSSP{\xdef\fc@DSSP{y}} \def\secondcolumnDSSP{\xdef\fc@DSSP{n}} @@ -11669,6 +12028,66 @@ \fi \ifnum\loopcount<\seq@count \repeat} +\def\T@coffee@shade{% + \loopcount=0 + \expandafter\ifx\csname tint@seq0\endcsname\y@ + \expandafter\xdef\csname tint@seq0\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq0\endcsname\y@ + \expandafter\xdef\csname emph@seq0\endcsname{n} + \xdef\first@{,\first@}\fi + \xdef\second@{\csname TC@num0\endcsname} + \xdef\consensus{\consensus\second@\n@m@tch} + \xdef\constopo{\constopo\second@} + \loop + \advance\loopcount by 1 + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\second@{\csname TC@num\the\loopcount\endcsname} + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\gap@char}\def\second@{*} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \fi + \fi + \fi + \xdef\third@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + *\first@} + \else + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + \second@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat} + \def\getregion@fromstack@first{% \expandafter\getregion@fromstack{\the\loopcount} \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd @@ -12089,6 +12508,18 @@ \multiply\temp@count by 2 \divide\temp@count by \innerloopcount \xdef\cons@val{\the\temp@count} + \ifx\T@coffee@bcons\y@ + \xdef\cons@val{\csname TC@num0\endcsname} + \if\cons@val * + \xdef\cons@val{99} + \fi \message{(b(\cons@val)b)} + \fi + \ifx\T@coffee@ccons\y@ + \xdef\cons@val{\csname TC@num0\endcsname} + \if\cons@val * + \xdef\cons@val{99} + \fi \message{(c(\cons@val)c)} + \fi \fi } @@ -12989,10 +13420,15 @@ \def\c@nsensus{% \ifnum\pos@count>\res@perline \else + \loopcount=0 \global\advance\cons@count by 1\relax \ifnum\cons@count=0\relax \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi \fi + \ifT@coffee + \xdef\TC@line{\csname T@coffee0\endcsname} + \expandafter\TC@get\TC@line + \fi \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} \ifx\hide@true\y@ \expandafter\ifx\csname hidestart0\endcsname\ampers@nd @@ -13009,9 +13445,13 @@ \fi \fi \fi - \loopcount=0 \loop \advance\loopcount by 1 + \ifT@coffee + \xdef\TC@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\TC@line + \xdef\TC@first@{\csname TC@num\the\loopcount\endcsname} + \fi \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\residue@get\seq@line \xdef\first@{\csname res\the\loopcount\endcsname} @@ -13075,6 +13515,14 @@ \ifnum\v@lseqttop=\loopcount \xdef\v@lttop{\v@lttop,\csname \ffourth@ttop\first@\endcsname} \fi\fi + \ifx\collect@valtttop\yes + \ifnum\v@lseqtttop=\loopcount + \xdef\v@ltttop{\v@ltttop,\csname \ffourth@tttop\first@\endcsname} + \fi\fi + \ifx\collect@valttttop\yes + \ifnum\v@lseqttttop=\loopcount + \xdef\v@lttttop{\v@lttttop,\csname \ffourth@ttttop\first@\endcsname} + \fi\fi \ifx\collect@valbottom\yes \ifnum\v@lseqbottom=\loopcount \xdef\v@lbottom{\v@lbottom,\csname \ffourth@bottom\first@\endcsname} @@ -13083,6 +13531,14 @@ \ifnum\v@lseqbbottom=\loopcount \xdef\v@lbbottom{\v@lbbottom,\csname \ffourth@bbottom\first@\endcsname} \fi\fi + \ifx\collect@valbbbottom\yes + \ifnum\v@lseqbbbottom=\loopcount + \xdef\v@lbbbottom{\v@lbbbottom,\csname \ffourth@bbbottom\first@\endcsname} + \fi\fi + \ifx\collect@valbbbbottom\yes + \ifnum\v@lseqbbbbottom=\loopcount + \xdef\v@lbbbbottom{\v@lbbbbottom,\csname \ffourth@bbbbottom\first@\endcsname} + \fi\fi \fi \ifx\collect@restop\yes \ifnum\tr@nsseqtop=\loopcount @@ -13108,6 +13564,30 @@ \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countttop{\the\innerloopcount} \fi\fi + \ifx\collect@restttop\yes + \ifnum\tr@nsseqtttop=\loopcount + \xdef\last@restttop{\last@@restttop} + \xdef\last@@restttop{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatetttop{\tr@nslatetttop\first@} + \fi + \innerloopcount=\triple@counttttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@counttttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resttttop\yes + \ifnum\tr@nsseqttttop=\loopcount + \xdef\last@resttttop{\last@@resttttop} + \xdef\last@@resttttop{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatettttop{\tr@nslatettttop\first@} + \fi + \innerloopcount=\triple@countttttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countttttop{\the\innerloopcount} + \fi\fi \ifx\collect@resbottom\yes \ifnum\tr@nsseqbottom=\loopcount \xdef\last@resbottom{\last@@resbottom} @@ -13132,6 +13612,30 @@ \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countbbottom{\the\innerloopcount} \fi\fi + \ifx\collect@resbbbottom\yes + \ifnum\tr@nsseqbbbottom=\loopcount + \xdef\last@resbbbottom{\last@@resbbbottom} + \xdef\last@@resbbbottom{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@} + \fi + \innerloopcount=\triple@countbbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbbottom{\the\innerloopcount} + \fi\fi + \ifx\collect@resbbbbottom\yes + \ifnum\tr@nsseqbbbbottom=\loopcount + \xdef\last@resbbbbottom{\last@@resbbbbottom} + \xdef\last@@resbbbbottom{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@} + \fi + \innerloopcount=\triple@countbbbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbbbottom{\the\innerloopcount} + \fi\fi \innerloopcount=\csname mol@weight\the\loopcount\endcsname \advance\innerloopcount by \csname \prefix@ mw\first@\endcsname \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{% @@ -13151,6 +13655,14 @@ \ifnum\v@lseqttop=\loopcount \xdef\v@lttop{\v@lttop,N} \fi\fi + \ifx\collect@valtttop\yes + \ifnum\v@lseqtttop=\loopcount + \xdef\v@ltttop{\v@ltttop,N} + \fi\fi + \ifx\collect@valttttop\yes + \ifnum\v@lseqttttop=\loopcount + \xdef\v@lttttop{\v@lttttop,N} + \fi\fi \ifx\collect@valbottom\yes \ifnum\v@lseqbottom=\loopcount \xdef\v@lbottom{\v@lbottom,N} @@ -13159,6 +13671,14 @@ \ifnum\v@lseqbbottom=\loopcount \xdef\v@lbbottom{\v@lbbottom,N} \fi\fi + \ifx\collect@valbbbottom\yes + \ifnum\v@lseqbbbottom=\loopcount + \xdef\v@lbbbottom{\v@lbbbottom,N} + \fi\fi + \ifx\collect@valbbbbottom\yes + \ifnum\v@lseqbbbbottom=\loopcount + \xdef\v@lbbbbottom{\v@lbbbbottom,N} + \fi\fi \ifx\collect@restop\yes \ifnum\tr@nsseqtop=\loopcount \xdef\tr@nslatetop{\tr@nslatetop -} @@ -13167,6 +13687,14 @@ \ifnum\tr@nsseqttop=\loopcount \xdef\tr@nslatettop{\tr@nslatettop -} \fi\fi + \ifx\collect@restttop\yes + \ifnum\tr@nsseqtttop=\loopcount + \xdef\tr@nslatetttop{\tr@nslatetttop -} + \fi\fi + \ifx\collect@resttttop\yes + \ifnum\tr@nsseqttttop=\loopcount + \xdef\tr@nslatettttop{\tr@nslatettttop -} + \fi\fi \ifx\collect@resbottom\yes \ifnum\tr@nsseqbottom=\loopcount \xdef\tr@nslatebottom{\tr@nslatebottom -} @@ -13175,6 +13703,14 @@ \ifnum\tr@nsseqbbottom=\loopcount \xdef\tr@nslatebbottom{\tr@nslatebbottom -} \fi\fi + \ifx\collect@resbbbottom\yes + \ifnum\tr@nsseqbbbottom=\loopcount + \xdef\tr@nslatebbbottom{\tr@nslatebbbottom -} + \fi\fi + \ifx\collect@resbbbbottom\yes + \ifnum\tr@nsseqbbbbottom=\loopcount + \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom -} + \fi\fi \fi \fi \ifnum\loopcount<\seq@count \repeat @@ -13212,6 +13748,18 @@ \sum@up@cons \xdef\v@lttop{\v@lttop,\cons@val} \fi + \ifx\collect@cons@graphtttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@ltttop{\v@ltttop,\cons@val} + \fi + \ifx\collect@cons@graphttttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lttttop{\v@lttttop,\cons@val} + \fi \ifx\collect@cons@graphbottom\yes \outerloopcount=1\relax \temp@count=0\relax @@ -13224,6 +13772,18 @@ \sum@up@cons \xdef\v@lbbottom{\v@lbbottom,\cons@val} \fi + \ifx\collect@cons@graphbbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbbottom{\v@lbbbottom,\cons@val} + \fi + \ifx\collect@cons@graphbbbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbbbottom{\v@lbbbbottom,\cons@val} + \fi \ifx\collect@cons@colors\y@ \outerloopcount=1\relax \temp@count=0\relax @@ -13260,10 +13820,14 @@ \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 + \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi + \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi + \iftttopfeaturenow \xdef\bottop@{tttop} \calc@feature \fi + \ifttttopfeaturenow \xdef\bottop@{ttttop} \calc@feature \fi + \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \ifbbbottomfeaturenow \xdef\bottop@{bbbottom} \calc@feature \fi + \ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi \ifx\hide@now\y@ \xdef\hidebar@on{1} \ifnum\pos@count=\bar@pos @@ -13279,13 +13843,16 @@ \ifshow@logo \calc@logo \fi \ifall@fshade \all@funcshade \else - \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi - \xdef\match@case{0} \xdef\m@x{1} - \iffuncmode - \xdef\prfx{\prefix@} \xdef\prefix@{func} \xdef\c@se{3} \check@sim - \xdef\prefix@{\prfx} - \else \xdef\c@se{1} \check@ident \fi - \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi + \ifT@coffee \T@coffee@shade + \else + \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi + \xdef\match@case{0} \xdef\m@x{1} + \iffuncmode + \xdef\prfx{\prefix@} \xdef\prefix@{func} \xdef\c@se{3} \check@sim + \xdef\prefix@{\prfx} + \else \xdef\c@se{1} \check@ident \fi + \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi + \fi \fi %%%%%%%% \fi @@ -13297,10 +13864,14 @@ \global\stop@true \loopcount=\pos@count \advance\loopcount by -1 \relax \res@perline=\loopcount - \iftopfeature \xdef\bottop@{top} \calc@feature \fi - \ifttopfeature \xdef\bottop@{ttop} \calc@feature \fi - \ifbottomfeature \xdef\bottop@{bottom} \calc@feature \fi - \ifbbottomfeature \xdef\bottop@{bbottom} \calc@feature \fi + \iftopfeature \xdef\bottop@{top} \calc@feature \fi + \ifttopfeature \xdef\bottop@{ttop} \calc@feature \fi + \iftttopfeature \xdef\bottop@{tttop} \calc@feature \fi + \ifttttopfeature \xdef\bottop@{ttttop} \calc@feature \fi + \ifbottomfeature \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeature \xdef\bottop@{bbottom} \calc@feature \fi + \ifbbbottomfeature \xdef\bottop@{bbbottom} \calc@feature \fi + \ifbbbbottomfeature \xdef\bottop@{bbbbottom} \calc@feature \fi \pos@count=0 \fi \fi} @@ -13315,6 +13886,10 @@ \def\c@unt{% \advance\loopcount by 1 + \ifT@coffee + \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\seq@line + \fi \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\residue@get\seq@line \xdef\first@{\csname res\the\loopcount\endcsname} @@ -13339,6 +13914,10 @@ \advance\end@count by 1 \ifnum\end@count<\start@number \loopcount=0 + \ifT@coffee + \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\seq@line + \fi \c@unt \count@first \fi} @@ -13354,8 +13933,10 @@ \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse \framenowfalse \fi - \topfeaturenowfalse \bottomfeaturenowfalse - \ttopfeaturenowfalse \bbottomfeaturenowfalse + \topfeaturenowfalse \bottomfeaturenowfalse + \ttopfeaturenowfalse \bbottomfeaturenowfalse + \tttopfeaturenowfalse \bbbottomfeaturenowfalse + \ttttopfeaturenowfalse \bbbbottomfeaturenowfalse \innerloopcount=\cons@count \advance\innerloopcount by \res@perline \advance\innerloopcount by 1 \loopcount=0 @@ -13422,6 +14003,28 @@ \fi \fi \fi + \iftttopfeature + \xdef\bottop@{tttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \tttopfeaturenowtrue + \fi + \fi + \fi + \ifttttopfeature + \xdef\bottop@{ttttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttttopfeaturenowtrue + \fi + \fi + \fi \ifbottomfeature \xdef\bottop@{bottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd @@ -13444,12 +14047,35 @@ \fi \fi \fi + \ifbbbottomfeature + \xdef\bottop@{bbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbbottomfeature + \xdef\bottop@{bbbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbbottomfeaturenowtrue + \fi + \fi + \fi \loop \advance\loopcount by 1 \ifnumbers@left - \innerloopcount=\csname seq@len\the\loopcount\endcsname + \innerloopcount=\csname seq@len\the\loopcount\endcsname\relax \expandafter\ifnum\csname res@count\the\loopcount\endcsname=% \innerloopcount + \res@count=\innerloopcount \else \res@count=\csname res@count\the\loopcount\endcsname \advance\res@count by 1 @@ -13548,6 +14174,28 @@ \fi \fi \fi + \iftttopfeature + \xdef\bottop@{tttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \tttopfeaturenowtrue + \fi + \fi + \fi + \ifttttopfeature + \xdef\bottop@{ttttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttttopfeaturenowtrue + \fi + \fi + \fi \ifbottomfeature \xdef\bottop@{bottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd @@ -13570,6 +14218,28 @@ \fi \fi \fi + \ifbbbottomfeature + \xdef\bottop@{bbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbbottomfeature + \xdef\bottop@{bbbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbbottomfeaturenowtrue + \fi + \fi + \fi \ifnum\loopcount<\seq@count \repeat \c@nsensus} @@ -13588,6 +14258,115 @@ \fontfamily{\legend@family}% \fontseries{\legend@series}% \fontshape{\legend@shape}% + \ifT@coffee + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \def\res@@style{\csname no@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}% + \expandafter\ifx\csname n@m@tch\the\loopcount\endcsname\low@up% + \def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \textcolor{TC0}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{schlecht}% + \else\ifsp@nish\kern2ex\legend@size{mala}% + \else\kern2ex\legend@size{bad}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC1}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC2}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC3}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC4}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{Grad der}% + \else\ifsp@nish\kern2ex\legend@size{conservaci\'on}% + \else\kern2ex\legend@size{level of}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC5}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{Konservierung}% + \else\ifsp@nish\kern2ex\legend@size{}% + \else\kern2ex\legend@size{conservation}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC6}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC7}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC8}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC9}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{gut}% + \else\ifsp@nish\kern2ex\legend@size{buena}% + \else\kern2ex\legend@size{good}\fi\fi} + \newline\hbox{}% + \else \iffuncmode \ifnum\fgroup@num>0 \loopcount=0 @@ -13682,6 +14461,7 @@ \newline\hbox{}\noindent \fi \fi + \fi } \def\put@name<#1>#2@{% \ifnames@% @@ -13729,6 +14509,13 @@ \xdef\temp@@{}% \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% \else% + \ifT@coffee% + \xdef\boxc@l@r{\csname fg@color#1\endcsname}% + \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% + \def\res@@style{\csname func@style#1\endcsname}% + \if\last@ *\def\last@{0}\fi + \if\last@ /\def\last@{10}\fi + \else% \iffuncmode% \xdef\boxc@l@r{\csname fg@color#1\endcsname}% \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% @@ -13754,7 +14541,7 @@ \def\res@@style{\csname relax\endcsname}% \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \def\res@@style{\csname relax\endcsname}% - \fi\fi\fi% + \fi\fi\fi\fi% \ifx\second@\comm@% \def\temp@{\res@style}% \expandafter\get@second@\first@% @@ -13791,20 +14578,48 @@ \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% \else% \ifx\collect@cons@colors\y@% + \if\last@ *% + \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% + \else% + \if\last@ /% + \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \else% \expandafter\get@item\first@@@% \xdef\first@@@{\first@}% \ifx\box@scale\y@% \xdef\boxc@l@r{\c@nssc@le\fourth@}% \else% - \xdef\boxc@l@r{\c@nssc@le}% + \xdef\first@{T-Coffee}% + \ifx\first@\c@nssc@le% + \xdef\boxc@l@r{TC\last@}% + \else + \xdef\boxc@l@r{\c@nssc@le}% + \fi% \fi% \ifx\text@scale\y@% \xdef\textc@l@r{\c@nsc@l\fourth@}% \else% - \xdef\textc@l@r{\c@nsc@l}% - \fi% + \xdef\first@{T-Coffee}% + \ifx\first@\c@nsc@l% + \xdef\textc@l@r{TC\last@}% + \else + \xdef\textc@l@r{\c@nsc@l}% + \fi% + \fi\fi\fi% \def\res@@style{\csname relax\endcsname}% \else% + \ifT@coffee% + \if\last@ *% + \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% + \else% + \if\last@ /% + \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \else% + \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}% + \def\res@@style{\csname relax\endcsname}% + \fi% + \fi% + \else% \ifcase#1\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}% \def\res@@style{\all@style}% \or\xdef\boxc@l@r{\Identical}\xdef\textc@l@r{\TextIdentical}% @@ -13823,7 +14638,7 @@ \def\res@@style{\csname relax\endcsname}% \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \def\res@@style{\csname relax\endcsname}% - \fi\fi\fi% + \fi\fi\fi\fi% \xdef\first@{#3@}% \xdef\second@{#2}% \ifx\second@\comm@% @@ -14098,13 +14913,23 @@ \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% \else% \xdef\last@{ttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \xdef\last@{tttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \xdef\last@{ttttop}% \ifx\bottop@\last@% \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% \else% \raisebox{1.75\arrow@height}{\ensuremath{\underbrace{\hbox to % \second@\box@width{}}}}% - \fi\fi}% + \fi\fi\fi\fi}% \else% \xdef\last@{fill}% \ifx\second@@\last@% @@ -14169,12 +14994,15 @@ \ifx\second@@\N@\hbox to \box@width{\hss}% \else \loopcount=\second@@% - \advance\loopcount by -\pm@shift% - \advance\loopcount by 4% - \divide\loopcount by 5% - \multiply\loopcount by 5% - \ifnum\loopcount>100\loopcount=100\fi% - \ifnum\loopcount<5\loopcount=5\fi% + \ifx\T@coffee@ccons\y@% + \else% + \advance\loopcount by -\pm@shift% + \advance\loopcount by 4% + \divide\loopcount by 5% + \multiply\loopcount by 5% + \ifnum\loopcount>100\loopcount=100\fi% + \ifnum\loopcount<5\loopcount=5\fi% + \fi% \setlength\arrow@height{50\box@height}% \divide\arrow@height by 100\relax% \setlength\arrow@height{\sc@le@stretch\arrow@height}% @@ -14204,7 +15032,13 @@ {\vrule height\arrow@height width\box@width}}\hss}% \kern-\box@width% \fi% + \ifx\T@coffee@bcons\y@% + \ifnum\second@@=99 \xdef\second@@{0}\fi% + \fi \setlength\arrow@height{\second@@\box@height}% + \ifx\T@coffee@bcons\y@% + \setlength\arrow@height{11\arrow@height}% + \fi \divide\arrow@height by 100\relax% \setlength\arrow@height{\b@r@stretch\arrow@height}% \ifdim\arrow@height<0pt% @@ -14339,7 +15173,13 @@ \xdef\temp@{ttop}% \ifx\bottop@\temp@ \xdef\last@{0.25}% \else% - \xdef\last@{-0.25}\fi\fi% + \xdef\temp@{tttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\temp@{ttttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\last@{-0.25}\fi\fi\fi\fi% \textcolor{\f@color}{% \raisebox{\last@\arrow@height}{% \if\first@@ ,% @@ -14568,12 +15408,46 @@ \def\put@feature{% \vspace{-\baselineskip}% \newline\hbox{}% + \xdef\temp@{ttttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else% + \xdef\temp@{tttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else% \xdef\temp@{ttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -14583,14 +15457,14 @@ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{top}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -14600,12 +15474,12 @@ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -14615,14 +15489,14 @@ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% - \fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \fi\fi\fi\fi% \newline\hbox{}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -14632,14 +15506,31 @@ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{ttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \xdef\temp@{tttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -14649,12 +15540,29 @@ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \xdef\temp@{ttttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \xdef\first@{\csname textfeature\bottop@\endcsname @}% @@ -14665,8 +15573,8 @@ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% - \fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \fi\fi\fi\fi% \newline\hbox{}% } \def\put@@@frame#1{% @@ -15298,10 +16206,32 @@ \def\set@lines{% \pos@count=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}% + \xdef\featurepostop{1} \xdef\featureposbottom{1}% + \xdef\featureposttop{1} \xdef\featureposbbottom{1}% + \xdef\featurepostttop{1} \xdef\featureposbbbottom{1}% + \xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}% \findc@nsensus% \noindent% + \ifnum\feature@ttttop=1 + \ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi + \xdef\bottop@{ttttop}% + \put@feature% + \vspace{\tttt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi + \ifnum\feature@tttop=1 + \ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi + \xdef\bottop@{tttop}% + \put@feature% + \vspace{\ttt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi \ifnum\feature@ttop=1 \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi \xdef\bottop@{ttop}% @@ -15464,12 +16394,56 @@ \fi \fi \fi + \ifnum\feature@bbbottom=1 % + \ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi% + \xdef\bottop@{bbbottom}% + \vspace{\bbb@sp@ce}% + \if\bbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature% + \else + \iffix@ + \if\bbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbbottomfeature + \vspace{\bbb@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi + \fi + \fi + \ifnum\feature@bbbbottom=1 % + \ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi% + \xdef\bottop@{bbbbottom}% + \vspace{\bbbb@sp@ce}% + \if\bbbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature% + \else + \iffix@ + \if\bbbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbbbottomfeature + \vspace{\bbbb@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi + \fi + \fi \xdef\consensus{} \xdef\ruler@{} - \xdef\styleframe{} \xdef\stylehidebar{} - \xdef\textfeaturetop{} \xdef\textfeaturebottom{} - \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} - \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} - \xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{} + \xdef\styleframe{} \xdef\stylehidebar{} + \xdef\textfeaturetop{} \xdef\textfeaturebottom{} + \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} + \xdef\textfeaturetttop{} \xdef\textfeaturebbbottom{} + \xdef\textfeaturettttop{} \xdef\textfeaturebbbbottom{} + \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} + \xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{} + \xdef\stylefeaturetttop{} \xdef\stylefeaturebbbottom{} + \xdef\stylefeaturettttop{} \xdef\stylefeaturebbbbottom{} \loopcount=0 \loop \advance\loopcount by 1 @@ -15491,6 +16465,10 @@ \advance\loopcount by 1\relax \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\remove@fromseq\seq@line + \ifT@coffee + \xdef\TC@cons{\csname TC0\endcsname} + \expandafter\remove@fromTC\TC@cons + \fi \ifnum\loopcount<\seq@count \repeat \fi \ifstop@ @@ -15573,15 +16551,23 @@ \xdef\consensus{} \xdef\constopo{} \xdef\frame@on{0} - \xdef\textfeaturetop{} \xdef\featureontop{0} - \xdef\textfeaturettop{} \xdef\featureonttop{0} - \xdef\textfeaturebottom{} \xdef\featureonbottom{0} - \xdef\textfeaturebbottom{}\xdef\featureonbbottom{0} + \xdef\textfeaturetop{} \xdef\featureontop{0} + \xdef\textfeaturettop{} \xdef\featureonttop{0} + \xdef\textfeaturetttop{} \xdef\featureontttop{0} + \xdef\textfeaturettttop{} \xdef\featureonttttop{0} + \xdef\textfeaturebottom{} \xdef\featureonbottom{0} + \xdef\textfeaturebbottom{} \xdef\featureonbbottom{0} + \xdef\textfeaturebbbottom{} \xdef\featureonbbbottom{0} + \xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0} \xdef\styleframe{} \xdef\stylehidebar{} \xdef\stylefeaturetop{} \xdef\stylefeaturettop{} + \xdef\stylefeaturetttop{} + \xdef\stylefeaturettttop{} \xdef\stylefeaturebottom{} - \xdef\stylefeaturebbottom{}} + \xdef\stylefeaturebbottom{} + \xdef\stylefeaturebbbottom{} + \xdef\stylefeaturebbbbottom{}} \def\guess@protein{\seqtype{P}\message{}} \def\guess@DNA{\seqtype{N}\message{}} \def\residue@count{% @@ -15673,7 +16659,12 @@ \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 + \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi + \total@count=\end@count\relax + \xdef\first@{\csname res@count\start@seq\endcsname} + \advance\total@count by \first@\relax + \xdef\first@{\the\total@count} + \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi \ifshow@sublogo \prep@sublogo \fi \ifshow@logo \prep@logo \fi \ifnum\seq@pointer>\res@perline \block@output \fi @@ -15717,7 +16708,12 @@ \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 + \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi + \total@count=\end@count\relax + \xdef\first@{\csname res@count\start@seq\endcsname} + \advance\total@count by \first@\relax + \xdef\first@{\the\total@count} + \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi \ifshow@sublogo \prep@sublogo \fi \ifshow@logo \prep@logo \fi \ifnum\seq@pointer>\res@perline \block@output \fi @@ -15858,8 +16854,12 @@ \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes} @@ -15871,6 +16871,7 @@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{false} + \expandafter\xdef\csname hide@@@seq\the\loopcount\endcsname{false} \expandafter\xdef\csname hide@name\the\loopcount\endcsname{no} \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} \expandafter\xdef\csname hide@number\the\loopcount\endcsname{no} @@ -15882,8 +16883,12 @@ \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{no} \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{0} @@ -15925,10 +16930,14 @@ \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} - \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bbottom}\expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \fontfamily{\namestext@family} \fontseries{\namestext@series} \fontshape{\namestext@shape} @@ -15972,17 +16981,18 @@ \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} - \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bbottom}\expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \innerloopcount = \csname seq@len\the\loopcount\endcsname \advance\innerloopcount by \csname seq@start\the\loopcount\endcsname \advance\innerloopcount by -1 \expandafter\xdef\csname seq@len\the\loopcount\endcsname{\the\innerloopcount} - \ifsh@wg@ps - \expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999} - \fi \advance\loopcount by 1 \ifnum\loopcount>\seq@count \else \repeat \advance\name@width by 1em @@ -16192,23 +17202,29 @@ \advance\loopcount by 1\relax \xdef\@lign@count{\the\loopcount} \start@true \xdef\start@num{1} \xdef\start@seq{0} -\stop@false \xdef\end@num{99999999} \xdef\seq@regions{0} +\stop@false \xdef\end@num{n} \xdef\seq@regions{0} \cons@count=0 \expandafter\xdef\csname res@count0\endcsname{0} \xdef\allow@zero{n} \xdef\c@ns@shift{0} \regionalshadefalse\regionalemphfalse\regionaltintfalse \frame@false \xdef\ruler@rot{0} -\topfeaturefalse\bottomfeaturefalse -\ttopfeaturefalse\bbottomfeaturefalse +\topfeaturefalse \bottomfeaturefalse +\ttopfeaturefalse \bbottomfeaturefalse +\tttopfeaturefalse \bbbottomfeaturefalse +\ttttopfeaturefalse \bbbbottomfeaturefalse \all@fshadefalse\hidecharfalse \xdef\finger@linenum{0} \xdef\hide@seqs{n} \xdef\dssp@num{0} \xdef\stride@num{0} \xdef\PHD@num{0} \xdef\HMMTOP@num{0} -\xdef\bottop@{top} \expandafter\xdef\csname feature@\bottop@\endcsname{0} -\xdef\bottop@{ttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} -\xdef\bottop@{bottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} -\xdef\bottop@{bbottom}\expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{top} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{ttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{tttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{ttttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbbbottom}\expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\frame@{0} \xdef\show@Hdssp{no} \xdef\show@Gdssp{no} \xdef\show@Idssp{no} \xdef\show@Edssp{no} \xdef\show@Bdssp{no} \xdef\show@Tdssp{no} @@ -16218,23 +17234,36 @@ \xdef\show@itop{no} \xdef\show@etop{no} \xdef\show@TMtop{no} \xdef\show@i@HMMTOP{no} \xdef\show@e@HMMTOP{no} \xdef\show@TM@HMMTOP{no} \xdef\show@Hsec{no} \xdef\show@Esec{no} -\xdef\collect@restop{no} \xdef\collect@resttop{no} -\xdef\collect@resbottom{no} \xdef\collect@resbbottom{no} -\xdef\tr@nslatetop{} \xdef\tr@nslatettop{} -\xdef\tr@nslatebottom{} \xdef\tr@nslatebbottom{} -\xdef\tr@nsseqtop{0} \xdef\tr@nsseqttop{0} -\xdef\tr@nsseqbottom{0} \xdef\tr@nsseqbbottom{0} -\xdef\triple@counttop{0} \xdef\triple@countttop{0} -\xdef\triple@countbottom{0} \xdef\triple@countbbottom{0} -\xdef\last@@restop{} \xdef\last@@resttop{} -\xdef\last@@resbottom{} \xdef\last@@resbbottom{} -\xdef\out@put{y} \xdef\m@p{no} -\xdef\t@sp@ce{0mm} \xdef\tt@sp@ce{0mm} -\xdef\b@sp@ce{0mm} \xdef\bb@sp@ce{0mm} +\xdef\collect@restop{no} \xdef\collect@resttop{no} +\xdef\collect@restttop{no} \xdef\collect@resttttop{no} +\xdef\collect@resbottom{no} \xdef\collect@resbbottom{no} +\xdef\collect@resbbbottom{no}\xdef\collect@resbbbbottom{no} +\xdef\tr@nslatetop{} \xdef\tr@nslatettop{} +\xdef\tr@nslatetttop{} \xdef\tr@nslatettttop{} +\xdef\tr@nslatebottom{} \xdef\tr@nslatebbottom{} +\xdef\tr@nslatebbbottom{} \xdef\tr@nslatebbbbottom{} +\xdef\tr@nsseqtop{0} \xdef\tr@nsseqttop{0} +\xdef\tr@nsseqtttop{0} \xdef\tr@nsseqttttop{0} +\xdef\tr@nsseqbottom{0} \xdef\tr@nsseqbbottom{0} +\xdef\tr@nsseqbbbottom{0} \xdef\tr@nsseqbbbbottom{0} +\xdef\triple@counttop{0} \xdef\triple@countttop{0} +\xdef\triple@counttttop{0} \xdef\triple@countttttop{0} +\xdef\triple@countbottom{0} \xdef\triple@countbbottom{0} +\xdef\triple@countbbbottom{0}\xdef\triple@countbbbbottom{0} +\xdef\last@@restop{} \xdef\last@@resttop{} +\xdef\last@@restttop{} \xdef\last@@resttttop{} +\xdef\last@@resbottom{} \xdef\last@@resbbottom{} +\xdef\last@@resbbbottom{} \xdef\last@@resbbbbottom{} +\xdef\out@put{y} \xdef\m@p{no} +\xdef\t@sp@ce{0mm} \xdef\tt@sp@ce{0mm} +\xdef\ttt@sp@ce{0mm} \xdef\tttt@sp@ce{0mm} +\xdef\b@sp@ce{0mm} \xdef\bb@sp@ce{0mm} +\xdef\bbb@sp@ce{0mm} \xdef\bbbb@sp@ce{0mm} \xdef\seq@gap@num{0} \xdef\h@ndalign{no} \xdef\sep@space{0pt} \xdef\c@pshort{n} \xdef\bottom@stretch{n} \xdef\bbottom@stretch{n} +\xdef\bbbottom@stretch{n} \xdef\bbbbottom@stretch{n} \xdef\c@nscol{} \xdef\c@nssc@le{ColdHot} \xdef\collect@cons@colors{no} \xdef\cons@now{no} \xdef\res@numA{0} \xdef\res@numB{0} @@ -16283,6 +17312,7 @@ \xdef\divref@{0} \xdef\all@thresh@ld{100} \all@shadefalse \hidefeaturenames \hidefeaturestylenames +\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% @@ -16824,7 +17854,7 @@ AQP5.PRO MK........................KEVCSLAFFKAVFAEFLATLIFVFFGLGSALKWP 61 120 AQP1.PRO YPLERNQTLVQDNVKVSLAFGLSIATLAQSVGHISGAHSNPAVTLGLLLSCQISILRAVM AQP2.PRO ...SS....PPSVLQIAVAFGLGIGILVQALGHVSGAHINPAVTVACLVGCHVSFLRAAF -AQP3.PRO LSRGTHGGF....LTINLAFGFAVTLAILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPI +AQP3.PRO LSRGTH....GGFLTINLAFGFAVTLAILVAGQVSGAHLNPAVTFAMCFLAREPWIKLPI AQP4.PRO ...GSENPLPVDMVLISLCFGLSIATMVQCFGHISGGHINPAVTVAMVCTRKISIAKSVF AQP5.PRO ...SA....LPTILQISIAFGLAIGTLAQALGPVSGGHINPAITLALLIGNQISLLRAVF @@ -19070,6 +20100,70 @@ The best path: % % \end{macrocode} % \begin{macrocode} +%<*TCoffee> +T-COFFEE, Version_5.31(Fri Oct 26 17:01:36 2007) +Cedric Notredame +CPU TIME:1 sec. +SCORE=54 +* + BAD AVG GOOD +* +AQP1.PRO : 55 +AQP2.PRO : 58 +AQP3.PRO : 46 +AQP4.PRO : 55 +AQP5.PRO : 58 +cons : 54 + +AQP1.PRO 1 65------------------------3777666677777766666666556666666554 36 +AQP2.PRO 1 -2------------------------2776667777777777777667666666666654 35 +AQP3.PRO 1 5---------9644-----33322111------457777665555556555657555544 40 +AQP4.PRO 1 63DGAAARRW9644PPCSR33322113667667677777666666666666767666665 60 +AQP5.PRO 1 65------------------------4877667667777777776666666667666665 36 +cons 1 54--------9644-----33322113777667667777766666666666666666554 60 + + +AQP1.PRO 37 111221111223454555555555444444444554455555555544544445555444 96 +AQP2.PRO 36 ---33----323444444444444444454444455556666555555555455565555 88 +AQP3.PRO 41 111211----11444444444433333232333344455565555544444445555444 96 +AQP4.PRO 61 ---331111223554555555544444454455555666666666555555455555555 117 +AQP5.PRO 37 ---43----323555555555554444454455555555666555555555555565555 89 +cons 61 111331111323454545444444444444444455555665555555555455555555 120 + + +AQP1.PRO 97 5555555556555655555----------4444445555555555555555-----5555 141 +AQP2.PRO 89 6556666666666665555----------5555555566666666666666-----5556 133 +AQP3.PRO 97 4445555555555554443YYDAIWAFAG2322222333333344443454LDMVN4445 156 +AQP4.PRO 118 5556666666666665544----------4445545555555555665666-----6666 162 +AQP5.PRO 90 5555555556666665554----------4455555666666666666677-----6676 134 +cons 121 5555556666666655554----------4444444555555555555566-----5566 180 + + +AQP1.PRO 142 6677777777777766666666-5666656666666555666556677777778777766 200 +AQP2.PRO 134 5566777777777766666555-5565556666666555556556788888888888777 192 +AQP3.PRO 157 7666777777777777765444V3454455554444322222224577777777777665 216 +AQP4.PRO 163 7777777777777777776666-5555555555666555555555677777777777766 221 +AQP5.PRO 135 7777888788887777776666-5666666666666555555556677777777777776 193 +cons 181 7677777777777777666555-5565555565556544555555677777777777766 240 + + +AQP1.PRO 201 7766--666---------66666666665555666666555566544455555220111- 248 +AQP2.PRO 193 7766--666---------6666666665555555555555556664456666633-222- 239 +AQP3.PRO 217 5544LA2220EVFTTGQN223333434333334433332322------------------ 258 +AQP4.PRO 222 6555--555---------55655666656666655555555454-33345544100111- 268 +AQP5.PRO 194 6666--5440--------5555556655555555555544445664444555533-222T 242 +cons 241 6665--5550--------55555555555555555555444455544455555220221- 300 + + +AQP1.PRO 249 22222--2111111111----11000----------------------------3 269 +AQP2.PRO 240 33333--42222222223--3333333233322-------------------223 271 +AQP3.PRO 259 --------------------2111222122211122-111112221-------12 285 +AQP4.PRO 269 11111KG22111111123VE3222333233322122D111112221SSGEVL224 323 +AQP5.PRO 243 23333--33222223334--3333333---------------------------- 265 +cons 301 23322--32222222223--3222223233322122-111112221------223 355 +% +% \end{macrocode} +% \begin{macrocode} %<*Standard> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% diff --git a/Master/texmf-dist/source/latex/texshade/texshade.ins b/Master/texmf-dist/source/latex/texshade/texshade.ins index 26560329661..7f548d9cdb8 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 1999-2007 Eric Beitz +%% Copyright 1999-2008 Eric Beitz %% \def\batchfile{texshade.ins} @@ -31,6 +31,7 @@ See the file texshade.txt \file{AQP1.phd}{\from{texshade.dtx}{AQP1PHD}} \file{AQP_HMM.sgl}{\from{texshade.dtx}{AQPHMMsgl}} \file{AQP_HMM.ext}{\from{texshade.dtx}{AQPHMMext}} + \file{AQP_TC.asc}{\from{texshade.dtx}{TCoffee}} \file{standard.cod}{\from{texshade.dtx}{Standard}} \file{ciliate.cod}{\from{texshade.dtx}{Ciliate}}} diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty index 77a390d1fc3..a3cd5b24ade 100644 --- a/Master/texmf-dist/tex/latex/texshade/texshade.sty +++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty @@ -101,6 +101,7 @@ \newif\ifnumbers@left \newif\ifnumbers@right \newif\ifhide@cons \newif\ifshow@cons \newif\iffuncmode \newif\iflegend@ +\newif\ifT@coffee \newif\ifnumbers@ \newif\ifnames@ \newif\ifgerm@n \newif\ifsp@nish \newif\ifrpl@fix @@ -108,6 +109,8 @@ \newif\ifstart@ \newif\ifstop@ \newif\iftopfeature \newif\ifbottomfeature \newif\ifttopfeature \newif\ifbbottomfeature +\newif\iftttopfeature \newif\ifbbbottomfeature +\newif\ifttttopfeature\newif\ifbbbbottomfeature \newif\ifall@fshade \newif\ifregionalemph \newif\ifframe@ \newif\ifregionaltint \newif\ifshow@logo \newif\ifshow@sublogo @@ -118,8 +121,12 @@ \newif\ifregionalshadenow \newif\iftopfeaturenow \newif\ifttopfeaturenow +\newif\iftttopfeaturenow +\newif\ifttttopfeaturenow \newif\ifbottomfeaturenow \newif\ifbbottomfeaturenow +\newif\ifbbbottomfeaturenow +\newif\ifbbbbottomfeaturenow \newif\ifframenow \newif\iffix@ @@ -816,6 +823,17 @@ \definecolor{Gray95} {cmyk}{0,0,0,0.95} \definecolor{Black} {cmyk}{0,0,0,1} \definecolor{Gray100} {cmyk}{0,0,0,1} +\definecolor{TC0} {cmyk}{0.4,0.4,0,0} +\definecolor{TC1} {cmyk}{0.6,0,0.7,0} +\definecolor{TC2} {cmyk}{0.4,0,0.7,0} +\definecolor{TC3} {cmyk}{0.2,0,1,0} +\definecolor{TC4} {cmyk}{0,0,1,0} +\definecolor{TC5} {cmyk}{0,0.2,1,0} +\definecolor{TC6} {cmyk}{0,0.4,1,0} +\definecolor{TC7} {cmyk}{0,0.6,1,0} +\definecolor{TC8} {cmyk}{0,0.8,1,0} +\definecolor{TC9} {cmyk}{0,0.875,1,0} +\definecolor{TC99} {cmyk}{0,0,0,0} \definecolor{LightGreenYellow} {cmyk}{0.08,0,0.35,0} \definecolor{LightYellow} {cmyk}{0,0,0.50,0} \definecolor{LightGoldenrod} {cmyk}{0,0.05,0.42,0} @@ -907,6 +925,16 @@ \definecolor{LightGray95} {cmyk}{0,0,0,0.47} \definecolor{LightBlack} {cmyk}{0,0,0,0.50} \definecolor{LightGray100} {cmyk}{0,0,0,0.50} +\definecolor{LightTC0} {cmyk}{0.2,0.2,0,0} +\definecolor{LightTC1} {cmyk}{0.3,0,0.35,0} +\definecolor{LightTC2} {cmyk}{0.2,0,0.35,0} +\definecolor{LightTC3} {cmyk}{0.1,0,0.5,0} +\definecolor{LightTC4} {cmyk}{0,0,0.5,0} +\definecolor{LightTC5} {cmyk}{0,0.1,0.5,0} +\definecolor{LightTC6} {cmyk}{0,0.2,0.5,0} +\definecolor{LightTC7} {cmyk}{0,0.3,0.5,0} +\definecolor{LightTC8} {cmyk}{0,0.4,0.5,0} +\definecolor{LightTC99} {cmyk}{0,0,0,0} \definecolor{LightLightGreenYellow} {cmyk}{0.04,0,0.17,0} \definecolor{LightLightYellow} {cmyk}{0,0,0.25,0} \definecolor{LightLightGoldenrod} {cmyk}{0,0.02,0.21,0} @@ -998,6 +1026,16 @@ \definecolor{LightLightGray95} {cmyk}{0,0,0,0.23} \definecolor{LightLightBlack} {cmyk}{0,0,0,0.25} \definecolor{LightLightGray100} {cmyk}{0,0,0,0.25} +\definecolor{LightLightTC0} {cmyk}{0.1,0.1,0,0} +\definecolor{LightLightTC1} {cmyk}{0.15,0,0.175,0} +\definecolor{LightLightTC2} {cmyk}{0.1,0,0.175,0} +\definecolor{LightLightTC3} {cmyk}{0.05,0,0.25,0} +\definecolor{LightLightTC4} {cmyk}{0,0,0.25,0} +\definecolor{LightLightTC5} {cmyk}{0,0.05,0.25,0} +\definecolor{LightLightTC6} {cmyk}{0,0.1,0.25,0} +\definecolor{LightLightTC7} {cmyk}{0,0.15,0.25,0} +\definecolor{LightLightTC8} {cmyk}{0,0.2,0.25,0} +\definecolor{LightLightTC99} {cmyk}{0,0,0,0} \definecolor{LightLightLightGreenYellow} {cmyk}{0.02,0,0.08,0} \definecolor{LightLightLightYellow} {cmyk}{0,0,0.12,0} \definecolor{LightLightLightGoldenrod} {cmyk}{0,0.01,0.10,0} @@ -1090,6 +1128,16 @@ \definecolor{LightLightLightGray95} {cmyk}{0,0,0,0.115} \definecolor{LightLightLightBlack} {cmyk}{0,0,0,0.12} \definecolor{LightLightLightGray100} {cmyk}{0,0,0,0.125} +\definecolor{LightLightLightTC0} {cmyk}{0.05,0.05,0,0} +\definecolor{LightLightLightTC1} {cmyk}{0.075,0,0.086,0} +\definecolor{LightLightLightTC2} {cmyk}{0.05,0,0.086,0} +\definecolor{LightLightLightTC3} {cmyk}{0.025,0,0.125,0} +\definecolor{LightLightLightTC4} {cmyk}{0,0,0.125,0} +\definecolor{LightLightLightTC5} {cmyk}{0,0.025,0.125,0} +\definecolor{LightLightLightTC6} {cmyk}{0,0.05,0.125,0} +\definecolor{LightLightLightTC7} {cmyk}{0,0.0175,0.125,0} +\definecolor{LightLightLightTC8} {cmyk}{0,0.1,0.125,0} +\definecolor{LightLightLightTC99} {cmyk}{0,0,0,0} \definecolor{BlueRed5} {rgb} {0.15,0.17,0.55} \definecolor{BlueRed10} {rgb} {0.20,0.23,0.57} \definecolor{BlueRed15} {rgb} {0.24,0.29,0.60} @@ -1404,6 +1452,16 @@ \expandafter\xdef\csname res\the\loopcount\endcsname{\first@} \expandafter\xdef\csname sequence\the\loopcount\endcsname{#2@}} \def\remove@fromseq#1@{\expandafter\xdef\csname sequence\the\loopcount\endcsname{#1}} +\def\TC@get#1#2@{\xdef\char@num{`#1} + \ifnum\char@num=45 \xdef\TC@first@{*} + \else + \ifnum\char@num>57 \xdef\TC@first@{*} + \else + \xdef\TC@first@{#1} + \fi + \fi + \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\TC@first@} + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{#2@}} \def\sublogo@get#1 @{\xdef\first@{#1}} \def\re@write#1,#2@{% \xdef\third@{#2,@} @@ -1455,10 +1513,18 @@ \csname stack@@top#1\endcsname} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% \csname stack@@ttop#1\endcsname} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% + \csname stack@@tttop#1\endcsname} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% + \csname stack@@ttttop#1\endcsname} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% \csname stack@@bottom#1\endcsname} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% \csname stack@@bbottom#1\endcsname} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% + \csname stack@@bbbottom#1\endcsname} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% + \csname stack@@bbbbottom#1\endcsname} } \def\reorder@seqs#1{% \loopcount=0 @@ -1500,10 +1566,18 @@ \csname stack@top\the\loopcount\endcsname} \expandafter\xdef\csname stack@@ttop\the\loopcount\endcsname{% \csname stack@ttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@tttop\the\loopcount\endcsname{% + \csname stack@tttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@ttttop\the\loopcount\endcsname{% + \csname stack@ttttop\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bottom\the\loopcount\endcsname{% \csname stack@bottom\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bbottom\the\loopcount\endcsname{% \csname stack@bbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbbottom\the\loopcount\endcsname{% + \csname stack@bbbottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbbbottom\the\loopcount\endcsname{% + \csname stack@bbbbottom\the\loopcount\endcsname} \ifnum\loopcount<\killseq@count \repeat \xdef\third@{#1} \loopcount=0 \innerloopcount=0 \xdef\last@{kill} \xdef\second@{e} @@ -1779,10 +1853,18 @@ \csname stack@top\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% \csname stack@ttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% + \csname stack@tttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% + \csname stack@ttttop\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% \csname stack@bottom\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% \csname stack@bbottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% + \csname stack@bbbottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% + \csname stack@bbbbottom\the\innerloopcount\endcsname} \expandafter\xdef\csname res@count\the\loopcount\endcsname{% \csname res@count\the\innerloopcount\endcsname} \expandafter\xdef\csname hide@seq\the\innerloopcount\endcsname{kill} @@ -2586,6 +2668,97 @@ \fi \ifx\sim@char\ampers@nd\else\write@PHDtopo\fi } +\def\include@T@coffee{% + \bgroup + \immediate\openin\structurefile = \TC@first@\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\TC@first@' not found} + {\MessageBreak + The file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No T-Coffee shading will be displayed (using "similar"). \MessageBreak + Type to proceed. \MessageBreak + Type X to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \simmodetrue \funcmodefalse \T@coffeefalse + \else + \message{} + \xdef\first@{} \xdef\temp@{*} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\temp@ \xdef\temp@{y} + \read\structurefile to \readline + \read\structurefile to \readline + \fi + \fi + \ifx\temp@\y@ \else\repeat + \loopcount=0 + \xdef\temp@{cons} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \if\second@ : + \advance\loopcount by 1\relax + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} + \fi + \fi + \ifx\first@\temp@\expandafter\xdef\csname T@coffee0\endcsname{} \else\repeat + \xdef\temp@{\the\loopcount} + \loopcount=0 + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \advance\loopcount by 1 + \ifnum\loopcount=\temp@ \loopcount=0 \fi + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname \third@} + \fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \loopcount=0 + \loop + \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} + \advance\loopcount by 1 + \ifnum\loopcount=\temp@ \else\repeat + \egroup + \def\n@m@tch{{$\bullet$}} + \expandafter\def\csname fg@color0\endcsname{TC0} + \expandafter\def\csname fg@color1\endcsname{TC1} + \expandafter\def\csname fg@color2\endcsname{TC2} + \expandafter\def\csname fg@color3\endcsname{TC3} + \expandafter\def\csname fg@color4\endcsname{TC4} + \expandafter\def\csname fg@color5\endcsname{TC5} + \expandafter\def\csname fg@color6\endcsname{TC6} + \expandafter\def\csname fg@color7\endcsname{TC7} + \expandafter\def\csname fg@color8\endcsname{TC8} + \expandafter\def\csname fg@color9\endcsname{TC9} + \expandafter\def\csname fg@textcolor0\endcsname{Black} + \expandafter\def\csname fg@textcolor1\endcsname{Black} + \expandafter\def\csname fg@textcolor2\endcsname{Black} + \expandafter\def\csname fg@textcolor3\endcsname{Black} + \expandafter\def\csname fg@textcolor4\endcsname{Black} + \expandafter\def\csname fg@textcolor5\endcsname{Black} + \expandafter\def\csname fg@textcolor6\endcsname{Black} + \expandafter\def\csname fg@textcolor7\endcsname{Black} + \expandafter\def\csname fg@textcolor8\endcsname{Black} + \expandafter\def\csname fg@textcolor9\endcsname{Black} + \fi + } + \def\include@DSSP{% \xdef\first@{\csname optiondssp\the\loopcount\endcsname} \xdef\bottop@{\csname bottopdssp\the\loopcount\endcsname} @@ -3875,10 +4048,18 @@ \ifx\bottop@\temp@ \topfeaturetrue\fi \xdef\temp@{ttop} \ifx\bottop@\temp@ \ttopfeaturetrue\fi + \xdef\temp@{tttop} + \ifx\bottop@\temp@ \tttopfeaturetrue\fi + \xdef\temp@{ttttop} + \ifx\bottop@\temp@ \ttttopfeaturetrue\fi \xdef\temp@{bottom} \ifx\bottop@\temp@ \bottomfeaturetrue\fi \xdef\temp@{bbottom} \ifx\bottop@\temp@ \bbottomfeaturetrue\fi + \xdef\temp@{bbbottom} + \ifx\bottop@\temp@ \bbbottomfeaturetrue\fi + \xdef\temp@{bbbbottom} + \ifx\bottop@\temp@ \bbbbottomfeaturetrue\fi \xdef\seq@{#2} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ @@ -3943,6 +4124,10 @@ \ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi \xdef\temp@{bbottom} \ifx\bottop@\temp@ \xdef\bbottom@stretch{y}\fi + \xdef\temp@{bbbottom} + \ifx\bottop@\temp@ \xdef\bbbottom@stretch{y}\fi + \xdef\temp@{bbbbottom} + \ifx\bottop@\temp@ \xdef\bbbbottom@stretch{y}\fi \else \xdef\last@{color} \ifx\second@@\last@ @@ -3987,6 +4172,11 @@ \xdef\last@{bcons} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\last@{T-Coffee} + \ifx\f@color\last@ + \xdef\T@coffee@bcons{y} + \xdef\f@color{Gray50} + \fi \xdef\style@{cons[bar]:cons[\f@color][0]} \else \xdef\last@{ch} @@ -4007,6 +4197,11 @@ \xdef\last@{ccons} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{ColdHot}\fi + \xdef\last@{T-Coffee} + \ifx\f@color\last@ + \xdef\T@coffee@ccons{y} + \xdef\f@color{TC} + \fi \xdef\style@{cons[color]:cons[\f@color][0]} \else \xdef\style@{#4} \expandafter\getarrow@shape\temp@ @@ -4030,9 +4225,11 @@ \def\showfeaturename#1#2{\expandafter\xdef\csname featuretextn@me#1\endcsname{#2}} \def\showfeaturestylename#1#2{\expandafter\xdef\csname featurestylesn@me#1\endcsname{#2}} \def\hidefeaturename#1{\expandafter\xdef\csname featuretextn@me#1\endcsname{}} -\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{}} +\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{} + \xdef\featuretextn@metttop{}\xdef\featuretextn@mettttop{}\xdef\featuretextn@mebbbbottom{}\xdef\featuretextn@mebbbottom{}} \def\hidefeaturestylename#1{\expandafter\xdef\csname featurestylesn@me#1\endcsname{}} -\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{}} +\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{} + \xdef\featurestylesn@metttop{}\xdef\featurestylesn@mettttop{}\xdef\featurestylesn@mebbbbottom{}\xdef\featurestylesn@mebbbottom{}} \def\seqtype#1{\xdef\seq@type{#1} \if\seq@type P \xdef\prefix@{pep} \else \if\seq@type p \xdef\seq@type{P} \xdef\prefix@{pep} @@ -4092,8 +4289,12 @@ \def\vblockspace#1{\def\block@skip{\vspace{#1}}} \def\topspace#1{\def\t@sp@ce{#1}} \def\ttopspace#1{\def\tt@sp@ce{#1}} +\def\tttopspace#1{\def\ttt@sp@ce{#1}} +\def\ttttopspace#1{\def\tttt@sp@ce{#1}} \def\bottomspace#1{\def\b@sp@ce{#1}} \def\bbottomspace#1{\def\bb@sp@ce{#1}} +\def\bbbottomspace#1{\def\bbb@sp@ce{#1}} +\def\bbbbottomspace#1{\def\bbbb@sp@ce{#1}} \def\fixblockspace{\fix@true} \def\flexblockspace{\fix@false} \def\nosepline{\def\seq@skip{\relax}} @@ -4117,6 +4318,7 @@ \fi \fi} \newcommand{\shadingmode}[2][-1]{% + \T@coffeefalse \xdef\last@{#2} \xdef\first@{identical} \ifx\first@\last@ @@ -4162,6 +4364,12 @@ \else \simmodefalse \funcmodetrue \func@shading{#1} \xdef\seq@type{P} \xdef\prefix@{pep} \fi \else + \xdef\first@{T-Coffee} + \ifx\first@\last@ + \simmodefalse \funcmodefalse \T@coffeetrue + \xdef\second@{#1 @} \expandafter\check@letter\second@ + \ifletter \xdef\TC@first@{#1}\include@T@coffee\fi + \else \xdef\first@{diverse} \ifx\first@\last@ \xdef\last@{#1} @@ -4180,7 +4388,7 @@ \else \message{} \simmodetrue \funcmodefalse - \fi\fi\fi\fi} + \fi\fi\fi\fi\fi} \newcommand\allmatchspecial[1][100]{% \ifnum#1<0 \xdef\all@thresh@ld{0} @@ -4197,8 +4405,8 @@ \ifx\first@\second@\def\gap@char{o} \else\def\gap@char{#1}\fi} \def\gaprule#1{\def\gap@rulethick{#1}} -\def\setends#1#2{% - \xdef\start@seq{#1} +\newcommand{\setends}[3][&]{% + \xdef\start@seq{#2} \xdef\temp@{consensus} \ifx\start@seq\temp@ \message{<\noexpand\setends does not accept `consensus'>} @@ -4208,14 +4416,14 @@ \xdef\first@{\start@seq} \ifletter \get@name@number \xdef\start@seq{\first@} \fi \ifnum\start@seq>\seq@count - \message{<\noexpand\setends{} error: sequence `#1' not defined>} + \message{<\noexpand\setends{} error: sequence `#2' not defined>} \xdef\start@seq{0} \else \ifnum\start@seq<1 - \message{<\noexpand\setends{} error: sequence `#1' not defined>} + \message{<\noexpand\setends{} error: sequence `#2' not defined>} \xdef\start@seq{0} \else - \xdef\second@{#2@} \expandafter\get@nums\second@ + \xdef\second@{#3@} \expandafter\get@nums\second@ \xdef\start@num{\first@} \xdef\end@num{\second@} \ifnum\start@num=0 \xdef\allow@zero{y}\fi \ifnum\end@num=0 \xdef\allow@zero{y}\fi @@ -4223,20 +4431,21 @@ \fi \fi \fi + \xdef\first@{#1}\ifx\first@\ampers@nd\else\startnumber{#2}{#1}\fi } -\def\startnumber#1#2{% - \xdef\first@{#1} \xdef\second@{consensus} +\newcommand{\startnumber}[3][&]{% + \xdef\first@{#2} \xdef\second@{consensus} \ifx\first@\second@ - \ifnum#2=0 \xdef\allow@zero{y} \fi + \ifnum#3=0 \xdef\allow@zero{y} \fi \expandafter\xdef\csname seq@start0\endcsname{#2} - \cons@count=#2 \advance\cons@count by -1\relax + \cons@count=#3 \advance\cons@count by -1\relax \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} \else - \xdef\first@{#1 @} \expandafter\check@letter\first@ - \xdef\first@{#1} \ifletter \get@name@number \fi - \ifnum\first@>\seq@count \message{} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count \message{} \else - \xdef\second@{#2} + \xdef\second@{#3} \ifnum\second@=0 \xdef\allow@zero{y} \fi \expandafter\xdef\csname seq@start\first@\endcsname{\second@} \res@count=\second@ @@ -4244,6 +4453,7 @@ \expandafter\xdef\csname res@count\first@\endcsname{\the\res@count} \fi \fi + \xdef\first@{#1}\ifx\first@\ampers@nd\else\setends{#2}{#1}\fi } \def\seqlength#1#2{% \xdef\first@{#1 @} \expandafter\check@letter\first@ @@ -5208,16 +5418,24 @@ \ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi \fi\fi\fi\fi} \def\featurenamescolor#1{% + \expandafter\xdef\csname ftext@fg@ttttop\endcsname{#1} + \expandafter\xdef\csname ftext@fg@tttop\endcsname{#1} \expandafter\xdef\csname ftext@fg@ttop\endcsname{#1} \expandafter\xdef\csname ftext@fg@top\endcsname{#1} \expandafter\xdef\csname ftext@fg@bottom\endcsname{#1} \expandafter\xdef\csname ftext@fg@bbottom\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bbbottom\endcsname{#1} + \expandafter\xdef\csname ftext@fg@bbbbottom\endcsname{#1} } \def\featurestylenamescolor#1{% + \expandafter\xdef\csname fstyles@fg@ttttop\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@tttop\endcsname{#1} \expandafter\xdef\csname fstyles@fg@ttop\endcsname{#1} \expandafter\xdef\csname fstyles@fg@top\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bottom\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bbottom\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bbbottom\endcsname{#1} + \expandafter\xdef\csname fstyles@fg@bbbbottom\endcsname{#1} } \def\featurenamecolor#1#2{\expandafter\xdef\csname ftext@fg@#1\endcsname{#2}} \def\featurestylenamecolor#1#2{\expandafter\xdef\csname fstyles@fg@#1\endcsname{#2}} @@ -5328,6 +5546,9 @@ \logo@rule\kern-\wd1\textcolor{White}{\texttt{d}}% \texttt{e}} +\def\includeTCoffee#1{% + \xdef\TC@first@{#1}\include@T@coffee} + \def\firstcolumnDSSP{\xdef\fc@DSSP{y}} \def\secondcolumnDSSP{\xdef\fc@DSSP{n}} @@ -6386,6 +6607,66 @@ \fi \ifnum\loopcount<\seq@count \repeat} +\def\T@coffee@shade{% + \loopcount=0 + \expandafter\ifx\csname tint@seq0\endcsname\y@ + \expandafter\xdef\csname tint@seq0\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq0\endcsname\y@ + \expandafter\xdef\csname emph@seq0\endcsname{n} + \xdef\first@{,\first@}\fi + \xdef\second@{\csname TC@num0\endcsname} + \xdef\consensus{\consensus\second@\n@m@tch} + \xdef\constopo{\constopo\second@} + \loop + \advance\loopcount by 1 + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\second@{\csname TC@num\the\loopcount\endcsname} + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\gap@char}\def\second@{*} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\second@{*} + \else + \def\first@{{}} \def\second@{/} + \fi + \fi + \fi + \fi + \xdef\third@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + *\first@} + \else + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + \second@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat} + \def\getregion@fromstack@first{% \expandafter\getregion@fromstack{\the\loopcount} \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd @@ -6804,6 +7085,18 @@ \multiply\temp@count by 2 \divide\temp@count by \innerloopcount \xdef\cons@val{\the\temp@count} + \ifx\T@coffee@bcons\y@ + \xdef\cons@val{\csname TC@num0\endcsname} + \if\cons@val * + \xdef\cons@val{99} + \fi \message{(b(\cons@val)b)} + \fi + \ifx\T@coffee@ccons\y@ + \xdef\cons@val{\csname TC@num0\endcsname} + \if\cons@val * + \xdef\cons@val{99} + \fi \message{(c(\cons@val)c)} + \fi \fi } @@ -7700,10 +7993,15 @@ \def\c@nsensus{% \ifnum\pos@count>\res@perline \else + \loopcount=0 \global\advance\cons@count by 1\relax \ifnum\cons@count=0\relax \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi \fi + \ifT@coffee + \xdef\TC@line{\csname T@coffee0\endcsname} + \expandafter\TC@get\TC@line + \fi \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} \ifx\hide@true\y@ \expandafter\ifx\csname hidestart0\endcsname\ampers@nd @@ -7720,9 +8018,13 @@ \fi \fi \fi - \loopcount=0 \loop \advance\loopcount by 1 + \ifT@coffee + \xdef\TC@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\TC@line + \xdef\TC@first@{\csname TC@num\the\loopcount\endcsname} + \fi \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\residue@get\seq@line \xdef\first@{\csname res\the\loopcount\endcsname} @@ -7786,6 +8088,14 @@ \ifnum\v@lseqttop=\loopcount \xdef\v@lttop{\v@lttop,\csname \ffourth@ttop\first@\endcsname} \fi\fi + \ifx\collect@valtttop\yes + \ifnum\v@lseqtttop=\loopcount + \xdef\v@ltttop{\v@ltttop,\csname \ffourth@tttop\first@\endcsname} + \fi\fi + \ifx\collect@valttttop\yes + \ifnum\v@lseqttttop=\loopcount + \xdef\v@lttttop{\v@lttttop,\csname \ffourth@ttttop\first@\endcsname} + \fi\fi \ifx\collect@valbottom\yes \ifnum\v@lseqbottom=\loopcount \xdef\v@lbottom{\v@lbottom,\csname \ffourth@bottom\first@\endcsname} @@ -7794,6 +8104,14 @@ \ifnum\v@lseqbbottom=\loopcount \xdef\v@lbbottom{\v@lbbottom,\csname \ffourth@bbottom\first@\endcsname} \fi\fi + \ifx\collect@valbbbottom\yes + \ifnum\v@lseqbbbottom=\loopcount + \xdef\v@lbbbottom{\v@lbbbottom,\csname \ffourth@bbbottom\first@\endcsname} + \fi\fi + \ifx\collect@valbbbbottom\yes + \ifnum\v@lseqbbbbottom=\loopcount + \xdef\v@lbbbbottom{\v@lbbbbottom,\csname \ffourth@bbbbottom\first@\endcsname} + \fi\fi \fi \ifx\collect@restop\yes \ifnum\tr@nsseqtop=\loopcount @@ -7819,6 +8137,30 @@ \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countttop{\the\innerloopcount} \fi\fi + \ifx\collect@restttop\yes + \ifnum\tr@nsseqtttop=\loopcount + \xdef\last@restttop{\last@@restttop} + \xdef\last@@restttop{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatetttop{\tr@nslatetttop\first@} + \fi + \innerloopcount=\triple@counttttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@counttttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resttttop\yes + \ifnum\tr@nsseqttttop=\loopcount + \xdef\last@resttttop{\last@@resttttop} + \xdef\last@@resttttop{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatettttop{\tr@nslatettttop\first@} + \fi + \innerloopcount=\triple@countttttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countttttop{\the\innerloopcount} + \fi\fi \ifx\collect@resbottom\yes \ifnum\tr@nsseqbottom=\loopcount \xdef\last@resbottom{\last@@resbottom} @@ -7843,6 +8185,30 @@ \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countbbottom{\the\innerloopcount} \fi\fi + \ifx\collect@resbbbottom\yes + \ifnum\tr@nsseqbbbottom=\loopcount + \xdef\last@resbbbottom{\last@@resbbbottom} + \xdef\last@@resbbbottom{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@} + \fi + \innerloopcount=\triple@countbbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbbottom{\the\innerloopcount} + \fi\fi + \ifx\collect@resbbbbottom\yes + \ifnum\tr@nsseqbbbbottom=\loopcount + \xdef\last@resbbbbottom{\last@@resbbbbottom} + \xdef\last@@resbbbbottom{\first@} + \ifx\hide@now\n@ + \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@} + \fi + \innerloopcount=\triple@countbbbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbbbottom{\the\innerloopcount} + \fi\fi \innerloopcount=\csname mol@weight\the\loopcount\endcsname \advance\innerloopcount by \csname \prefix@ mw\first@\endcsname \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{% @@ -7862,6 +8228,14 @@ \ifnum\v@lseqttop=\loopcount \xdef\v@lttop{\v@lttop,N} \fi\fi + \ifx\collect@valtttop\yes + \ifnum\v@lseqtttop=\loopcount + \xdef\v@ltttop{\v@ltttop,N} + \fi\fi + \ifx\collect@valttttop\yes + \ifnum\v@lseqttttop=\loopcount + \xdef\v@lttttop{\v@lttttop,N} + \fi\fi \ifx\collect@valbottom\yes \ifnum\v@lseqbottom=\loopcount \xdef\v@lbottom{\v@lbottom,N} @@ -7870,6 +8244,14 @@ \ifnum\v@lseqbbottom=\loopcount \xdef\v@lbbottom{\v@lbbottom,N} \fi\fi + \ifx\collect@valbbbottom\yes + \ifnum\v@lseqbbbottom=\loopcount + \xdef\v@lbbbottom{\v@lbbbottom,N} + \fi\fi + \ifx\collect@valbbbbottom\yes + \ifnum\v@lseqbbbbottom=\loopcount + \xdef\v@lbbbbottom{\v@lbbbbottom,N} + \fi\fi \ifx\collect@restop\yes \ifnum\tr@nsseqtop=\loopcount \xdef\tr@nslatetop{\tr@nslatetop -} @@ -7878,6 +8260,14 @@ \ifnum\tr@nsseqttop=\loopcount \xdef\tr@nslatettop{\tr@nslatettop -} \fi\fi + \ifx\collect@restttop\yes + \ifnum\tr@nsseqtttop=\loopcount + \xdef\tr@nslatetttop{\tr@nslatetttop -} + \fi\fi + \ifx\collect@resttttop\yes + \ifnum\tr@nsseqttttop=\loopcount + \xdef\tr@nslatettttop{\tr@nslatettttop -} + \fi\fi \ifx\collect@resbottom\yes \ifnum\tr@nsseqbottom=\loopcount \xdef\tr@nslatebottom{\tr@nslatebottom -} @@ -7886,6 +8276,14 @@ \ifnum\tr@nsseqbbottom=\loopcount \xdef\tr@nslatebbottom{\tr@nslatebbottom -} \fi\fi + \ifx\collect@resbbbottom\yes + \ifnum\tr@nsseqbbbottom=\loopcount + \xdef\tr@nslatebbbottom{\tr@nslatebbbottom -} + \fi\fi + \ifx\collect@resbbbbottom\yes + \ifnum\tr@nsseqbbbbottom=\loopcount + \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom -} + \fi\fi \fi \fi \ifnum\loopcount<\seq@count \repeat @@ -7923,6 +8321,18 @@ \sum@up@cons \xdef\v@lttop{\v@lttop,\cons@val} \fi + \ifx\collect@cons@graphtttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@ltttop{\v@ltttop,\cons@val} + \fi + \ifx\collect@cons@graphttttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lttttop{\v@lttttop,\cons@val} + \fi \ifx\collect@cons@graphbottom\yes \outerloopcount=1\relax \temp@count=0\relax @@ -7935,6 +8345,18 @@ \sum@up@cons \xdef\v@lbbottom{\v@lbbottom,\cons@val} \fi + \ifx\collect@cons@graphbbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbbottom{\v@lbbbottom,\cons@val} + \fi + \ifx\collect@cons@graphbbbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbbbottom{\v@lbbbbottom,\cons@val} + \fi \ifx\collect@cons@colors\y@ \outerloopcount=1\relax \temp@count=0\relax @@ -7971,10 +8393,14 @@ \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 + \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi + \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi + \iftttopfeaturenow \xdef\bottop@{tttop} \calc@feature \fi + \ifttttopfeaturenow \xdef\bottop@{ttttop} \calc@feature \fi + \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \ifbbbottomfeaturenow \xdef\bottop@{bbbottom} \calc@feature \fi + \ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi \ifx\hide@now\y@ \xdef\hidebar@on{1} \ifnum\pos@count=\bar@pos @@ -7990,13 +8416,16 @@ \ifshow@logo \calc@logo \fi \ifall@fshade \all@funcshade \else - \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi - \xdef\match@case{0} \xdef\m@x{1} - \iffuncmode - \xdef\prfx{\prefix@} \xdef\prefix@{func} \xdef\c@se{3} \check@sim - \xdef\prefix@{\prfx} - \else \xdef\c@se{1} \check@ident \fi - \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi + \ifT@coffee \T@coffee@shade + \else + \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi + \xdef\match@case{0} \xdef\m@x{1} + \iffuncmode + \xdef\prfx{\prefix@} \xdef\prefix@{func} \xdef\c@se{3} \check@sim + \xdef\prefix@{\prfx} + \else \xdef\c@se{1} \check@ident \fi + \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi + \fi \fi %%%%%%%% \fi @@ -8008,10 +8437,14 @@ \global\stop@true \loopcount=\pos@count \advance\loopcount by -1 \relax \res@perline=\loopcount - \iftopfeature \xdef\bottop@{top} \calc@feature \fi - \ifttopfeature \xdef\bottop@{ttop} \calc@feature \fi - \ifbottomfeature \xdef\bottop@{bottom} \calc@feature \fi - \ifbbottomfeature \xdef\bottop@{bbottom} \calc@feature \fi + \iftopfeature \xdef\bottop@{top} \calc@feature \fi + \ifttopfeature \xdef\bottop@{ttop} \calc@feature \fi + \iftttopfeature \xdef\bottop@{tttop} \calc@feature \fi + \ifttttopfeature \xdef\bottop@{ttttop} \calc@feature \fi + \ifbottomfeature \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeature \xdef\bottop@{bbottom} \calc@feature \fi + \ifbbbottomfeature \xdef\bottop@{bbbottom} \calc@feature \fi + \ifbbbbottomfeature \xdef\bottop@{bbbbottom} \calc@feature \fi \pos@count=0 \fi \fi} @@ -8026,6 +8459,10 @@ \def\c@unt{% \advance\loopcount by 1 + \ifT@coffee + \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\seq@line + \fi \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\residue@get\seq@line \xdef\first@{\csname res\the\loopcount\endcsname} @@ -8050,6 +8487,10 @@ \advance\end@count by 1 \ifnum\end@count<\start@number \loopcount=0 + \ifT@coffee + \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} + \expandafter\TC@get\seq@line + \fi \c@unt \count@first \fi} @@ -8065,8 +8506,10 @@ \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse \framenowfalse \fi - \topfeaturenowfalse \bottomfeaturenowfalse - \ttopfeaturenowfalse \bbottomfeaturenowfalse + \topfeaturenowfalse \bottomfeaturenowfalse + \ttopfeaturenowfalse \bbottomfeaturenowfalse + \tttopfeaturenowfalse \bbbottomfeaturenowfalse + \ttttopfeaturenowfalse \bbbbottomfeaturenowfalse \innerloopcount=\cons@count \advance\innerloopcount by \res@perline \advance\innerloopcount by 1 \loopcount=0 @@ -8133,6 +8576,28 @@ \fi \fi \fi + \iftttopfeature + \xdef\bottop@{tttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \tttopfeaturenowtrue + \fi + \fi + \fi + \ifttttopfeature + \xdef\bottop@{ttttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttttopfeaturenowtrue + \fi + \fi + \fi \ifbottomfeature \xdef\bottop@{bottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd @@ -8155,12 +8620,35 @@ \fi \fi \fi + \ifbbbottomfeature + \xdef\bottop@{bbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbbottomfeature + \xdef\bottop@{bbbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbbottomfeaturenowtrue + \fi + \fi + \fi \loop \advance\loopcount by 1 \ifnumbers@left - \innerloopcount=\csname seq@len\the\loopcount\endcsname + \innerloopcount=\csname seq@len\the\loopcount\endcsname\relax \expandafter\ifnum\csname res@count\the\loopcount\endcsname=% \innerloopcount + \res@count=\innerloopcount \else \res@count=\csname res@count\the\loopcount\endcsname \advance\res@count by 1 @@ -8259,6 +8747,28 @@ \fi \fi \fi + \iftttopfeature + \xdef\bottop@{tttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \tttopfeaturenowtrue + \fi + \fi + \fi + \ifttttopfeature + \xdef\bottop@{ttttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttttopfeaturenowtrue + \fi + \fi + \fi \ifbottomfeature \xdef\bottop@{bottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd @@ -8281,6 +8791,28 @@ \fi \fi \fi + \ifbbbottomfeature + \xdef\bottop@{bbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbottomfeaturenowtrue + \fi + \fi + \fi + \ifbbbbottomfeature + \xdef\bottop@{bbbbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbbbottomfeaturenowtrue + \fi + \fi + \fi \ifnum\loopcount<\seq@count \repeat \c@nsensus} @@ -8299,6 +8831,115 @@ \fontfamily{\legend@family}% \fontseries{\legend@series}% \fontshape{\legend@shape}% + \ifT@coffee + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \def\res@@style{\csname no@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}% + \expandafter\ifx\csname n@m@tch\the\loopcount\endcsname\low@up% + \def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \textcolor{TC0}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{schlecht}% + \else\ifsp@nish\kern2ex\legend@size{mala}% + \else\kern2ex\legend@size{bad}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC1}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC2}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC3}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC4}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{Grad der}% + \else\ifsp@nish\kern2ex\legend@size{conservaci\'on}% + \else\kern2ex\legend@size{level of}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC5}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{Konservierung}% + \else\ifsp@nish\kern2ex\legend@size{}% + \else\kern2ex\legend@size{conservation}\fi\fi} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC6}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC7}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC8}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{\legend@size{}} + \newline\hbox{}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \textcolor{TC9}{\box@rule}% + \kern-\box@width\textcolor{Black}{\hbox to \box@width{% + \legend@size{\res@@style{\hss\temp@\hss}}}}% + \kern2ex\textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{gut}% + \else\ifsp@nish\kern2ex\legend@size{buena}% + \else\kern2ex\legend@size{good}\fi\fi} + \newline\hbox{}% + \else \iffuncmode \ifnum\fgroup@num>0 \loopcount=0 @@ -8393,6 +9034,7 @@ \newline\hbox{}\noindent \fi \fi + \fi } \def\put@name<#1>#2@{% \ifnames@% @@ -8440,6 +9082,13 @@ \xdef\temp@@{}% \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% \else% + \ifT@coffee% + \xdef\boxc@l@r{\csname fg@color#1\endcsname}% + \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% + \def\res@@style{\csname func@style#1\endcsname}% + \if\last@ *\def\last@{0}\fi + \if\last@ /\def\last@{10}\fi + \else% \iffuncmode% \xdef\boxc@l@r{\csname fg@color#1\endcsname}% \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% @@ -8465,7 +9114,7 @@ \def\res@@style{\csname relax\endcsname}% \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \def\res@@style{\csname relax\endcsname}% - \fi\fi\fi% + \fi\fi\fi\fi% \ifx\second@\comm@% \def\temp@{\res@style}% \expandafter\get@second@\first@% @@ -8502,20 +9151,48 @@ \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% \else% \ifx\collect@cons@colors\y@% + \if\last@ *% + \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% + \else% + \if\last@ /% + \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \else% \expandafter\get@item\first@@@% \xdef\first@@@{\first@}% \ifx\box@scale\y@% \xdef\boxc@l@r{\c@nssc@le\fourth@}% \else% - \xdef\boxc@l@r{\c@nssc@le}% + \xdef\first@{T-Coffee}% + \ifx\first@\c@nssc@le% + \xdef\boxc@l@r{TC\last@}% + \else + \xdef\boxc@l@r{\c@nssc@le}% + \fi% \fi% \ifx\text@scale\y@% \xdef\textc@l@r{\c@nsc@l\fourth@}% \else% - \xdef\textc@l@r{\c@nsc@l}% - \fi% + \xdef\first@{T-Coffee}% + \ifx\first@\c@nsc@l% + \xdef\textc@l@r{TC\last@}% + \else + \xdef\textc@l@r{\c@nsc@l}% + \fi% + \fi\fi\fi% \def\res@@style{\csname relax\endcsname}% \else% + \ifT@coffee% + \if\last@ *% + \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% + \else% + \if\last@ /% + \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \else% + \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}% + \def\res@@style{\csname relax\endcsname}% + \fi% + \fi% + \else% \ifcase#1\xdef\boxc@l@r{\Allmatch}\xdef\textc@l@r{\TextAllmatch}% \def\res@@style{\all@style}% \or\xdef\boxc@l@r{\Identical}\xdef\textc@l@r{\TextIdentical}% @@ -8534,7 +9211,7 @@ \def\res@@style{\csname relax\endcsname}% \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \def\res@@style{\csname relax\endcsname}% - \fi\fi\fi% + \fi\fi\fi\fi% \xdef\first@{#3@}% \xdef\second@{#2}% \ifx\second@\comm@% @@ -8809,13 +9486,23 @@ \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% \else% \xdef\last@{ttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \xdef\last@{tttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \xdef\last@{ttttop}% \ifx\bottop@\last@% \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% \else% \raisebox{1.75\arrow@height}{\ensuremath{\underbrace{\hbox to % \second@\box@width{}}}}% - \fi\fi}% + \fi\fi\fi\fi}% \else% \xdef\last@{fill}% \ifx\second@@\last@% @@ -8880,12 +9567,15 @@ \ifx\second@@\N@\hbox to \box@width{\hss}% \else \loopcount=\second@@% - \advance\loopcount by -\pm@shift% - \advance\loopcount by 4% - \divide\loopcount by 5% - \multiply\loopcount by 5% - \ifnum\loopcount>100\loopcount=100\fi% - \ifnum\loopcount<5\loopcount=5\fi% + \ifx\T@coffee@ccons\y@% + \else% + \advance\loopcount by -\pm@shift% + \advance\loopcount by 4% + \divide\loopcount by 5% + \multiply\loopcount by 5% + \ifnum\loopcount>100\loopcount=100\fi% + \ifnum\loopcount<5\loopcount=5\fi% + \fi% \setlength\arrow@height{50\box@height}% \divide\arrow@height by 100\relax% \setlength\arrow@height{\sc@le@stretch\arrow@height}% @@ -8915,7 +9605,13 @@ {\vrule height\arrow@height width\box@width}}\hss}% \kern-\box@width% \fi% + \ifx\T@coffee@bcons\y@% + \ifnum\second@@=99 \xdef\second@@{0}\fi% + \fi \setlength\arrow@height{\second@@\box@height}% + \ifx\T@coffee@bcons\y@% + \setlength\arrow@height{11\arrow@height}% + \fi \divide\arrow@height by 100\relax% \setlength\arrow@height{\b@r@stretch\arrow@height}% \ifdim\arrow@height<0pt% @@ -9050,7 +9746,13 @@ \xdef\temp@{ttop}% \ifx\bottop@\temp@ \xdef\last@{0.25}% \else% - \xdef\last@{-0.25}\fi\fi% + \xdef\temp@{tttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\temp@{ttttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\last@{-0.25}\fi\fi\fi\fi% \textcolor{\f@color}{% \raisebox{\last@\arrow@height}{% \if\first@@ ,% @@ -9279,12 +9981,46 @@ \def\put@feature{% \vspace{-\baselineskip}% \newline\hbox{}% + \xdef\temp@{ttttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else% + \xdef\temp@{tttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featuretext% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \else% \xdef\temp@{ttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9294,14 +10030,14 @@ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{top}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9311,12 +10047,12 @@ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9326,14 +10062,14 @@ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% - \fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \fi\fi\fi\fi% \newline\hbox{}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9343,14 +10079,31 @@ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{ttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \xdef\temp@{tttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% @@ -9360,12 +10113,29 @@ \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \else + \xdef\temp@{ttttop}% + \ifx\temp@\bottop@% + \ifnames@right\else\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \loopcount=\res@perline% + \put@featurestyle% + \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifnames@right\ifnames@% + \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% + \selectfont% + \kern1em\hbox to \loopcount\box@width{\hss}% + \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \xdef\first@{\csname textfeature\bottop@\endcsname @}% @@ -9376,8 +10146,8 @@ \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% - \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% - \fi\fi% + \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% + \fi\fi\fi\fi% \newline\hbox{}% } \def\put@@@frame#1{% @@ -10009,10 +10779,32 @@ \def\set@lines{% \pos@count=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}% + \xdef\featurepostop{1} \xdef\featureposbottom{1}% + \xdef\featureposttop{1} \xdef\featureposbbottom{1}% + \xdef\featurepostttop{1} \xdef\featureposbbbottom{1}% + \xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}% \findc@nsensus% \noindent% + \ifnum\feature@ttttop=1 + \ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi + \xdef\bottop@{ttttop}% + \put@feature% + \vspace{\tttt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi + \ifnum\feature@tttop=1 + \ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi + \xdef\bottop@{tttop}% + \put@feature% + \vspace{\ttt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi \ifnum\feature@ttop=1 \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi \xdef\bottop@{ttop}% @@ -10175,12 +10967,56 @@ \fi \fi \fi + \ifnum\feature@bbbottom=1 % + \ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi% + \xdef\bottop@{bbbottom}% + \vspace{\bbb@sp@ce}% + \if\bbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature% + \else + \iffix@ + \if\bbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbbottomfeature + \vspace{\bbb@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi + \fi + \fi + \ifnum\feature@bbbbottom=1 % + \ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi% + \xdef\bottop@{bbbbottom}% + \vspace{\bbbb@sp@ce}% + \if\bbbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature% + \else + \iffix@ + \if\bbbbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbbbottomfeature + \vspace{\bbbb@sp@ce}\newline\hbox{}\newline\hbox{}% + \fi + \fi + \fi \xdef\consensus{} \xdef\ruler@{} - \xdef\styleframe{} \xdef\stylehidebar{} - \xdef\textfeaturetop{} \xdef\textfeaturebottom{} - \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} - \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} - \xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{} + \xdef\styleframe{} \xdef\stylehidebar{} + \xdef\textfeaturetop{} \xdef\textfeaturebottom{} + \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} + \xdef\textfeaturetttop{} \xdef\textfeaturebbbottom{} + \xdef\textfeaturettttop{} \xdef\textfeaturebbbbottom{} + \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} + \xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{} + \xdef\stylefeaturetttop{} \xdef\stylefeaturebbbottom{} + \xdef\stylefeaturettttop{} \xdef\stylefeaturebbbbottom{} \loopcount=0 \loop \advance\loopcount by 1 @@ -10202,6 +11038,10 @@ \advance\loopcount by 1\relax \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\remove@fromseq\seq@line + \ifT@coffee + \xdef\TC@cons{\csname TC0\endcsname} + \expandafter\remove@fromTC\TC@cons + \fi \ifnum\loopcount<\seq@count \repeat \fi \ifstop@ @@ -10284,15 +11124,23 @@ \xdef\consensus{} \xdef\constopo{} \xdef\frame@on{0} - \xdef\textfeaturetop{} \xdef\featureontop{0} - \xdef\textfeaturettop{} \xdef\featureonttop{0} - \xdef\textfeaturebottom{} \xdef\featureonbottom{0} - \xdef\textfeaturebbottom{}\xdef\featureonbbottom{0} + \xdef\textfeaturetop{} \xdef\featureontop{0} + \xdef\textfeaturettop{} \xdef\featureonttop{0} + \xdef\textfeaturetttop{} \xdef\featureontttop{0} + \xdef\textfeaturettttop{} \xdef\featureonttttop{0} + \xdef\textfeaturebottom{} \xdef\featureonbottom{0} + \xdef\textfeaturebbottom{} \xdef\featureonbbottom{0} + \xdef\textfeaturebbbottom{} \xdef\featureonbbbottom{0} + \xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0} \xdef\styleframe{} \xdef\stylehidebar{} \xdef\stylefeaturetop{} \xdef\stylefeaturettop{} + \xdef\stylefeaturetttop{} + \xdef\stylefeaturettttop{} \xdef\stylefeaturebottom{} - \xdef\stylefeaturebbottom{}} + \xdef\stylefeaturebbottom{} + \xdef\stylefeaturebbbottom{} + \xdef\stylefeaturebbbbottom{}} \def\guess@protein{\seqtype{P}\message{}} \def\guess@DNA{\seqtype{N}\message{}} \def\residue@count{% @@ -10384,7 +11232,12 @@ \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 + \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi + \total@count=\end@count\relax + \xdef\first@{\csname res@count\start@seq\endcsname} + \advance\total@count by \first@\relax + \xdef\first@{\the\total@count} + \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi \ifshow@sublogo \prep@sublogo \fi \ifshow@logo \prep@logo \fi \ifnum\seq@pointer>\res@perline \block@output \fi @@ -10428,7 +11281,12 @@ \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 + \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi + \total@count=\end@count\relax + \xdef\first@{\csname res@count\start@seq\endcsname} + \advance\total@count by \first@\relax + \xdef\first@{\the\total@count} + \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi \ifshow@sublogo \prep@sublogo \fi \ifshow@logo \prep@logo \fi \ifnum\seq@pointer>\res@perline \block@output \fi @@ -10568,8 +11426,12 @@ \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes} @@ -10581,6 +11443,7 @@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{false} + \expandafter\xdef\csname hide@@@seq\the\loopcount\endcsname{false} \expandafter\xdef\csname hide@name\the\loopcount\endcsname{no} \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} \expandafter\xdef\csname hide@number\the\loopcount\endcsname{no} @@ -10592,8 +11455,12 @@ \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{no} \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{0} @@ -10635,10 +11502,14 @@ \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} - \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bbottom}\expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \fontfamily{\namestext@family} \fontseries{\namestext@series} \fontshape{\namestext@shape} @@ -10682,17 +11553,18 @@ \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} - \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} - \xdef\bottop@{bbottom}\expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \innerloopcount = \csname seq@len\the\loopcount\endcsname \advance\innerloopcount by \csname seq@start\the\loopcount\endcsname \advance\innerloopcount by -1 \expandafter\xdef\csname seq@len\the\loopcount\endcsname{\the\innerloopcount} - \ifsh@wg@ps - \expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999} - \fi \advance\loopcount by 1 \ifnum\loopcount>\seq@count \else \repeat \advance\name@width by 1em @@ -10902,23 +11774,29 @@ \advance\loopcount by 1\relax \xdef\@lign@count{\the\loopcount} \start@true \xdef\start@num{1} \xdef\start@seq{0} -\stop@false \xdef\end@num{99999999} \xdef\seq@regions{0} +\stop@false \xdef\end@num{n} \xdef\seq@regions{0} \cons@count=0 \expandafter\xdef\csname res@count0\endcsname{0} \xdef\allow@zero{n} \xdef\c@ns@shift{0} \regionalshadefalse\regionalemphfalse\regionaltintfalse \frame@false \xdef\ruler@rot{0} -\topfeaturefalse\bottomfeaturefalse -\ttopfeaturefalse\bbottomfeaturefalse +\topfeaturefalse \bottomfeaturefalse +\ttopfeaturefalse \bbottomfeaturefalse +\tttopfeaturefalse \bbbottomfeaturefalse +\ttttopfeaturefalse \bbbbottomfeaturefalse \all@fshadefalse\hidecharfalse \xdef\finger@linenum{0} \xdef\hide@seqs{n} \xdef\dssp@num{0} \xdef\stride@num{0} \xdef\PHD@num{0} \xdef\HMMTOP@num{0} -\xdef\bottop@{top} \expandafter\xdef\csname feature@\bottop@\endcsname{0} -\xdef\bottop@{ttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} -\xdef\bottop@{bottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} -\xdef\bottop@{bbottom}\expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{top} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{ttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{tttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{ttttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} +\xdef\bottop@{bbbbottom}\expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\frame@{0} \xdef\show@Hdssp{no} \xdef\show@Gdssp{no} \xdef\show@Idssp{no} \xdef\show@Edssp{no} \xdef\show@Bdssp{no} \xdef\show@Tdssp{no} @@ -10928,23 +11806,36 @@ \xdef\show@itop{no} \xdef\show@etop{no} \xdef\show@TMtop{no} \xdef\show@i@HMMTOP{no} \xdef\show@e@HMMTOP{no} \xdef\show@TM@HMMTOP{no} \xdef\show@Hsec{no} \xdef\show@Esec{no} -\xdef\collect@restop{no} \xdef\collect@resttop{no} -\xdef\collect@resbottom{no} \xdef\collect@resbbottom{no} -\xdef\tr@nslatetop{} \xdef\tr@nslatettop{} -\xdef\tr@nslatebottom{} \xdef\tr@nslatebbottom{} -\xdef\tr@nsseqtop{0} \xdef\tr@nsseqttop{0} -\xdef\tr@nsseqbottom{0} \xdef\tr@nsseqbbottom{0} -\xdef\triple@counttop{0} \xdef\triple@countttop{0} -\xdef\triple@countbottom{0} \xdef\triple@countbbottom{0} -\xdef\last@@restop{} \xdef\last@@resttop{} -\xdef\last@@resbottom{} \xdef\last@@resbbottom{} -\xdef\out@put{y} \xdef\m@p{no} -\xdef\t@sp@ce{0mm} \xdef\tt@sp@ce{0mm} -\xdef\b@sp@ce{0mm} \xdef\bb@sp@ce{0mm} +\xdef\collect@restop{no} \xdef\collect@resttop{no} +\xdef\collect@restttop{no} \xdef\collect@resttttop{no} +\xdef\collect@resbottom{no} \xdef\collect@resbbottom{no} +\xdef\collect@resbbbottom{no}\xdef\collect@resbbbbottom{no} +\xdef\tr@nslatetop{} \xdef\tr@nslatettop{} +\xdef\tr@nslatetttop{} \xdef\tr@nslatettttop{} +\xdef\tr@nslatebottom{} \xdef\tr@nslatebbottom{} +\xdef\tr@nslatebbbottom{} \xdef\tr@nslatebbbbottom{} +\xdef\tr@nsseqtop{0} \xdef\tr@nsseqttop{0} +\xdef\tr@nsseqtttop{0} \xdef\tr@nsseqttttop{0} +\xdef\tr@nsseqbottom{0} \xdef\tr@nsseqbbottom{0} +\xdef\tr@nsseqbbbottom{0} \xdef\tr@nsseqbbbbottom{0} +\xdef\triple@counttop{0} \xdef\triple@countttop{0} +\xdef\triple@counttttop{0} \xdef\triple@countttttop{0} +\xdef\triple@countbottom{0} \xdef\triple@countbbottom{0} +\xdef\triple@countbbbottom{0}\xdef\triple@countbbbbottom{0} +\xdef\last@@restop{} \xdef\last@@resttop{} +\xdef\last@@restttop{} \xdef\last@@resttttop{} +\xdef\last@@resbottom{} \xdef\last@@resbbottom{} +\xdef\last@@resbbbottom{} \xdef\last@@resbbbbottom{} +\xdef\out@put{y} \xdef\m@p{no} +\xdef\t@sp@ce{0mm} \xdef\tt@sp@ce{0mm} +\xdef\ttt@sp@ce{0mm} \xdef\tttt@sp@ce{0mm} +\xdef\b@sp@ce{0mm} \xdef\bb@sp@ce{0mm} +\xdef\bbb@sp@ce{0mm} \xdef\bbbb@sp@ce{0mm} \xdef\seq@gap@num{0} \xdef\h@ndalign{no} \xdef\sep@space{0pt} \xdef\c@pshort{n} \xdef\bottom@stretch{n} \xdef\bbottom@stretch{n} +\xdef\bbbottom@stretch{n} \xdef\bbbbottom@stretch{n} \xdef\c@nscol{} \xdef\c@nssc@le{ColdHot} \xdef\collect@cons@colors{no} \xdef\cons@now{no} \xdef\res@numA{0} \xdef\res@numB{0} @@ -10993,6 +11884,7 @@ \xdef\divref@{0} \xdef\all@thresh@ld{100} \all@shadefalse \hidefeaturenames \hidefeaturestylenames +\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% -- cgit v1.2.3