From 1335c8dc79c73826f03e31bdd3fb30cbe415839f Mon Sep 17 00:00:00 2001 From: Karl Berry Date: Fri, 13 Jan 2006 00:08:56 +0000 Subject: texshade git-svn-id: svn://tug.org/texlive/trunk@1381 c570f23f-e606-0410-a88d-b1316a301751 --- Master/texmf-dist/tex/latex/texshade/texshade.def | 167 + Master/texmf-dist/tex/latex/texshade/texshade.sty | 8425 +++++++++++++++++++++ 2 files changed, 8592 insertions(+) create mode 100644 Master/texmf-dist/tex/latex/texshade/texshade.def create mode 100644 Master/texmf-dist/tex/latex/texshade/texshade.sty (limited to 'Master/texmf-dist') diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.def b/Master/texmf-dist/tex/latex/texshade/texshade.def new file mode 100644 index 00000000000..be63e0f7c69 --- /dev/null +++ b/Master/texmf-dist/tex/latex/texshade/texshade.def @@ -0,0 +1,167 @@ + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% This example file contains all standard settings of the TeXshade %%%%% +%%%%% package. It can be used as a template for the creation of perso- %%%%% +%%%%% nal parameter files. All TeXshade user commands are allowed and %%%%% +%%%%% functional when specified here. %%%%% +%%%%% %%%%% +%%%%% To activate these settings for your alignment load this file by %%%%% +%%%%% naming it as optional parameter at the beginning of the texshade %%%%% +%%%%% environment, e.g. %%%%% +%%%%% %%%%% +%%%%% \begin{texshade}[myparameterfile]{alignmentfile} %%%%% +%%%%% . %%%%% +%%%%% . %%%%% +%%%%% \end{texshade} %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +\shadingmode{identical} % Shade identical residues only +\shadingcolors{blues} % Select the blue color scheme for shading +\constoallseqs % Calculate consensus considering all seqs +\threshold{50} % Consensus threshold percentage is 50 +\residuesperline{999} % As many residues as possible per line +\numberingwidth{9999} % Assign space for 4 digit numbering +\charstretch{1.15} % Stretch character width 1.15fold +\linestretch{1} % Do not stretch lines +\gapchar{.} % . is printed in sequence gaps +\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt +\gapcolors{Black}{White} % Gap symbols appear `Black on White' +\numberingcolor{Black} % Numbering color is `Black' +\shownumbering{left} % Show sequence numbering on the left +\namescolor{Black} % Names' color is `Black' +\shownames{right} % Show sequence names on the right +\consensuscolors{Black}{White} % All consensus symbols/letters + {Black}{White} % appear `Black on White' + {Black}{White} % +\showconsensus{bottom} % Show consensus line at bottom with +\defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match +\rulercolor{Black} % Ruler's color is `Black' +\hideruler % Do not show the ruler +\showleadinggaps % Show gap symbols before sequence start +\rulersteps{10} % Ruler ticks every 10 residues +\legendcolor{Black} % Legend text color is `Black' +\hidelegend % Do not show the legend +\alignment{center} % Center alignment on page +\medsepline % Medium height if separation line is on +\medblockskip % Medium skip between sequence blocks +\flexblockspace % Use optimized space between blocks +\featurerule{0.5ex} % Set feature rule thickness to 1/5 ex +\bargraphstretch{1} % Do not stretch bars in feature graphs +\colorscalestretch{1} % Do not stretch color scales in features +\backtranstext{horizontal} % Horizontal triplets in feature texts +\backtranslabel{alternating} % Alternating triplets in feature styles +\setfamily{residues}{tt} % Use typewriter family for residues +\setseries{residues}{md} % Use normal series for residues +\setshape {residues}{up} % Use upright shape for residues +\setsize {residues}{normalsize} % Use normal size for residues +\setfamily{numbering}{tt} % Use typewriter family for numbering +\setseries{numbering}{md} % Use normal series for numbering +\setshape {numbering}{up} % Use upright shape for numbering +\setsize {numbering}{normalsize} % Use normal size for numbering +\setfamily{names}{tt} % Use typewriter family for names +\setseries{names}{md} % Use normal series for names +\setshape {names}{up} % Use upright shape for names +\setsize {names}{normalsize} % Use normal size for names +\setfamily{features}{rm} % Use roman family for feature texts +\setseries{features}{md} % Use normal series for feature texts +\setshape {features}{it} % Use italics shape for feature texts +\setsize {features}{normalsize} % Use normal size for feature texts +\setfamily{legend}{tt} % Use typewriter family for legend texts +\setseries{legend}{md} % Use normal series for legend texts +\setshape {legend}{up} % Use upright shape for legend texts +\setsize {legend}{normalsize} % Use normal size for legend texts +\tintdefault{medium} % Use medium tint intensity +\emphdefault{it} % Use italics to emphasize regions +\showonPHDsec{alpha,beta} % Show helices and strands (PHD input) +\showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input) +\showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input) +\showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input) +\showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input) +\secondcolumnDSSP % Use numbering from 2. column in DSSP +\appearance{PHDtopo}{internal} % \ + {bottom}{'-'} % \ + {int.\ \Alphacount} % | +\appearance{PHDtopo}{external} % | + {top}{,-,} % | + {ext.\ \Alphacount} % | +\appearance{PHDtopo}{TM}{top} % | + {box[LightGray]:TM\numcount}{} % | +\appearance{HMMTOP}{internal} % | + {bottom}{---} % | + {int.\ \Alphacount} % | +\appearance{HMMTOP}{external} % | + {top}{---} % | + {ext.\ \Alphacount} % | +\appearance{HMMTOP}{TM}{top} % | + {helix}{TM\numcount} % | +\appearance{PHDsec}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{PHDsec}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | Definitions for the appearance of +\appearance{STRIDE}{3-10}{top} % \ + {fill:$\circ$}{3$_{10}$} % > secondary structures included from| +\appearance{STRIDE}{pi} % / + {top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files. +\appearance{STRIDE}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{STRIDE}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{DSSP}{3-10}{top} % | + {fill:$\circ$}{3$_{10}$} % | +\appearance{DSSP}{pi} % | + {top}{---}{$\pi$} % | +\appearance{DSSP}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{DSSP}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{DSSP}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{bend}{top} % / + {fill:$\diamond$}{} % / + +\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity + +\pepsims{F}{YW} % Y and W are similar to F +\pepsims{Y}{WF} % W and F are similar to Y +\pepsims{W}{YF} % Y and F are similar to W + +\pepsims{I}{LVM} % L, V and M are similar to I +\pepsims{L}{VMI} % V, M and I are similar to L +\pepsims{V}{MIL} % M, I and L are similar to V + +\pepsims{R}{KH} % K and H are similar to R +\pepsims{K}{HR} % H and R are similar to K +\pepsims{H}{RK} % R and K are similar to H + +\pepsims{A}{GS} % G and S are similar to A +\pepsims{G}{A} % A (but not S) is similar to G + +\pepsims{S}{TA} % T and A are similar to S +\pepsims{T}{S} % S (but not A) is similar to T + +\pepsims{D}{EN} % E and N (but not Q) are similar to D +\pepsims{E}{DQ} % D and Q (but not N) are similar to E +\pepsims{N}{QD} % Q and D (but not E) are similar to N +\pepsims{Q}{NE} % N and E (but not D) are similar to Q + +\DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity + +\DNAsims{A}{GR} % G and R are similar to A +\DNAsims{G}{AR} % A and R are similar to G +\DNAsims{R}{AG} % A and G are similar to R + +\DNAsims{C}{TY} % T and Y are similar to C +\DNAsims{T}{CY} % C and Y are similar to T +\DNAsims{Y}{CT} % C and T are similar to Y diff --git a/Master/texmf-dist/tex/latex/texshade/texshade.sty b/Master/texmf-dist/tex/latex/texshade/texshade.sty new file mode 100644 index 00000000000..2ba3a2cdc1f --- /dev/null +++ b/Master/texmf-dist/tex/latex/texshade/texshade.sty @@ -0,0 +1,8425 @@ +%% +%% This is file `texshade.sty', +%% generated with the docstrip utility. +%% +%% The original source files were: +%% +%% texshade.dtx (with options: `texshade') +%% +%% LaTeX package for typesetting nucleotide and peptide alignments +%% +%% Copyright (C) 1999-2005 Eric Beitz +%% See the file texshade.txt +%% + +\NeedsTeXFormat{LaTeX2e} +\ProvidesPackage{texshade}[2005/04/13 LaTeX TeXshade (v1.12)] +\message{Package `texshade', Version 1.12 of 2005/09/20.} + +\PassOptionsToPackage{dvips}{color} +\DeclareOption*{% + \PassOptionsToPackage{\CurrentOption}{color}% +} +\ProcessOptions +\RequirePackage{color} + +\expandafter\ifx\csname TeXshade\endcsname\relax \else \endinput \fi + +\expandafter\ifx\csname TeXtopo\endcsname\relax \else + \PackageError{TeXtopo} + {TeXtopo loaded before TeXshade} + {\MessageBreak + For the proper function of the TeXtopo/TeXshade combo the \MessageBreak + TeXshade package must be loaded before the TeXtopo package.\MessageBreak + Please change the order of the \noexpand\usepackage commands in your + \MessageBreak + document header section or use the `biotex.sty'.\MessageBreak\MessageBreak + Quit here by typing \space X . \MessageBreak +} +\fi + +\catcode`\@11 + +\newread\structurefile \newwrite\featurefile +\newread\alignfile + +\expandafter\ifx\csname blacktriangleright\endcsname\relax + \openin\structurefile = amssymb.sty + \ifeof\structurefile + \message{} + \def\blacktriangleright{% + \rule[\width@tmp]{0.65ex}{\temp@@length}\kern-0.55ex\ensuremath{\bullet}% + } + \def\blacktriangleleft{% + \ensuremath{\bullet}\kern-0.55ex\rule[\width@tmp]{0.65ex}{\temp@@length}% + } + \else \RequirePackage[]{amssymb} \fi + \closein\structurefile +\fi + +\newcount\loopcount \newcount\innerloopcount \newcount\outerloopcount +\newcount\seq@count \newcount\killseq@count +\newcount\seq@percent \newcount\res@count +\newcount\seq@pointer \newcount\pos@count +\newcount\res@perline \newcount\end@count +\newcount\cons@count \expandafter\newcount\csname res@count0\endcsname +\newcount\temp@count \newcount\triple@count + +\newlength\box@width \newlength\name@width +\newlength\box@depth \newlength\width@tmp +\newlength\box@height \newlength\number@width +\newlength\char@stretch \newlength\line@stretch +\newlength\center@fill \newlength\arrow@width +\newlength\arrow@height \newlength\rule@thick +\newlength\arrow@thick +\newlength\equal@width \newlength\equal@tmp +\newlength\equal@height \newlength\temp@@length +\newlength\vspace@legend +\newlength\hspace@legend + +\newif\ifletter \newif\ifnumber +\newif\ifnewres \newif\ifall@shade +\newif\ifnames@right \newif\ifnumbers@left +\newif\ifhide@cons \newif\ifshow@cons +\newif\iffuncmode \newif\iflegend@ +\newif\ifnumbers@ \newif\ifnames@ +\newif\ifgerm@n \newif\ifsp@nish +\newif\ifrpl@fix +\newif\ifnosh@de \newif\ifregionalshade +\newif\ifstart@ \newif\ifstop@ +\newif\iftopfeature \newif\ifbottomfeature +\newif\ifttopfeature \newif\ifbbottomfeature +\newif\ifall@fshade \newif\ifregionalemph +\newif\ifframe@ \newif\ifregionaltint +\newif\ifhidechar \newif\ifsh@wg@ps +\newif\ifsimmode +\newif\ifregionaltintnow +\newif\ifregionalemphnow +\newif\ifregionalshadenow +\newif\iftopfeaturenow +\newif\ifttopfeaturenow +\newif\ifbottomfeaturenow +\newif\ifbbottomfeaturenow +\newif\ifframenow +\newif\iffix@ + +\expandafter\ifx\csname mdqon\endcsname\relax + \germ@nfalse \sp@nishfalse \def\cons@name{consensus} +\else \germ@ntrue \sp@nishfalse \def\cons@name{Konsensus} \fi + +\def\n@me{Name:} \def\@msf{MSF:} \def\he@derend{//} \def\ampers@nd{&} +\def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:} +\def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H} +\def\gap@char{.} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.} +\def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}} +\def\fgroup@num{0} \def\max@seqnumber{0} \def\@lign@count{0} +\def\resn@m@tch{upper} \def\ressimm@tch{upper} +\def\resm@tch{upper} \def\res@llm@tch{upper} +\def\tr@ns{translate} \def\gr@ydef@ult{GrayDefault} +\xdef\par@{\expandafter\string\par} +\expandafter\def\csname fg@textcolor/\endcsname{White} +\expandafter\def\csname fg@color/\endcsname{White} +\expandafter\def\csname func@style/\endcsname{\csname textup\endcsname} +\expandafter\def\csname func@style*\endcsname{\csname textup\endcsname} +\expandafter\def\csname funcm@tch/\endcsname{upper} +\expandafter\def\csname funcm@tch*\endcsname{upper} + +\setlength\hspace@legend{0pt} \setlength\vspace@legend{0pt} +\triple@count=0 \cons@count=0 + +\def\clear@sims{% + \expandafter\xdef\csname \prfx simA\endcsname{(1)A} + \expandafter\xdef\csname \prfx simB\endcsname{(1)B} + \expandafter\xdef\csname \prfx simC\endcsname{(1)C} + \expandafter\xdef\csname \prfx simD\endcsname{(1)D} + \expandafter\xdef\csname \prfx simE\endcsname{(1)E} + \expandafter\xdef\csname \prfx simF\endcsname{(1)F} + \expandafter\xdef\csname \prfx simG\endcsname{(1)G} + \expandafter\xdef\csname \prfx simH\endcsname{(1)H} + \expandafter\xdef\csname \prfx simI\endcsname{(1)I} + \expandafter\xdef\csname \prfx simJ\endcsname{(1)J} + \expandafter\xdef\csname \prfx simK\endcsname{(1)K} + \expandafter\xdef\csname \prfx simL\endcsname{(1)L} + \expandafter\xdef\csname \prfx simM\endcsname{(1)M} + \expandafter\xdef\csname \prfx simN\endcsname{(1)N} + \expandafter\xdef\csname \prfx simO\endcsname{(1)O} + \expandafter\xdef\csname \prfx simP\endcsname{(1)P} + \expandafter\xdef\csname \prfx simQ\endcsname{(1)Q} + \expandafter\xdef\csname \prfx simR\endcsname{(1)R} + \expandafter\xdef\csname \prfx simS\endcsname{(1)S} + \expandafter\xdef\csname \prfx simT\endcsname{(1)T} + \expandafter\xdef\csname \prfx simU\endcsname{(1)U} + \expandafter\xdef\csname \prfx simV\endcsname{(1)V} + \expandafter\xdef\csname \prfx simW\endcsname{(1)W} + \expandafter\xdef\csname \prfx simX\endcsname{(1)X} + \expandafter\xdef\csname \prfx simY\endcsname{(1)Y} + \expandafter\xdef\csname \prfx simZ\endcsname{(1)Z} +} + +\xdef\pepmwA{711} \xdef\pepmwB{1146} \xdef\pepmwC{1032} +\xdef\pepmwD{1151} \xdef\pepmwE{1291} \xdef\pepmwF{1472} +\xdef\pepmwG{571} \xdef\pepmwH{1372} \xdef\pepmwI{1132} +\xdef\pepmwJ{0} \xdef\pepmwK{1282} \xdef\pepmwL{1132} +\xdef\pepmwM{1312} \xdef\pepmwN{1141} \xdef\pepmwO{0} +\xdef\pepmwP{971} \xdef\pepmwQ{1281} \xdef\pepmwR{1562} +\xdef\pepmwS{871} \xdef\pepmwT{1011} \xdef\pepmwU{0} +\xdef\pepmwV{991} \xdef\pepmwW{1862} \xdef\pepmwX{1282} +\xdef\pepmwY{1632} \xdef\pepmwZ{1286} + +\xdef\DNAmwA{3462} \xdef\DNAmwB{0} \xdef\DNAmwC{3222} +\xdef\DNAmwD{0} \xdef\DNAmwE{0} \xdef\DNAmwF{0} +\xdef\DNAmwG{3622} \xdef\DNAmwH{0} \xdef\DNAmwI{0} +\xdef\DNAmwJ{0} \xdef\DNAmwK{0} \xdef\DNAmwL{0} +\xdef\DNAmwM{0} \xdef\DNAmwN{0} \xdef\DNAmwO{0} +\xdef\DNAmwP{0} \xdef\DNAmwQ{0} \xdef\DNAmwR{0} +\xdef\DNAmwS{0} \xdef\DNAmwT{3372} \xdef\DNAmwU{3232} +\xdef\DNAmwV{0} \xdef\DNAmwW{0} \xdef\DNAmwX{0} +\xdef\DNAmwY{0} \xdef\DNAmwZ{0} + +\xdef\pepchargeA{0} \xdef\pepchargeB{0} \xdef\pepchargeC{-30} +\xdef\pepchargeD{-1000} \xdef\pepchargeE{-1000} \xdef\pepchargeF{0} +\xdef\pepchargeG{0} \xdef\pepchargeH{165} \xdef\pepchargeI{0} +\xdef\pepchargeJ{0} \xdef\pepchargeK{1000} \xdef\pepchargeL{0} +\xdef\pepchargeM{0} \xdef\pepchargeN{0} \xdef\pepchargeO{0} +\xdef\pepchargeP{0} \xdef\pepchargeQ{0} \xdef\pepchargeR{1000} +\xdef\pepchargeS{0} \xdef\pepchargeT{0} \xdef\pepchargeU{0} +\xdef\pepchargeV{0} \xdef\pepchargeW{0} \xdef\pepchargeX{0} +\xdef\pepchargeY{0} \xdef\pepchargeZ{0} +\xdef\chargeNterm{910} \xdef\chargeCterm{-1000} + +\xdef\chargeA{0} \xdef\chargeB{0} \xdef\chargeC{0} +\xdef\chargeD{-50} \xdef\chargeE{-50} \xdef\chargeF{0} +\xdef\chargeG{0} \xdef\chargeH{30} \xdef\chargeI{0} +\xdef\chargeJ{0} \xdef\chargeK{50} \xdef\chargeL{0} +\xdef\chargeM{0} \xdef\chargeN{0} \xdef\chargeO{0} +\xdef\chargeP{0} \xdef\chargeQ{0} \xdef\chargeR{50} +\xdef\chargeS{0} \xdef\chargeT{0} \xdef\chargeU{0} +\xdef\chargeV{0} \xdef\chargeW{0} \xdef\chargeX{0} +\xdef\chargeY{0} \xdef\chargeZ{0} + +\xdef\molwA{11} \xdef\molwB{45} \xdef\molwC{36} +\xdef\molwD{45} \xdef\molwE{66} \xdef\molwF{70} +\xdef\molwG{1} \xdef\molwH{62} \xdef\molwI{44} +\xdef\molwJ{N} \xdef\molwK{55} \xdef\molwL{44} +\xdef\molwM{58} \xdef\molwN{44} \xdef\molwO{N} +\xdef\molwP{31} \xdef\molwQ{55} \xdef\molwR{77} +\xdef\molwS{19} \xdef\molwT{34} \xdef\molwU{N} +\xdef\molwV{33} \xdef\molwW{100} \xdef\molwX{55} +\xdef\molwY{82} \xdef\molwZ{66} + +\xdef\HydroA{21} \xdef\HydroB{N} \xdef\HydroC{10} +\xdef\HydroD{-31} \xdef\HydroE{-25} \xdef\HydroF{41} +\xdef\HydroG{16} \xdef\HydroH{-14} \xdef\HydroI{47} +\xdef\HydroJ{N} \xdef\HydroK{-52} \xdef\HydroL{36} +\xdef\HydroM{22} \xdef\HydroN{-27} \xdef\HydroO{N} +\xdef\HydroP{4} \xdef\HydroQ{-29} \xdef\HydroR{-53} +\xdef\HydroS{-6} \xdef\HydroT{-2} \xdef\HydroU{N} +\xdef\HydroV{37} \xdef\HydroW{28} \xdef\HydroX{N} +\xdef\HydroY{9} \xdef\HydroZ{N} + +\xdef\consCC{100} \xdef\consCS{67} \xdef\consCT{33} \xdef\consCP{33} \xdef\consCA{33} +\xdef\consCG{50} \xdef\consCN{33} \xdef\consCD{17} \xdef\consCE{0} \xdef\consCQ{17} +\xdef\consCH{33} \xdef\consCR{33} \xdef\consCK{0} \xdef\consCM{33} \xdef\consCI{33} +\xdef\consCL{33} \xdef\consCV{33} \xdef\consCF{50} \xdef\consCY{50} \xdef\consCW{50} +\expandafter\xdef\csname consC.\endcsname{0} + +\xdef\consSC{67} \xdef\consSS{100} \xdef\consST{83} \xdef\consSP{67} \xdef\consSA{83} +\xdef\consSG{83} \xdef\consSN{83} \xdef\consSD{67} \xdef\consSE{50} \xdef\consSQ{50} +\xdef\consSH{50} \xdef\consSR{50} \xdef\consSK{50} \xdef\consSM{33} \xdef\consSI{33} +\xdef\consSL{33} \xdef\consSV{67} \xdef\consSF{50} \xdef\consSY{50} \xdef\consSW{33} +\expandafter\xdef\csname consS.\endcsname{0} + +\xdef\consTC{33} \xdef\consTS{83} \xdef\consTT{100} \xdef\consTP{67} \xdef\consTA{83} +\xdef\consTG{67} \xdef\consTN{67} \xdef\consTD{50} \xdef\consTE{50} \xdef\consTQ{50} +\xdef\consTH{33} \xdef\consTR{50} \xdef\consTK{67} \xdef\consTM{50} \xdef\consTI{50} +\xdef\consTL{33} \xdef\consTV{67} \xdef\consTF{33} \xdef\consTY{33} \xdef\consTW{17} +\expandafter\xdef\csname consT.\endcsname{0} + +\xdef\consPC{33} \xdef\consPS{67} \xdef\consPT{67} \xdef\consPP{100} \xdef\consPA{83} +\xdef\consPG{67} \xdef\consPN{33} \xdef\consPD{50} \xdef\consPE{50} \xdef\consPQ{50} +\xdef\consPH{50} \xdef\consPR{50} \xdef\consPK{33} \xdef\consPM{33} \xdef\consPI{33} +\xdef\consPL{50} \xdef\consPV{67} \xdef\consPF{50} \xdef\consPY{33} \xdef\consPW{33} +\expandafter\xdef\csname consP.\endcsname{0} + +\xdef\consAC{33} \xdef\consAS{83} \xdef\consAT{83} \xdef\consAP{83} \xdef\consAA{100} +\xdef\consAG{83} \xdef\consAN{50} \xdef\consAD{67} \xdef\consAE{67} \xdef\consAQ{50} +\xdef\consAH{33} \xdef\consAR{33} \xdef\consAK{50} \xdef\consAM{50} \xdef\consAI{33} +\xdef\consAL{33} \xdef\consAV{83} \xdef\consAF{50} \xdef\consAY{33} \xdef\consAW{33} +\expandafter\xdef\csname consA.\endcsname{0} + +\xdef\consGC{50} \xdef\consGS{83} \xdef\consGT{67} \xdef\consGP{67} \xdef\consGA{83} +\xdef\consGG{100} \xdef\consGN{50} \xdef\consGD{67} \xdef\consGE{67} \xdef\consGQ{33} +\xdef\consGH{17} \xdef\consGR{50} \xdef\consGK{33} \xdef\consGM{17} \xdef\consGI{33} +\xdef\consGL{33} \xdef\consGV{67} \xdef\consGF{33} \xdef\consGY{33} \xdef\consGW{50} +\expandafter\xdef\csname consG.\endcsname{0} + +\xdef\consNC{33} \xdef\consNS{83} \xdef\consNT{67} \xdef\consNP{33} \xdef\consNA{50} +\xdef\consNG{50} \xdef\consNN{100} \xdef\consND{83} \xdef\consNE{67} \xdef\consNQ{50} +\xdef\consNH{67} \xdef\consNR{50} \xdef\consNK{67} \xdef\consNM{17} \xdef\consNI{33} +\xdef\consNL{17} \xdef\consNV{33} \xdef\consNF{33} \xdef\consNY{50} \xdef\consNW{0} +\expandafter\xdef\csname consN.\endcsname{0} + +\xdef\consDC{17} \xdef\consDS{67} \xdef\consDT{50} \xdef\consDP{50} \xdef\consDA{67} +\xdef\consDG{67} \xdef\consDN{83} \xdef\consDD{100} \xdef\consDE{83} \xdef\consDQ{67} +\xdef\consDH{50} \xdef\consDR{33} \xdef\consDK{50} \xdef\consDM{33} \xdef\consDI{17} +\xdef\consDL{17} \xdef\consDV{50} \xdef\consDF{17} \xdef\consDY{33} \xdef\consDW{0} +\expandafter\xdef\csname consD.\endcsname{0} + +\xdef\consEC{0} \xdef\consES{50} \xdef\consET{50} \xdef\consEP{50} \xdef\consEA{67} +\xdef\consEG{67} \xdef\consEN{67} \xdef\consED{83} \xdef\consEE{100} \xdef\consEQ{67} +\xdef\consEH{33} \xdef\consER{50} \xdef\consEK{67} \xdef\consEM{33} \xdef\consEI{17} +\xdef\consEL{17} \xdef\consEV{67} \xdef\consEF{33} \xdef\consEY{17} \xdef\consEW{17} +\expandafter\xdef\csname consE.\endcsname{0} + +\xdef\consQC{17} \xdef\consQS{50} \xdef\consQT{50} \xdef\consQP{50} \xdef\consQA{50} +\xdef\consQG{33} \xdef\consQN{50} \xdef\consQD{67} \xdef\consQE{67} \xdef\consQQ{100} +\xdef\consQH{67} \xdef\consQR{50} \xdef\consQK{67} \xdef\consQM{33} \xdef\consQI{17} +\xdef\consQL{33} \xdef\consQV{33} \xdef\consQF{17} \xdef\consQY{33} \xdef\consQW{17} +\expandafter\xdef\csname consQ.\endcsname{0} + +\xdef\consHC{33} \xdef\consHS{50} \xdef\consHT{33} \xdef\consHP{50} \xdef\consHA{33} +\xdef\consHG{17} \xdef\consHN{67} \xdef\consHD{50} \xdef\consHE{33} \xdef\consHQ{67} +\xdef\consHH{100} \xdef\consHR{67} \xdef\consHK{50} \xdef\consHM{33} \xdef\consHI{33} +\xdef\consHL{50} \xdef\consHV{17} \xdef\consHF{33} \xdef\consHY{50} \xdef\consHW{17} +\expandafter\xdef\csname consH.\endcsname{0} + +\xdef\consRC{33} \xdef\consRS{50} \xdef\consRT{50} \xdef\consRP{50} \xdef\consRA{33} +\xdef\consRG{50} \xdef\consRN{50} \xdef\consRD{33} \xdef\consRE{50} \xdef\consRQ{50} +\xdef\consRH{67} \xdef\consRR{100} \xdef\consRK{83} \xdef\consRM{33} \xdef\consRI{33} +\xdef\consRL{33} \xdef\consRV{33} \xdef\consRF{17} \xdef\consRY{17} \xdef\consRW{33} +\expandafter\xdef\csname consR.\endcsname{0} + +\xdef\consKC{0} \xdef\consKS{50} \xdef\consKT{67} \xdef\consKP{33} \xdef\consKA{50} +\xdef\consKG{33} \xdef\consKN{67} \xdef\consKD{50} \xdef\consKE{67} \xdef\consKQ{67} +\xdef\consKH{50} \xdef\consKR{83} \xdef\consKK{100} \xdef\consKM{33} \xdef\consKI{33} +\xdef\consKL{33} \xdef\consKV{50} \xdef\consKF{17} \xdef\consKY{17} \xdef\consKW{17} +\expandafter\xdef\csname consK.\endcsname{0} + +\xdef\consMC{33} \xdef\consMS{50} \xdef\consMT{50} \xdef\consMP{33} \xdef\consMA{50} +\xdef\consMG{17} \xdef\consMN{17} \xdef\consMD{33} \xdef\consME{33} \xdef\consMQ{33} +\xdef\consMH{33} \xdef\consMR{33} \xdef\consMK{33} \xdef\consMM{100} \xdef\consMI{67} +\xdef\consML{83} \xdef\consMV{67} \xdef\consMF{50} \xdef\consMY{33} \xdef\consMW{50} +\expandafter\xdef\csname consM.\endcsname{0} + +\xdef\consIC{33} \xdef\consIS{33} \xdef\consIT{50} \xdef\consIP{33} \xdef\consIA{33} +\xdef\consIG{33} \xdef\consIN{33} \xdef\consID{17} \xdef\consIE{17} \xdef\consIQ{17} +\xdef\consIH{33} \xdef\consIR{33} \xdef\consIK{33} \xdef\consIM{67} \xdef\consII{100} +\xdef\consIL{83} \xdef\consIV{33} \xdef\consIF{67} \xdef\consIY{50} \xdef\consIW{50} +\expandafter\xdef\csname consI.\endcsname{0} + +\xdef\consLC{33} \xdef\consLS{33} \xdef\consLT{33} \xdef\consLP{50} \xdef\consLA{33} +\xdef\consLG{33} \xdef\consLN{17} \xdef\consLD{17} \xdef\consLE{17} \xdef\consLQ{33} +\xdef\consLH{50} \xdef\consLR{33} \xdef\consLK{33} \xdef\consLM{83} \xdef\consLI{83} +\xdef\consLL{100} \xdef\consLV{33} \xdef\consLF{67} \xdef\consLY{50} \xdef\consLW{67} +\expandafter\xdef\csname consL.\endcsname{0} + +\xdef\consVC{33} \xdef\consVS{67} \xdef\consVT{67} \xdef\consVP{67} \xdef\consVA{83} +\xdef\consVG{67} \xdef\consVN{33} \xdef\consVD{50} \xdef\consVE{67} \xdef\consVQ{33} +\xdef\consVH{17} \xdef\consVR{33} \xdef\consVK{50} \xdef\consVM{67} \xdef\consVI{33} +\xdef\consVL{33} \xdef\consVV{100} \xdef\consVF{67} \xdef\consVY{50} \xdef\consVW{50} +\expandafter\xdef\csname consV.\endcsname{0} + +\xdef\consFC{50} \xdef\consFS{50} \xdef\consFT{33} \xdef\consFP{50} \xdef\consFA{50} +\xdef\consFG{33} \xdef\consFN{33} \xdef\consFD{17} \xdef\consFE{33} \xdef\consFQ{17} +\xdef\consFH{33} \xdef\consFR{17} \xdef\consFK{17} \xdef\consFM{50} \xdef\consFI{67} +\xdef\consFL{67} \xdef\consFV{67} \xdef\consFF{100} \xdef\consFY{83} \xdef\consFW{50} +\expandafter\xdef\csname consF.\endcsname{0} + +\xdef\consYC{50} \xdef\consYS{50} \xdef\consYT{33} \xdef\consYP{33} \xdef\consYA{33} +\xdef\consYG{33} \xdef\consYN{50} \xdef\consYD{33} \xdef\consYE{17} \xdef\consYQ{33} +\xdef\consYH{50} \xdef\consYR{17} \xdef\consYK{17} \xdef\consYM{33} \xdef\consYI{50} +\xdef\consYL{50} \xdef\consYV{50} \xdef\consYF{83} \xdef\consYY{100} \xdef\consYW{50} +\expandafter\xdef\csname consY.\endcsname{0} + +\xdef\consWC{50} \xdef\consWS{33} \xdef\consWT{17} \xdef\consWP{33} \xdef\consWA{33} +\xdef\consWG{50} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{17} \xdef\consWQ{17} +\xdef\consWH{17} \xdef\consWR{33} \xdef\consWK{17} \xdef\consWM{50} \xdef\consWI{50} +\xdef\consWL{67} \xdef\consWV{50} \xdef\consWF{50} \xdef\consWY{50} \xdef\consWW{100} +\expandafter\xdef\csname consW.\endcsname{0} + +\expandafter\xdef\csname cons.C\endcsname{0} +\expandafter\xdef\csname cons.S\endcsname{0} +\expandafter\xdef\csname cons.T\endcsname{0} +\expandafter\xdef\csname cons.P\endcsname{0} +\expandafter\xdef\csname cons.A\endcsname{0} +\expandafter\xdef\csname cons.G\endcsname{0} +\expandafter\xdef\csname cons.N\endcsname{0} +\expandafter\xdef\csname cons.D\endcsname{0} +\expandafter\xdef\csname cons.E\endcsname{0} +\expandafter\xdef\csname cons.Q\endcsname{0} +\expandafter\xdef\csname cons.H\endcsname{0} +\expandafter\xdef\csname cons.R\endcsname{0} +\expandafter\xdef\csname cons.K\endcsname{0} +\expandafter\xdef\csname cons.M\endcsname{0} +\expandafter\xdef\csname cons.I\endcsname{0} +\expandafter\xdef\csname cons.L\endcsname{0} +\expandafter\xdef\csname cons.V\endcsname{0} +\expandafter\xdef\csname cons.F\endcsname{0} +\expandafter\xdef\csname cons.Y\endcsname{0} +\expandafter\xdef\csname cons.W\endcsname{0} +\expandafter\xdef\csname cons..\endcsname{0} + +\def\c@d@ns{% +\codon{A}{GCA,GCG,GCC,GCT,GCU,GCN} +\codon{B}{---} +\codon{C}{TGC,TGT,UGC,UGU,TGY} +\codon{D}{GAC,GAT,GAU,GAY} +\codon{E}{GAA,GAG,GAR} +\codon{F}{TTC,TTT,UUC,UUU,TTY} +\codon{G}{GGA,GGG,GGC,GGT,GGU,GGN} +\codon{H}{CAC,CAT,CAY} +\codon{I}{ATA,ATC,ATT,AUA,AUC,AUU,ATH} +\codon{J}{---} +\codon{K}{AAA,AAG,AAG,AAR} +\codon{L}{CTA,CTG,CTC,CTT,TTA,TTG,CUG,CUG,CUC,CUU,UUA,UUG,YTN} +\codon{M}{ATG,AUG,ATG} +\codon{N}{AAC,AAT,AAU,AAY} +\codon{O}{---} +\codon{P}{CCA,CCG,CCC,CCT,CCU,CCN} +\codon{Q}{CAA,CAG,CAR} +\codon{R}{AGA,AGG,CGA,CGG,CGC,CGT,CGU,MGN} +\codon{S}{TCT,TCC,TCG,TCA,AGT,AGC,UCU,UCC,UCG,UCA,AGU,WSN} +\codon{T}{ACT,ACC,ACG,ACA,ACU,ACN} +\codon{U}{---} +\codon{V}{GTA,GTG,GTC,GTT,GUA,GUG,GUC,GUU,GTN} +\codon{W}{TGG,UGG,TGG} +\codon{X}{---} +\codon{Y}{TAC,TAT,UAC,UAU,TAY} +\codon{Z}{---} +\codon{.}{TAA,TAG,TGA,UAA,UAG,UGA,TRR} +} + +\definecolor{GreenYellow} {cmyk}{0.15,0,0.69,0} +\definecolor{Yellow} {cmyk}{0,0,1,0} +\definecolor{Goldenrod} {cmyk}{0,0.10,0.84,0} +\definecolor{Dandelion} {cmyk}{0,0.29,0.84,0} +\definecolor{Apricot} {cmyk}{0,0.32,0.52,0} +\definecolor{Peach} {cmyk}{0,0.50,0.70,0} +\definecolor{Melon} {cmyk}{0,0.46,0.50,0} +\definecolor{YellowOrange} {cmyk}{0,0.42,1,0} +\definecolor{Orange} {cmyk}{0,0.61,0.87,0} +\definecolor{BurntOrange} {cmyk}{0,0.51,1,0} +\definecolor{Bittersweet} {cmyk}{0,0.75,1,0.24} +\definecolor{RedOrange} {cmyk}{0,0.77,0.87,0} +\definecolor{Mahagony} {cmyk}{0,0.85,0.87,0.35} +\definecolor{Maroon} {cmyk}{0,0.87,0.68,0.32} +\definecolor{BrickRed} {cmyk}{0,0.89,0.94,0.28} +\definecolor{Red} {cmyk}{0,1,1,0} +\definecolor{OrangeRed} {cmyk}{0,1,0.50,0} +\definecolor{RubineRed} {cmyk}{0,1,0.13,0} +\definecolor{WildStrawberry}{cmyk}{0,0.96,0.39,0} +\definecolor{Salmon} {cmyk}{0,0.53,0.38,0} +\definecolor{CarnationPink} {cmyk}{0,0.63,0,0} +\definecolor{Magenta} {cmyk}{0,1,0,0} +\definecolor{VioletRed} {cmyk}{0,0.81,0,0} +\definecolor{Rhodamine} {cmyk}{0,0.82,0,0} +\definecolor{Mulberry} {cmyk}{0.34,0.90,0,0.02} +\definecolor{RedViolet} {cmyk}{0.07,0.90,0,0.34} +\definecolor{Fuchsia} {cmyk}{0.47,0.91,0,0.08} +\definecolor{Lavender} {cmyk}{0,0.48,0,0} +\definecolor{Thistle} {cmyk}{0.12,0.59,0,0} +\definecolor{Orchid} {cmyk}{0.32,0.64,0,0} +\definecolor{DarkOrchid} {cmyk}{0.40,0.80,0.20,0} +\definecolor{Purple} {cmyk}{0.45,0.86,0,0} +\definecolor{Plum} {cmyk}{0.50,1,0,0} +\definecolor{Violet} {cmyk}{0.79,0.88,0,0} +\definecolor{RoyalPurple} {cmyk}{0.75,0.90,0,0} +\definecolor{BlueViolet} {cmyk}{0.86,0.91,0,0.04} +\definecolor{Periwinkle} {cmyk}{0.57,0.55,0,0} +\definecolor{CadetBlue} {cmyk}{0.62,0.57,0.23,0} +\definecolor{CornflowerBlue}{cmyk}{0.65,0.13,0,0} +\definecolor{MidnightBlue} {cmyk}{0.98,0.13,0,0.43} +\definecolor{NavyBlue} {cmyk}{0.94,0.54,0,0} +\definecolor{RoyalBlue} {cmyk}{1,0.50,0,0} +\definecolor{Blue} {cmyk}{1,1,0,0} +\definecolor{Cerulean} {cmyk}{0.94,0.11,0,0} +\definecolor{Cyan} {cmyk}{1,0,0,0} +\definecolor{ProcessBlue} {cmyk}{0.96,0,0,0} +\definecolor{SkyBlue} {cmyk}{0.62,0,0.12,0} +\definecolor{TurquoisQ} {cmyk}{0.85,0,0.20,0} +\definecolor{TealBlue} {cmyk}{0.86,0,0.34,0.02} +\definecolor{Aquamarine} {cmyk}{0.82,0,0.30,0} +\definecolor{BlueGreen} {cmyk}{0.85,0,0.33,0} +\definecolor{Emerald} {cmyk}{1,0,0.50,0} +\definecolor{JungleGreen} {cmyk}{0.99,0,0.52,0} +\definecolor{SeaGreen} {cmyk}{0.69,0,0.50,0} +\definecolor{Green} {cmyk}{1,0,1,0} +\definecolor{ForestGreen} {cmyk}{0.91,0,0.88,0.12} +\definecolor{PineGreen} {cmyk}{0.92,0,0.59,0.25} +\definecolor{LimeGreen} {cmyk}{0.50,0,1,0} +\definecolor{YellowGreen} {cmyk}{0.44,0,0.74,0} +\definecolor{SpringGreen} {cmyk}{0.26,0,0.76,0} +\definecolor{OliveGreen} {cmyk}{0.64,0,0.95,0.40} +\definecolor{RawSienna} {cmyk}{0,0.72,1,0.45} +\definecolor{Sepia} {cmyk}{0,0.83,1,0.70} +\definecolor{Brown} {cmyk}{0,0.81,1,0.60} +\definecolor{Tan} {cmyk}{0.14,0.42,0.56,0} +\definecolor{White} {cmyk}{0,0,0,0} +\definecolor{Gray0} {cmyk}{0,0,0,0} +\definecolor{Gray5} {cmyk}{0,0,0,0.05} +\definecolor{Gray10} {cmyk}{0,0,0,0.10} +\definecolor{Gray15} {cmyk}{0,0,0,0.15} +\definecolor{Gray20} {cmyk}{0,0,0,0.20} +\definecolor{Gray25} {cmyk}{0,0,0,0.25} +\definecolor{Gray30} {cmyk}{0,0,0,0.30} +\definecolor{LightGray} {cmyk}{0,0,0,0.33} +\definecolor{Gray35} {cmyk}{0,0,0,0.35} +\definecolor{Gray40} {cmyk}{0,0,0,0.40} +\definecolor{Gray45} {cmyk}{0,0,0,0.45} +\definecolor{Gray50} {cmyk}{0,0,0,0.50} +\definecolor{Gray} {cmyk}{0,0,0,0.50} +\definecolor{GrayDefault} {cmyk}{0,0,0,0.50} +\definecolor{Gray55} {cmyk}{0,0,0,0.55} +\definecolor{Gray60} {cmyk}{0,0,0,0.60} +\definecolor{Gray65} {cmyk}{0,0,0,0.65} +\definecolor{DarkGray} {cmyk}{0,0,0,0.66} +\definecolor{Gray70} {cmyk}{0,0,0,0.70} +\definecolor{Gray75} {cmyk}{0,0,0,0.75} +\definecolor{Gray80} {cmyk}{0,0,0,0.80} +\definecolor{Gray85} {cmyk}{0,0,0,0.85} +\definecolor{Gray90} {cmyk}{0,0,0,0.90} +\definecolor{Gray95} {cmyk}{0,0,0,0.95} +\definecolor{Black} {cmyk}{0,0,0,1} +\definecolor{Gray100} {cmyk}{0,0,0,1} +\definecolor{LightGreenYellow} {cmyk}{0.08,0,0.35,0} +\definecolor{LightYellow} {cmyk}{0,0,0.50,0} +\definecolor{LightGoldenrod} {cmyk}{0,0.05,0.42,0} +\definecolor{LightDandelion} {cmyk}{0,0.15,0.42,0} +\definecolor{LightApricot} {cmyk}{0,0.16,0.26,0} +\definecolor{LightPeach} {cmyk}{0,0.25,0.35,0} +\definecolor{LightMelon} {cmyk}{0,0.23,0.25,0} +\definecolor{LightYellowOrange} {cmyk}{0,0.21,0.50,0} +\definecolor{LightOrange} {cmyk}{0,0.31,0.44,0} +\definecolor{LightBurntOrange} {cmyk}{0,0.26,0.50,0} +\definecolor{LightBittersweet} {cmyk}{0,0.38,0.50,0.12} +\definecolor{LightRedOrange} {cmyk}{0,0.39,0.44,0} +\definecolor{LightMahagony} {cmyk}{0,0.43,0.44,0.18} +\definecolor{LightMaroon} {cmyk}{0,0.44,0.34,0.16} +\definecolor{LightBrickRed} {cmyk}{0,0.45,0.47,0.14} +\definecolor{LightRed} {cmyk}{0,0.50,0.50,0} +\definecolor{LightOrangeRed} {cmyk}{0,0.50,0.25,0} +\definecolor{LightRubineRed} {cmyk}{0,0.50,0.07,0} +\definecolor{LightWildStrawberry}{cmyk}{0,0.48,0.20,0} +\definecolor{LightSalmon} {cmyk}{0,0.27,0.19,0} +\definecolor{LightCarnationPink} {cmyk}{0,0.32,0,0} +\definecolor{LightMagenta} {cmyk}{0,0.50,0,0} +\definecolor{LightVioletRed} {cmyk}{0,0.40,0,0} +\definecolor{LightRhodamine} {cmyk}{0,0.41,0,0} +\definecolor{LightMulberry} {cmyk}{0.17,0.45,0,0.01} +\definecolor{LightRedViolet} {cmyk}{0.04,0.45,0,0.17} +\definecolor{LightFuchsia} {cmyk}{0.24,0.46,0,0.04} +\definecolor{LightLavender} {cmyk}{0,0.24,0,0} +\definecolor{LightThistle} {cmyk}{0.06,0.30,0,0} +\definecolor{LightOrchid} {cmyk}{0.16,0.32,0,0} +\definecolor{LightDarkOrchid} {cmyk}{0.20,0.40,0.10,0} +\definecolor{LightPurple} {cmyk}{0.23,0.43,0,0} +\definecolor{LightPlum} {cmyk}{0.25,0.50,0,0} +\definecolor{LightViolet} {cmyk}{0.40,0.44,0,0} +\definecolor{LightRoyalPurple} {cmyk}{0.38,0.45,0,0} +\definecolor{LightBlueViolet} {cmyk}{0.43,0.46,0,0.02} +\definecolor{LightPeriwinkle} {cmyk}{0.29,0.28,0,0} +\definecolor{LightCadetBlue} {cmyk}{0.31,0.29,0.12,0} +\definecolor{LightCornflowerBlue}{cmyk}{0.33,0.07,0,0} +\definecolor{LightMidnightBlue} {cmyk}{0.49,0.07,0,0.22} +\definecolor{LightNavyBlue} {cmyk}{0.47,0.27,0,0} +\definecolor{LightRoyalBlue} {cmyk}{0.50,0.25,0,0} +\definecolor{LightBlue} {cmyk}{0.50,0.50,0,0} +\definecolor{LightCerulean} {cmyk}{0.47,0.06,0,0} +\definecolor{LightCyan} {cmyk}{0.50,0,0,0} +\definecolor{LightProcessBlue} {cmyk}{0.48,0,0,0} +\definecolor{LightSkyBlue} {cmyk}{0.31,0,0.06,0} +\definecolor{LightTurquoise} {cmyk}{0.43,0,0.10,0} +\definecolor{LightTealBlue} {cmyk}{0.43,0,0.17,0.01} +\definecolor{LightAquamarine} {cmyk}{0.41,0,0.15,0} +\definecolor{LightBlueGreen} {cmyk}{0.43,0,0.17,0} +\definecolor{LightEmerald} {cmyk}{0.50,0,0.25,0} +\definecolor{LightJungleGreen} {cmyk}{0.50,0,0.26,0} +\definecolor{LightSeaGreen} {cmyk}{0.35,0,0.25,0} +\definecolor{LightGreen} {cmyk}{0.50,0,0.50,0} +\definecolor{LightForestGreen} {cmyk}{0.46,0,0.44,0.06} +\definecolor{LightPineGreen} {cmyk}{0.46,0,0.30,0.13} +\definecolor{LightLimeGreen} {cmyk}{0.25,0,0.50,0} +\definecolor{LightYellowGreen} {cmyk}{0.22,0,0.37,0} +\definecolor{LightSpringGreen} {cmyk}{0.13,0,0.38,0} +\definecolor{LightOliveGreen} {cmyk}{0.32,0,0.48,0.20} +\definecolor{LightRawSienna} {cmyk}{0,0.36,0.50,0.23} +\definecolor{LightSepia} {cmyk}{0,0.44,0.50,0.35} +\definecolor{LightBrown} {cmyk}{0,0.41,0.50,0.30} +\definecolor{LightTan} {cmyk}{0.07,0.21,0.28,0} +\definecolor{LightWhite} {cmyk}{0,0,0,0} +\definecolor{LightGray0} {cmyk}{0,0,0,0} +\definecolor{LightGray5} {cmyk}{0,0,0,0.02} +\definecolor{LightGray10} {cmyk}{0,0,0,0.05} +\definecolor{LightGray15} {cmyk}{0,0,0,0.07} +\definecolor{LightGray20} {cmyk}{0,0,0,0.10} +\definecolor{LightGray25} {cmyk}{0,0,0,0.12} +\definecolor{LightGray30} {cmyk}{0,0,0,0.15} +\definecolor{LightLightGray} {cmyk}{0,0,0,0.16} +\definecolor{LightGray35} {cmyk}{0,0,0,0.17} +\definecolor{LightGray40} {cmyk}{0,0,0,0.20} +\definecolor{LightGray45} {cmyk}{0,0,0,0.22} +\definecolor{LightGray50} {cmyk}{0,0,0,0.25} +\definecolor{LightGray} {cmyk}{0,0,0,0.25} +\definecolor{LightGray55} {cmyk}{0,0,0,0.27} +\definecolor{LightGray60} {cmyk}{0,0,0,0.30} +\definecolor{LightGray65} {cmyk}{0,0,0,0.32} +\definecolor{LightDarkGray} {cmyk}{0,0,0,0.33} +\definecolor{LightGray70} {cmyk}{0,0,0,0.35} +\definecolor{LightGray75} {cmyk}{0,0,0,0.37} +\definecolor{LightGray80} {cmyk}{0,0,0,0.40} +\definecolor{LightGray85} {cmyk}{0,0,0,0.42} +\definecolor{LightGray90} {cmyk}{0,0,0,0.45} +\definecolor{LightGray95} {cmyk}{0,0,0,0.47} +\definecolor{LightBlack} {cmyk}{0,0,0,0.50} +\definecolor{LightGray100} {cmyk}{0,0,0,0.50} +\definecolor{LightLightGreenYellow} {cmyk}{0.04,0,0.17,0} +\definecolor{LightLightYellow} {cmyk}{0,0,0.25,0} +\definecolor{LightLightGoldenrod} {cmyk}{0,0.02,0.21,0} +\definecolor{LightLightDandelion} {cmyk}{0,0.07,0.21,0} +\definecolor{LightLightApricot} {cmyk}{0,0.08,0.13,0} +\definecolor{LightLightPeach} {cmyk}{0,0.12,0.17,0} +\definecolor{LightLightMelon} {cmyk}{0,0.11,0.12,0} +\definecolor{LightLightYellowOrange} {cmyk}{0,0.10,0.25,0} +\definecolor{LightLightOrange} {cmyk}{0,0.15,0.22,0} +\definecolor{LightLightBurntOrange} {cmyk}{0,0.13,0.25,0} +\definecolor{LightLightBittersweet} {cmyk}{0,0.19,0.25,0.06} +\definecolor{LightLightRedOrange} {cmyk}{0,0.14,0.22,0} +\definecolor{LightLightMahagony} {cmyk}{0,0.21,0.22,0.09} +\definecolor{LightLightMaroon} {cmyk}{0,0.22,0.17,0.08} +\definecolor{LightLightBrickRed} {cmyk}{0,0.22,0.23,0.07} +\definecolor{LightLightRed} {cmyk}{0,0.25,0.25,0} +\definecolor{LightLightOrangeRed} {cmyk}{0,0.25,0.12,0} +\definecolor{LightLightRubineRed} {cmyk}{0,0.25,0.03,0} +\definecolor{LightLightWildStrawberry}{cmyk}{0,0.24,0.10,0} +\definecolor{LightLightSalmon} {cmyk}{0,0.13,0.09,0} +\definecolor{LightLightCarnationPink} {cmyk}{0,0.16,0,0} +\definecolor{LightLightMagenta} {cmyk}{0,0.25,0,0} +\definecolor{LightLightVioletRed} {cmyk}{0,0.20,0,0} +\definecolor{LightLightRhodamine} {cmyk}{0,0.20,0,0} +\definecolor{LightLightMulberry} {cmyk}{0.08,0.22,0,0.005} +\definecolor{LightLightRedViolet} {cmyk}{0.02,0.22,0,0.08} +\definecolor{LightLightFuchsia} {cmyk}{0.12,0.23,0,0.02} +\definecolor{LightLightLavender} {cmyk}{0,0.12,0,0} +\definecolor{LightLightThistle} {cmyk}{0.03,0.15,0,0} +\definecolor{LightLightOrchid} {cmyk}{0.08,0.16,0,0} +\definecolor{LightLightDarkOrchid} {cmyk}{0.10,0.20,0.05,0} +\definecolor{LightLightPurple} {cmyk}{0.11,0.21,0,0} +\definecolor{LightLightPlum} {cmyk}{0.12,0.25,0,0} +\definecolor{LightLightViolet} {cmyk}{0.20,0.22,0,0} +\definecolor{LightLightRoyalPurple} {cmyk}{0.19,0.22,0,0} +\definecolor{LightLightBlueViolet} {cmyk}{0.21,0.23,0,0.01} +\definecolor{LightLightPeriwinkle} {cmyk}{0.14,0.14,0,0} +\definecolor{LightLightCadetBlue} {cmyk}{0.15,0.14,0.06,0} +\definecolor{LightLightCornflowerBlue}{cmyk}{0.16,0.03,0,0} +\definecolor{LightLightMidnightBlue} {cmyk}{0.24,0.03,0,0.11} +\definecolor{LightLightNavyBlue} {cmyk}{0.23,0.13,0,0} +\definecolor{LightLightRoyalBlue} {cmyk}{0.25,0.12,0,0} +\definecolor{LightLightBlue} {cmyk}{0.25,0.25,0,0} +\definecolor{LightLightCerulean} {cmyk}{0.23,0.03,0,0} +\definecolor{LightLightCyan} {cmyk}{0.25,0,0,0} +\definecolor{LightLightProcessBlue} {cmyk}{0.24,0,0,0} +\definecolor{LightLightSkyBlue} {cmyk}{0.15,0,0.03,0} +\definecolor{LightLightTurquoise} {cmyk}{0.21,0,0.05,0} +\definecolor{LightLightTealBlue} {cmyk}{0.21,0,0.08,0.005} +\definecolor{LightLightAquamarine} {cmyk}{0.20,0,0.07,0} +\definecolor{LightLightBlueGreen} {cmyk}{0.21,0,0.08,0} +\definecolor{LightLightEmerald} {cmyk}{0.25,0,0.12,0} +\definecolor{LightLightJungleGreen} {cmyk}{0.25,0,0.13,0} +\definecolor{LightLightSeaGreen} {cmyk}{0.17,0,0.12,0} +\definecolor{LightLightGreen} {cmyk}{0.25,0,0.25,0} +\definecolor{LightLightForestGreen} {cmyk}{0.23,0,0.22,0.03} +\definecolor{LightLightPineGreen} {cmyk}{0.23,0,0.15,0.06} +\definecolor{LightLightLimeGreen} {cmyk}{0.12,0,0.25,0} +\definecolor{LightLightYellowGreen} {cmyk}{0.11,0,0.18,0} +\definecolor{LightLightSpringGreen} {cmyk}{0.06,0,0.19,0} +\definecolor{LightLightOliveGreen} {cmyk}{0.16,0,0.24,0.10} +\definecolor{LightLightRawSienna} {cmyk}{0,0.18,0.25,0.11} +\definecolor{LightLightSepia} {cmyk}{0,0.22,0.25,0.17} +\definecolor{LightLightBrown} {cmyk}{0,0.20,0.25,0.15} +\definecolor{LightLightTan} {cmyk}{0.03,0.10,0.14,0} +\definecolor{LightLightWhite} {cmyk}{0,0,0,0} +\definecolor{LightLightGray0} {cmyk}{0,0,0,0} +\definecolor{LightLightGray5} {cmyk}{0,0,0,0.01} +\definecolor{LightLightGray10} {cmyk}{0,0,0,0.02} +\definecolor{LightLightGray15} {cmyk}{0,0,0,0.03} +\definecolor{LightLightGray20} {cmyk}{0,0,0,0.05} +\definecolor{LightLightGray25} {cmyk}{0,0,0,0.06} +\definecolor{LightLightGray30} {cmyk}{0,0,0,0.07} +\definecolor{LightLightLightGray} {cmyk}{0,0,0,0.08} +\definecolor{LightLightGray35} {cmyk}{0,0,0,0.09} +\definecolor{LightLightGray40} {cmyk}{0,0,0,0.10} +\definecolor{LightLightGray45} {cmyk}{0,0,0,0.11} +\definecolor{LightLightGray50} {cmyk}{0,0,0,0.12} +\definecolor{LightLightGray} {cmyk}{0,0,0,0.13} +\definecolor{LightLightGray55} {cmyk}{0,0,0,0.14} +\definecolor{LightLightGray60} {cmyk}{0,0,0,0.15} +\definecolor{LightLightGray65} {cmyk}{0,0,0,0.16} +\definecolor{LightLightDarkGray} {cmyk}{0,0,0,0.17} +\definecolor{LightLightGray70} {cmyk}{0,0,0,0.18} +\definecolor{LightLightGray75} {cmyk}{0,0,0,0.19} +\definecolor{LightLightGray80} {cmyk}{0,0,0,0.20} +\definecolor{LightLightGray85} {cmyk}{0,0,0,0.21} +\definecolor{LightLightGray90} {cmyk}{0,0,0,0.22} +\definecolor{LightLightGray95} {cmyk}{0,0,0,0.23} +\definecolor{LightLightBlack} {cmyk}{0,0,0,0.25} +\definecolor{LightLightGray100} {cmyk}{0,0,0,0.25} +\definecolor{LightLightLightGreenYellow} {cmyk}{0.02,0,0.08,0} +\definecolor{LightLightLightYellow} {cmyk}{0,0,0.12,0} +\definecolor{LightLightLightGoldenrod} {cmyk}{0,0.01,0.10,0} +\definecolor{LightLightLightDandelion} {cmyk}{0,0.03,0.10,0} +\definecolor{LightLightLightApricot} {cmyk}{0,0.04,0.06,0} +\definecolor{LightLightLightPeach} {cmyk}{0,0.06,0.08,0} +\definecolor{LightLightLightMelon} {cmyk}{0,0.05,0.06,0} +\definecolor{LightLightLightYellowOrange} {cmyk}{0,0.05,0.12,0} +\definecolor{LightLightLightOrange} {cmyk}{0,0.07,0.11,0} +\definecolor{LightLightLightBurntOrange} {cmyk}{0,0.06,0.12,0} +\definecolor{LightLightLightBittersweet} {cmyk}{0,0.09,0.12,0.03} +\definecolor{LightLightLightRedOrange} {cmyk}{0,0.07,0.11,0} +\definecolor{LightLightLightMahagony} {cmyk}{0,0.10,0.11,0.04} +\definecolor{LightLightLightMaroon} {cmyk}{0,0.11,0.08,0.04} +\definecolor{LightLightLightBrickRed} {cmyk}{0,0.11,0.11,0.03} +\definecolor{LightLightLightRed} {cmyk}{0,0.12,0.12,0} +\definecolor{LightLightLightOrangeRed} {cmyk}{0,0.12,0.06,0} +\definecolor{LightLightLightRubineRed} {cmyk}{0,0.12,0.01,0} +\definecolor{LightLightLightWildStrawberry}{cmyk}{0,0.12,0.05,0} +\definecolor{LightLightLightSalmon} {cmyk}{0,0.06,0.04,0} +\definecolor{LightLightLightCarnationPink} {cmyk}{0,0.08,0,0} +\definecolor{LightLightLightMagenta} {cmyk}{0,0.12,0,0} +\definecolor{LightLightLightVioletRed} {cmyk}{0,0.10,0,0} +\definecolor{LightLightLightRhodamine} {cmyk}{0,0.10,0,0} +\definecolor{LightLightLightMulberry} {cmyk}{0.04,0.11,0,0.002} +\definecolor{LightLightLightRedViolet} {cmyk}{0.01,0.11,0,0.04} +\definecolor{LightLightLightFuchsia} {cmyk}{0.06,0.11,0,0.01} +\definecolor{LightLightLightLavender} {cmyk}{0,0.06,0,0} +\definecolor{LightLightLightThistle} {cmyk}{0.01,0.07,0,0} +\definecolor{LightLightLightOrchid} {cmyk}{0.04,0.08,0,0} +\definecolor{LightLightLightDarkOrchid} {cmyk}{0.05,0.10,0.02,0} +\definecolor{LightLightLightPurple} {cmyk}{0.05,0.10,0,0} +\definecolor{LightLightLightPlum} {cmyk}{0.06,0.12,0,0} +\definecolor{LightLightLightViolet} {cmyk}{0.10,0.11,0,0} +\definecolor{LightLightLightRoyalPurple} {cmyk}{0.09,0.11,0,0} +\definecolor{LightLightLightBlueViolet} {cmyk}{0.10,0.11,0,0.005} +\definecolor{LightLightLightPeriwinkle} {cmyk}{0.07,0.07,0,0} +\definecolor{LightLightLightCadetBlue} {cmyk}{0.07,0.07,0.03,0} +\definecolor{LightLightLightCornflowerBlue}{cmyk}{0.08,0.01,0,0} +\definecolor{LightLightLightMidnightBlue} {cmyk}{0.12,0.01,0,0.05} +\definecolor{LightLightLightNavyBlue} {cmyk}{0.11,0.06,0,0} +\definecolor{LightLightLightRoyalBlue} {cmyk}{0.12,0.06,0,0} +\definecolor{LightLightLightBlue} {cmyk}{0.12,0.12,0,0} +\definecolor{LightLightLightCerulean} {cmyk}{0.11,0.01,0,0} +\definecolor{LightLightLightCyan} {cmyk}{0.12,0,0,0} +\definecolor{LightLightLightProcessBlue} {cmyk}{0.12,0,0,0} +\definecolor{LightLightLightSkyBlue} {cmyk}{0.07,0,0.01,0} +\definecolor{LightLightLightTurquoise} {cmyk}{0.10,0,0.02,0} +\definecolor{LightLightLightTealBlue} {cmyk}{0.10,0,0.04,0.002} +\definecolor{LightLightLightAquamarine} {cmyk}{0.10,0,0.03,0} +\definecolor{LightLightLightBlueGreen} {cmyk}{0.10,0,0.04,0} +\definecolor{LightLightLightEmerald} {cmyk}{0.12,0,0.06,0} +\definecolor{LightLightLightJungleGreen} {cmyk}{0.12,0,0.06,0} +\definecolor{LightLightLightSeaGreen} {cmyk}{0.08,0,0.06,0} +\definecolor{LightLightLightGreen} {cmyk}{0.12,0,0.12,0} +\definecolor{LightLightLightForestGreen} {cmyk}{0.11,0,0.11,0.01} +\definecolor{LightLightLightPineGreen} {cmyk}{0.11,0,0.07,0.03} +\definecolor{LightLightLightLimeGreen} {cmyk}{0.06,0,0.12,0} +\definecolor{LightLightLightYellowGreen} {cmyk}{0.05,0,0.09,0} +\definecolor{LightLightLightSpringGreen} {cmyk}{0.03,0,0.09,0} +\definecolor{LightLightLightOliveGreen} {cmyk}{0.08,0,0.12,0.05} +\definecolor{LightLightLightRawSienna} {cmyk}{0,0.09,0.12,0.05} +\definecolor{LightLightLightSepia} {cmyk}{0,0.11,0.12,0.06} +\definecolor{LightLightLightBrown} {cmyk}{0,0.10,0.12,0.07} +\definecolor{LightLightLightTan} {cmyk}{0.01,0.05,0.07,0} +\definecolor{LightLightLightWhite} {cmyk}{0,0,0,0} +\definecolor{LightLightLightGray0} {cmyk}{0,0,0,0} +\definecolor{LightLightLightGray5} {cmyk}{0,0,0,0.005} +\definecolor{LightLightLightGray10} {cmyk}{0,0,0,0.01} +\definecolor{LightLightLightGray15} {cmyk}{0,0,0,0.015} +\definecolor{LightLightLightGray20} {cmyk}{0,0,0,0.025} +\definecolor{LightLightLightGray25} {cmyk}{0,0,0,0.03} +\definecolor{LightLightLightGray30} {cmyk}{0,0,0,0.035} +\definecolor{LightLightLightLightGray} {cmyk}{0,0,0,0.04} +\definecolor{LightLightLightGray35} {cmyk}{0,0,0,0.045} +\definecolor{LightLightLightGray40} {cmyk}{0,0,0,0.05} +\definecolor{LightLightLightGray45} {cmyk}{0,0,0,0.055} +\definecolor{LightLightLightGray50} {cmyk}{0,0,0,0.06} +\definecolor{LightLightLightGray} {cmyk}{0,0,0,0.065} +\definecolor{LightLightLightGray55} {cmyk}{0,0,0,0.07} +\definecolor{LightLightLightGray60} {cmyk}{0,0,0,0.075} +\definecolor{LightLightLightGray65} {cmyk}{0,0,0,0.08} +\definecolor{LightLightLightDarkGray} {cmyk}{0,0,0,0.085} +\definecolor{LightLightLightGray70} {cmyk}{0,0,0,0.09} +\definecolor{LightLightLightGray75} {cmyk}{0,0,0,0.095} +\definecolor{LightLightLightGray80} {cmyk}{0,0,0,0.10} +\definecolor{LightLightLightGray85} {cmyk}{0,0,0,0.105} +\definecolor{LightLightLightGray90} {cmyk}{0,0,0,0.11} +\definecolor{LightLightLightGray95} {cmyk}{0,0,0,0.115} +\definecolor{LightLightLightBlack} {cmyk}{0,0,0,0.12} +\definecolor{LightLightLightGray100} {cmyk}{0,0,0,0.125} +\definecolor{BlueRed5} {rgb} {0.15,0.17,0.55} +\definecolor{BlueRed10} {rgb} {0.20,0.23,0.57} +\definecolor{BlueRed15} {rgb} {0.24,0.29,0.60} +\definecolor{BlueRed20} {rgb} {0.33,0.35,0.64} +\definecolor{BlueRed25} {rgb} {0.43,0.43,0.68} +\definecolor{BlueRed30} {rgb} {0.52,0.52,0.73} +\definecolor{BlueRed35} {rgb} {0.60,0.60,0.78} +\definecolor{BlueRed40} {rgb} {0.70,0.70,0.84} +\definecolor{BlueRed45} {rgb} {0.80,0.80,0.85} +\definecolor{BlueRed50} {rgb} {0.86,0.82,0.82} +\definecolor{BlueRed55} {rgb} {0.87,0.73,0.73} +\definecolor{BlueRed60} {rgb} {0.89,0.64,0.64} +\definecolor{BlueRed65} {rgb} {0.90,0.55,0.55} +\definecolor{BlueRed70} {rgb} {0.91,0.47,0.46} +\definecolor{BlueRed75} {rgb} {0.91,0.39,0.37} +\definecolor{BlueRed80} {rgb} {0.90,0.33,0.28} +\definecolor{BlueRed85} {rgb} {0.89,0.25,0.20} +\definecolor{BlueRed90} {rgb} {0.88,0.23,0.14} +\definecolor{BlueRed95} {rgb} {0.87,0.21,0.09} +\definecolor{BlueRed100} {rgb} {0.87,0.16,0.04} +\definecolor{RedBlue100} {rgb} {0.15,0.17,0.55} +\definecolor{RedBlue95} {rgb} {0.15,0.17,0.55} +\definecolor{RedBlue90} {rgb} {0.20,0.23,0.57} +\definecolor{RedBlue85} {rgb} {0.24,0.29,0.60} +\definecolor{RedBlue80} {rgb} {0.33,0.35,0.64} +\definecolor{RedBlue75} {rgb} {0.43,0.43,0.68} +\definecolor{RedBlue70} {rgb} {0.52,0.52,0.73} +\definecolor{RedBlue65} {rgb} {0.60,0.60,0.78} +\definecolor{RedBlue60} {rgb} {0.70,0.70,0.84} +\definecolor{RedBlue55} {rgb} {0.80,0.80,0.85} +\definecolor{RedBlue50} {rgb} {0.86,0.82,0.82} +\definecolor{RedBlue45} {rgb} {0.87,0.73,0.73} +\definecolor{RedBlue40} {rgb} {0.89,0.64,0.64} +\definecolor{RedBlue35} {rgb} {0.90,0.55,0.55} +\definecolor{RedBlue30} {rgb} {0.91,0.47,0.46} +\definecolor{RedBlue25} {rgb} {0.91,0.39,0.37} +\definecolor{RedBlue20} {rgb} {0.90,0.33,0.28} +\definecolor{RedBlue15} {rgb} {0.89,0.25,0.20} +\definecolor{RedBlue10} {rgb} {0.88,0.23,0.14} +\definecolor{RedBlue5} {rgb} {0.87,0.21,0.09} +\definecolor{GreenRed5} {rgb} {0,1,0} +\definecolor{GreenRed10} {rgb} {0.05,0.95,0} +\definecolor{GreenRed15} {rgb} {0.10,0.90,0} +\definecolor{GreenRed20} {rgb} {0.15,0.85,0} +\definecolor{GreenRed25} {rgb} {0.20,0.80,0} +\definecolor{GreenRed30} {rgb} {0.25,0.75,0} +\definecolor{GreenRed35} {rgb} {0.30,0.70,0} +\definecolor{GreenRed40} {rgb} {0.35,0.65,0} +\definecolor{GreenRed45} {rgb} {0.40,0.60,0} +\definecolor{GreenRed50} {rgb} {0.45,0.55,0} +\definecolor{GreenRed55} {rgb} {0.50,0.50,0} +\definecolor{GreenRed60} {rgb} {0.55,0.45,0} +\definecolor{GreenRed65} {rgb} {0.60,0.40,0} +\definecolor{GreenRed70} {rgb} {0.65,0.35,0} +\definecolor{GreenRed75} {rgb} {0.70,0.30,0} +\definecolor{GreenRed80} {rgb} {0.75,0.25,0} +\definecolor{GreenRed85} {rgb} {0.80,0.20,0} +\definecolor{GreenRed90} {rgb} {0.85,0.15,0} +\definecolor{GreenRed95} {rgb} {0.90,0.10,0} +\definecolor{GreenRed100} {rgb} {0.95,0.05,0} +\definecolor{RedGreen100} {rgb} {0.05,0.95,0} +\definecolor{RedGreen95} {rgb} {0.10,0.90,0} +\definecolor{RedGreen90} {rgb} {0.15,0.85,0} +\definecolor{RedGreen85} {rgb} {0.20,0.80,0} +\definecolor{RedGreen80} {rgb} {0.25,0.75,0} +\definecolor{RedGreen75} {rgb} {0.30,0.70,0} +\definecolor{RedGreen70} {rgb} {0.35,0.65,0} +\definecolor{RedGreen65} {rgb} {0.40,0.60,0} +\definecolor{RedGreen60} {rgb} {0.45,0.55,0} +\definecolor{RedGreen55} {rgb} {0.50,0.50,0} +\definecolor{RedGreen50} {rgb} {0.55,0.45,0} +\definecolor{RedGreen45} {rgb} {0.60,0.40,0} +\definecolor{RedGreen40} {rgb} {0.65,0.35,0} +\definecolor{RedGreen35} {rgb} {0.70,0.30,0} +\definecolor{RedGreen30} {rgb} {0.75,0.25,0} +\definecolor{RedGreen25} {rgb} {0.80,0.20,0} +\definecolor{RedGreen20} {rgb} {0.85,0.15,0} +\definecolor{RedGreen15} {rgb} {0.90,0.10,0} +\definecolor{RedGreen10} {rgb} {0.95,0.05,0} +\definecolor{RedGreen5} {rgb} {1,0,0} +\definecolor{ColdHot5} {rgb} {0,0.08,1} +\definecolor{ColdHot10} {rgb} {0,0.29,1} +\definecolor{ColdHot15} {rgb} {0,0.49,1} +\definecolor{ColdHot20} {rgb} {0,0.70,1} +\definecolor{ColdHot25} {rgb} {0,0.90,1} +\definecolor{ColdHot30} {rgb} {0,1,0.87} +\definecolor{ColdHot35} {rgb} {0,1,0.68} +\definecolor{ColdHot40} {rgb} {0,1,0.46} +\definecolor{ColdHot45} {rgb} {0,1,0.25} +\definecolor{ColdHot50} {rgb} {0,1,0.04} +\definecolor{ColdHot55} {rgb} {0.16,1,0} +\definecolor{ColdHot60} {rgb} {0.35,1,0} +\definecolor{ColdHot65} {rgb} {0.56,1,0} +\definecolor{ColdHot70} {rgb} {0.79,1,0} +\definecolor{ColdHot75} {rgb} {0.98,1,0} +\definecolor{ColdHot80} {rgb} {1,0.82,0} +\definecolor{ColdHot85} {rgb} {1,0.60,0} +\definecolor{ColdHot90} {rgb} {1,0.40,0} +\definecolor{ColdHot95} {rgb} {1,0.20,0} +\definecolor{ColdHot100} {rgb} {0.91,0,0} +\definecolor{HotCold100} {rgb} {0,0.08,1} +\definecolor{HotCold95} {rgb} {0,0.29,1} +\definecolor{HotCold90} {rgb} {0,0.49,1} +\definecolor{HotCold85} {rgb} {0,0.70,1} +\definecolor{HotCold80} {rgb} {0,0.90,1} +\definecolor{HotCold75} {rgb} {0,1,0.87} +\definecolor{HotCold70} {rgb} {0,1,0.68} +\definecolor{HotCold65} {rgb} {0,1,0.46} +\definecolor{HotCold60} {rgb} {0,1,0.25} +\definecolor{HotCold55} {rgb} {0,1,0.04} +\definecolor{HotCold50} {rgb} {0.16,1,0} +\definecolor{HotCold45} {rgb} {0.35,1,0} +\definecolor{HotCold40} {rgb} {0.56,1,0} +\definecolor{HotCold35} {rgb} {0.79,1,0} +\definecolor{HotCold30} {rgb} {0.98,1,0} +\definecolor{HotCold25} {rgb} {1,0.82,0} +\definecolor{HotCold20} {rgb} {1,0.60,0} +\definecolor{HotCold15} {rgb} {1,0.40,0} +\definecolor{HotCold10} {rgb} {1,0.20,0} +\definecolor{HotCold5} {rgb} {0.91,0,0} + +\def\make@lower{% +\if\first@ A\xdef\first@{a}\else \if\first@ B\xdef\first@{b}\else +\if\first@ C\xdef\first@{c}\else \if\first@ D\xdef\first@{d}\else +\if\first@ E\xdef\first@{e}\else \if\first@ F\xdef\first@{f}\else +\if\first@ G\xdef\first@{g}\else \if\first@ H\xdef\first@{h}\else +\if\first@ I\xdef\first@{i}\else \if\first@ J\xdef\first@{j}\else +\if\first@ K\xdef\first@{k}\else \if\first@ L\xdef\first@{l}\else +\if\first@ M\xdef\first@{m}\else \if\first@ N\xdef\first@{n}\else +\if\first@ O\xdef\first@{o}\else \if\first@ P\xdef\first@{p}\else +\if\first@ Q\xdef\first@{q}\else \if\first@ R\xdef\first@{r}\else +\if\first@ S\xdef\first@{s}\else \if\first@ T\xdef\first@{t}\else +\if\first@ U\xdef\first@{u}\else \if\first@ V\xdef\first@{v}\else +\if\first@ W\xdef\first@{w}\else \if\first@ X\xdef\first@{x}\else +\if\first@ Y\xdef\first@{y}\else \if\first@ Z\xdef\first@{z}\else +\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi} + +\def\make@upper{% +\if\first@ a\xdef\first@{A}\else \if\first@ b\xdef\first@{B}\else +\if\first@ c\xdef\first@{C}\else \if\first@ d\xdef\first@{D}\else +\if\first@ e\xdef\first@{E}\else \if\first@ f\xdef\first@{F}\else +\if\first@ g\xdef\first@{G}\else \if\first@ h\xdef\first@{H}\else +\if\first@ i\xdef\first@{I}\else \if\first@ j\xdef\first@{J}\else +\if\first@ k\xdef\first@{K}\else \if\first@ l\xdef\first@{L}\else +\if\first@ m\xdef\first@{M}\else \if\first@ n\xdef\first@{N}\else +\if\first@ o\xdef\first@{O}\else \if\first@ p\xdef\first@{P}\else +\if\first@ q\xdef\first@{Q}\else \if\first@ r\xdef\first@{R}\else +\if\first@ s\xdef\first@{S}\else \if\first@ t\xdef\first@{T}\else +\if\first@ u\xdef\first@{U}\else \if\first@ v\xdef\first@{V}\else +\if\first@ w\xdef\first@{W}\else \if\first@ x\xdef\first@{X}\else +\if\first@ y\xdef\first@{Y}\else \if\first@ z\xdef\first@{Z}\else +\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi} + +\def\type@get#1 MSF: #2 Type: #3 #4@{\def\seq@type{#3}} +\def\inf@@get#1 #2 #3 #4 #5 #6@{% + \def\first@{#1} + \def\second@{#2} + \def\third@{#3} + \xdef\fourth@{#4 @} + \expandafter\check@letter\fourth@ + \ifnumber + \def\fourth@{#4} + \else + \xdef\fourth@{#5 @} + \expandafter\check@letter\fourth@ + \ifnumber + \def\fourth@{#5} + \else + \def\fourth@{99999999} + \fi + \fi + \def\fifth@{#5} + \def\last@{#6}} +\def\check@char#1{\letterfalse \ifnum\catcode`#1=11 \lettertrue \fi + \numberfalse \ifnum\catcode`#1=12 \numbertrue \fi + \xdef\code@num{\the\catcode`#1}} +\def\check@letter#1#2@{\letterfalse \ifnum\catcode`#1=11 \lettertrue \fi + \numberfalse \ifnum\catcode`#1=12 \numbertrue \fi} +\def\seq@get#1 #2@{\def\first@{#1} \def\seq@line{#2}} +\def\res@get#1#2@{\def\first@{#1} \def\seq@line{#2&@}} +\def\firstchar@get#1#2@{\def\first@{#1} \def\third@{#2@}} +\def\residue@get#1#2@{\xdef\first@{#1} + \ifnum`#1>96 \make@upper \fi + \ifnum`#1=45 \xdef\first@{\d@t} \fi + \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\re@write#1,#2@{% + \xdef\third@{#2,@} + \xdef\first@{\csname hide@@@seq#1\endcsname} + \ifx\first@\last@ + \else + \xdef\first@{#1&} + \ifx\first@\ampers@nd \else \advance\innerloopcount by 1 \fi + \if\second@ e \xdef\second@{\csname @rd#1\endcsname} + \else \xdef\second@{\second@,\csname @rd#1\endcsname}\fi + \fi + } +\def\order@set#1,#2@{% + \xdef\second@{#2,@} + \expandafter\xdef\csname @rd#1\endcsname{\the\loopcount} + \csname res@count\the\loopcount\endcsname=% + \csname pos#1\endcsname + \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{% + \csname hide@@seq#1\endcsname} + \expandafter\xdef\csname hide@name\the\loopcount\endcsname{% + \csname hide@@name#1\endcsname} + \expandafter\xdef\csname hide@number\the\loopcount\endcsname{% + \csname hide@@number#1\endcsname} + \expandafter\xdef\csname seq@start\the\loopcount\endcsname{% + \csname seq@@start#1\endcsname} + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{% + \csname seq@@len#1\endcsname} + \expandafter\xdef\csname seqname\the\loopcount\endcsname{% + \csname seq@name#1\endcsname} + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% + \csname newseq@name#1\endcsname} + \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{% + \csname seq@@gap#1\endcsname} + \expandafter\xdef\csname name@col\the\loopcount\endcsname{% + \csname name@@col#1\endcsname} + \expandafter\xdef\csname number@col\the\loopcount\endcsname{% + \csname number@@col#1\endcsname} + \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{% + \csname stack@@reg#1\endcsname} + \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% + \csname stack@@tintreg#1\endcsname} + \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% + \csname stack@@emphreg#1\endcsname} + \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% + \csname stack@@framereg#1\endcsname} + \expandafter\xdef\csname stack@top\the\loopcount\endcsname{% + \csname stack@@top#1\endcsname} + \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% + \csname stack@@ttop#1\endcsname} + \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% + \csname stack@@bottom#1\endcsname} + \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% + \csname stack@@bbottom#1\endcsname} +} +\def\reorder@seqs#1{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \csname pos\the\loopcount\endcsname=% + \csname res@count\the\loopcount\endcsname + \expandafter\xdef\csname hide@@seq\the\loopcount\endcsname{% + \csname hide@seq\the\loopcount\endcsname} + \expandafter\xdef\csname hide@@name\the\loopcount\endcsname{% + \csname hide@name\the\loopcount\endcsname} + \expandafter\xdef\csname hide@@number\the\loopcount\endcsname{% + \csname hide@number\the\loopcount\endcsname} + \expandafter\xdef\csname seq@@start\the\loopcount\endcsname{% + \csname seq@start\the\loopcount\endcsname} + \expandafter\xdef\csname seq@@len\the\loopcount\endcsname{% + \csname seq@len\the\loopcount\endcsname} + \expandafter\xdef\csname seq@name\the\loopcount\endcsname{% + \csname seqname\the\loopcount\endcsname} + \expandafter\xdef\csname newseq@name\the\loopcount\endcsname{% + \csname newseqname\the\loopcount\endcsname} + \expandafter\xdef\csname seq@@gap\the\loopcount\endcsname{% + \csname seq@gap\the\loopcount\endcsname} + \expandafter\xdef\csname name@@col\the\loopcount\endcsname{% + \csname name@col\the\loopcount\endcsname} + \expandafter\xdef\csname number@@col\the\loopcount\endcsname{% + \csname number@col\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@reg\the\loopcount\endcsname{% + \csname stack@reg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{% + \csname stack@tintreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{% + \csname stack@emphreg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{% + \csname stack@framereg\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@top\the\loopcount\endcsname{% + \csname stack@top\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@ttop\the\loopcount\endcsname{% + \csname stack@ttop\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bottom\the\loopcount\endcsname{% + \csname stack@bottom\the\loopcount\endcsname} + \expandafter\xdef\csname stack@@bbottom\the\loopcount\endcsname{% + \csname stack@bbottom\the\loopcount\endcsname} + \ifnum\loopcount<\killseq@count \repeat + \xdef\third@{#1} + \loopcount=0 \innerloopcount=0 \xdef\last@{kill} \xdef\second@{e} + \loop + \advance\loopcount by 1 + \expandafter\re@write\third@ + \ifnum\loopcount<\seq@count \repeat + \ifnum\innerloopcount<\killseq@count + \@latex@error{Not enough sequences specified in `orderseqs' + (\the\innerloopcount/\the\killseq@count)}\@ehc + \fi + \loopcount=0 \xdef\second@{\second@,@} + \loop + \advance\loopcount by 1 + \expandafter\order@set\second@ + \ifnum\loopcount<\killseq@count \repeat + \ifnum\cons@num>0 \xdef\cons@num{\csname @rd\cons@num\endcsname} \fi + \ifnum\rule@num>0 \xdef\rule@num{\csname @rd\rule@num\endcsname} \fi + \loopcount=0 + \loop + \advance\loopcount by 1 + \csname pos\the\loopcount\endcsname=0 + \ifnum\loopcount<\killseq@count \repeat +} +\def\group@get#1,#2@{% + \def\group@set{\expandafter\residue@get\second@ + \ifx\first@\ampers@nd + \else \expandafter\xdef\csname \prfx grp\first@\endcsname{\the\loopcount} + \xdef\second@{\csname sequence\the\loopcount\endcsname} \group@set + \fi} + \xdef\second@{#1 &@} \xdef\third@{#2&,@} \group@set} +\def\get@item#1,#2@{\xdef\first@{#2@}\xdef\first@@{#2}\xdef\fourth@{#1}} +\def\get@first@@#1-#2@{\xdef\first@@{#1}} +\def\get@digit#1,#2@{% + \def\check@series##1-##2##3@{% + \xdef\first@@{##2}\xdef\fourth@{##1}\xdef\fourth@@{##3}} + \xdef\first@{#2@} + \xdef\fourth@{#1-&@} + \expandafter\check@series\fourth@ + \ifx\first@@\ampers@nd + \else + \xdef\first@@{\first@@\fourth@@-&@} + \expandafter\get@first@@\first@@ + \loopcount=\fourth@ + \ifnum\first@@>\fourth@ + \advance\loopcount by 1 + \xdef\first@{\the\loopcount-\first@@,#2@} + \else + \ifnum\first@@<\fourth@ + \advance\loopcount by -1 + \xdef\first@{\the\loopcount-\first@@,#2@} + \fi + \fi + \fi +} +\def\donot@shade{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\first@\endcsname{noshade} + \fi + \xdef\first@{\first@@ @} + \donot@shade + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\fourth@\endcsname{noshade} + \fi + \donot@shade + \fi + \fi} +\def\hideseq@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\first@\endcsname{true} + \fi + \xdef\first@{\first@@ @} + \hideseq@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\fourth@\endcsname{true} + \fi + \hideseq@ + \fi + \fi} +\def\hidename@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \expandafter\xdef\csname hide@name\first@\endcsname{yes} + \xdef\first@{\first@@ @} + \hidename@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \expandafter\xdef\csname hide@name\fourth@\endcsname{yes} + \hidename@ + \fi + \fi} +\def\hidenumber@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \expandafter\xdef\csname hide@number\first@\endcsname{yes} + \xdef\first@{\first@@ @} + \hidenumber@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \expandafter\xdef\csname hide@number\fourth@\endcsname{yes} + \hidenumber@ + \fi + \fi} +\def\namecolor@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \expandafter\xdef\csname name@col\first@\endcsname{\third@} + \xdef\first@{\first@@ @} + \namecolor@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \expandafter\xdef\csname name@col\fourth@\endcsname{\third@} + \namecolor@ + \fi + \fi} +\def\numbercolor@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \expandafter\xdef\csname number@col\first@\endcsname{\third@} + \xdef\first@{\first@@ @} + \numbercolor@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \expandafter\xdef\csname number@col\fourth@\endcsname{\third@} + \numbercolor@ + \fi + \fi} +\def\killseq@{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \ifnum\first@>\seq@count + \else + \ifnum\killseq@count>1 + \xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\first@\endcsname{kill} + \expandafter\xdef\csname hide@@@seq\first@\endcsname{kill} + \ifnum\first@=\cons@num \xdef\cons@num{0} \fi + \advance\killseq@count by -1 + \seq@percent=100 \divide\seq@percent by \killseq@count + \fi + \fi\fi + \xdef\first@{\first@@ @} + \killseq@ + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \ifnum\fourth@>\seq@count + \else + \ifnum\killseq@count>1 + \xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill} + \ifx\third@\second@ + \else + \expandafter\xdef\csname hide@seq\fourth@\endcsname{kill} + \expandafter\xdef\csname hide@@@seq\fourth@\endcsname{kill} + \ifnum\fourth@=\cons@num \xdef\cons@num{0} \fi + \advance\killseq@count by -1 + \seq@percent=100 \divide\seq@percent by \killseq@count + \fi + \fi\fi + \killseq@ + \fi + \fi} +\def\kill@loop{% + \advance\innerloopcount by 1 + \xdef\first@{\csname hide@seq\the\innerloopcount\endcsname} + \ifx\first@\second@ \kill@loop \fi} +\def\kill@seqnow{% + \xdef\first@{\csname hide@seq\the\loopcount\endcsname} \xdef\second@{kill} + \innerloopcount=\loopcount + \ifx\first@\second@ + \kill@loop + \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{% + \csname hide@seq\the\innerloopcount\endcsname} + \expandafter\xdef\csname seqname\the\loopcount\endcsname{% + \csname seqname\the\innerloopcount\endcsname} + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% + \csname newseqname\the\innerloopcount\endcsname} + \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{% + \csname seq@gap\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{% + \csname stack@reg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% + \csname stack@tintreg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% + \csname stack@emphreg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% + \csname stack@framereg\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@top\the\loopcount\endcsname{% + \csname stack@top\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% + \csname stack@ttop\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% + \csname stack@bottom\the\innerloopcount\endcsname} + \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% + \csname stack@bbottom\the\innerloopcount\endcsname} + \csname res@count\the\loopcount\endcsname=% + \csname res@count\the\innerloopcount\endcsname + \expandafter\xdef\csname hide@seq\the\innerloopcount\endcsname{kill} + \ifnum\loopcount=\rule@num \hideruler \fi + \fi + \expandafter\xdef\csname @rd\the\innerloopcount\endcsname{\the\loopcount} + \advance\loopcount by 1 + \ifnum\loopcount>\killseq@count + \ifnum\rule@num>0\xdef\rule@num{\csname @rd\rule@num\endcsname}\fi + \ifnum\cons@num>0\xdef\cons@num{\csname @rd\cons@num\endcsname}\fi + \else + \kill@seqnow + \fi} +\def\set@maxseqnumber#1{% + \ifnum#1>\max@seqnumber + \loopcount=\max@seqnumber \xdef\max@seqnumber{\the #1} + \loop + \advance\loopcount by 1 + \expandafter\newcount\csname pos\the\loopcount\endcsname + \expandafter\newcount\csname res@count\the\loopcount\endcsname + \ifnum\loopcount<\max@seqnumber \repeat + \fi} +\def\get@sim#1#2@{\xdef\sim@char{#1} \xdef\last@{#2 &@}} +\def\getsim@char{% + \advance\innerloopcount by 1 + \ifnum\innerloopcount>\m@x + \else + \expandafter\get@sim\last@ + \ifx\second@\sim@char \xdef\third@{2} \innerloopcount=\m@x \fi + \getsim@char + \fi} +\def\get@count(#1)#2@{\xdef\last@{#2 &@} \xdef\m@x{#1}} +\def\get@nums#1..#2@{\xdef\first@{#1} \xdef\second@{#2}} +\def\func@shading#1{% + \clearfuncgroups + \xdef\temp@{#1} + \xdef\second@{charge} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{basisch ($+$)}{KRH}{White}{Blue}{upper}{up} + \else + \ifsp@nish + \funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up} + \else + \funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up} + \fi + \fi + \else + \xdef\second@{hydropathy} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{basisch ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{polar ungeladen}{YSTGNQC}{Black}{Yellow}{upper}{up} + \funcgroup{hydrophob unpolar}{AFPMWVIL}{White}{Green}{upper}{up} + \else + \ifsp@nish + \funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{polar sin carga}{YSTGNQC}{Black}{Yellow}{upper}{up} + \funcgroup{hidrof\'obico no polar}{AFPMWVIL}{White}{Green}{upper}{up} + \else + \funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{polar uncharged}{YSTGNQC}{Black}{Yellow}{upper}{up} + \funcgroup{hydrophobic nonpolar}{AFPMWVIL}{White}{Green}{upper}{up} + \fi + \fi + \else + \xdef\second@{chemical} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{aliphatisch}{AGVIL}{White}{Black}{upper}{up} + \funcgroup{Amid}{NQ}{White}{Green}{upper}{up} + \funcgroup{aromatisch}{FYW}{White}{Brown}{upper}{up} + \funcgroup{basisch (+)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{Hydroxyl}{ST}{Black}{Magenta}{upper}{up} + \funcgroup{Imin}{P}{Black}{Orange}{upper}{up} + \funcgroup{Schwefel}{CM}{Black}{Yellow}{upper}{up} + \else + \ifsp@nish + \funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{alif\'atico}{AGVIL}{White}{Black}{upper}{up} + \funcgroup{amida}{NQ}{White}{Green}{upper}{up} + \funcgroup{arom\'atico}{FYW}{White}{Brown}{upper}{up} + \funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{hidr\'oxido}{ST}{Black}{Magenta}{upper}{up} + \funcgroup{imino}{P}{Black}{Orange}{upper}{up} + \funcgroup{azufre}{CM}{Black}{Yellow}{upper}{up} + \else + \funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up} + \funcgroup{aliphatic}{AGVIL}{White}{Black}{upper}{up} + \funcgroup{amide}{NQ}{White}{Green}{upper}{up} + \funcgroup{aromatic}{FYW}{White}{Brown}{upper}{up} + \funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up} + \funcgroup{hydroxyl}{ST}{Black}{Magenta}{upper}{up} + \funcgroup{imino}{P}{Black}{Orange}{upper}{up} + \funcgroup{sulfur}{CM}{Black}{Yellow}{upper}{up} + \fi + \fi + \else + \xdef\second@{structure} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{extern}{DEHKNQR}{Black}{Orange}{upper}{up} + \funcgroup{ambivalent}{ACGPSTWY}{Black}{Yellow}{upper}{up} + \funcgroup{intern}{FILMV}{White}{Green}{upper}{up} + \else + \ifsp@nish + \funcgroup{externo}{DEHKNQR}{Black}{Orange}{upper}{up} + \funcgroup{ambivalente}{ACGPSTWY}{Black}{Yellow}{upper}{up} + \funcgroup{interno}{FILMV}{White}{Green}{upper}{up} + \else + \funcgroup{external}{DEHKNQR}{Black}{Orange}{upper}{up} + \funcgroup{ambivalent}{ACGPSTWY}{Black}{Yellow}{upper}{up} + \funcgroup{internal}{FILMV}{White}{Green}{upper}{up} + \fi + \fi + \else + \xdef\second@{standard area} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{\ 88,1 (G); Standard Seitenkettenfl\"ache % + (\AA$^2$)}% + {G}{Black}{BrickRed}{upper}{up} + \funcgroup{118,2 (A); 129,8 (S)}{AS}{Black}{Orange}{upper}{up} + \funcgroup{146,1 (C); 146,8 (P)}% + {CP}{Black}{Yellow}{upper}{up} + \funcgroup{152,5 (T); 158,7 (D); 164,5 (V); 165,5 (N)}% + {TDVN}{Black}{YellowGreen}{upper}{up} + \funcgroup{181,0 (I); 186,2 (E)}{IE}{White}{PineGreen}{upper}{up} + \funcgroup{193,1 (L); 193,2 (Q); 202,5 (H); 203,3 (M)}% + {LQHM}{Black}{SkyBlue}{upper}{up} + \funcgroup{222,8 (F); 225,8 (K)}{FK}{White}{RoyalPurple}{upper}{up} + \funcgroup{238,8 (Y)}{Y}{White}{RedViolet}{upper}{up} + \funcgroup{256,0 (R); 266,2 (W)}{RW}{White}{Black}{upper}{up} + \else + \ifsp@nish + \funcgroup{\ 88.1 (G); Superficie est\'andar de la cadena lateral (\AA$^2$)}% + {G}{Black}{BrickRed}{upper}{up} + \funcgroup{118.2 (A); 129.8 (S)}{AS}{Black}{Orange}{upper}{up} + \funcgroup{146.1 (C); 146.8 (P)}% + {CP}{Black}{Yellow}{upper}{up} + \funcgroup{152.5 (T); 158.7 (D); 164.5 (V); 165.5 (N)}% + {TDVN}{Black}{YellowGreen}{upper}{up} + \funcgroup{181.0 (I); 186.2 (E)}{IE}{White}{PineGreen}{upper}{up} + \funcgroup{193.1 (L); 193.2 (Q); 202.5 (H); 203.3 (M)}% + {LQHM}{Black}{SkyBlue}{upper}{up} + \funcgroup{222.8 (F); 225.8 (K)}{FK}{White}{RoyalPurple}{upper}{up} + \funcgroup{238.8 (Y)}{Y}{White}{RedViolet}{upper}{up} + \funcgroup{256.0 (R); 266.2 (W)}{RW}{White}{Black}{upper}{up} + \else + \funcgroup{\ 88.1 (G); Standard sidechain area (\AA$^2$)}% + {G}{Black}{BrickRed}{upper}{up} + \funcgroup{118.2 (A); 129.8 (S)}{AS}{Black}{Orange}{upper}{up} + \funcgroup{146.1 (C); 146.8 (P)}% + {CP}{Black}{Yellow}{upper}{up} + \funcgroup{152.5 (T); 158.7 (D); 164.5 (V); 165.5 (N)}% + {TDVN}{Black}{YellowGreen}{upper}{up} + \funcgroup{181.0 (I); 186.2 (E)}{IE}{White}{PineGreen}{upper}{up} + \funcgroup{193.1 (L); 193.2 (Q); 202.5 (H); 203.3 (M)}% + {LQHM}{Black}{SkyBlue}{upper}{up} + \funcgroup{222.8 (F); 225.8 (K)}{FK}{White}{RoyalPurple}{upper}{up} + \funcgroup{238.8 (Y)}{Y}{White}{RedViolet}{upper}{up} + \funcgroup{256.0 (R); 266.2 (W)}{RW}{White}{Black}{upper}{up} + \fi + \fi + \else + \xdef\second@{accessible area} + \ifx\temp@\second@ + \ifgerm@n + \funcgroup{\ 13,9 (C); Zug\"angliche Seitenkettenfl\"ache % + (\AA$^2$)}% + {CIV}{Black}{BrickRed}{upper}{up} + \funcgroup{\ 23,0 (I); 23,5 (V); 25,2 (G)}% + {IVG}{Black}{Orange}{upper}{up} + \funcgroup{\ 28,7 (F); 29,0 (L); 30,5 (M); 31,5 (A)}% + {FLMA}{Black}{Yellow}{upper}{up} + \funcgroup{\ 41,7 (W); 44,2 (S); 46,0 (T); 46,7 (H)}% + {WSTH}{Black}{YellowGreen}{upper}{up} + \funcgroup{\ 53,7 (P)}{P}{White}{PineGreen}{upper}{up} + \funcgroup{\ 59,1 (Y); 60,9 (D); 62,2 (N)}% + {YDN}{Black}{SkyBlue}{upper}{up} + \funcgroup{\ 72,3 (E); 74,0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up} + \funcgroup{\ 93,8 (R)}{R}{White}{RedViolet}{upper}{up} + \funcgroup{110,3 (K)}{K}{White}{Black}{upper}{up} + \else + \ifsp@nish + \funcgroup{\ 13.9 (C); Superficie accesible de la cadena lateral (\AA$^2$)}% + {CIV}{Black}{BrickRed}{upper}{up} + \funcgroup{\ 23.0 (I); 23.5 (V); 25.2 (G)}% + {IVG}{Black}{Orange}{upper}{up} + \funcgroup{\ 28.7 (F); 29.0 (L); 30.5 (M); 31.5 (A)}% + {FLMA}{Black}{Yellow}{upper}{up} + \funcgroup{\ 41.7 (W); 44.2 (S); 46.0 (T); 46.7 (H)}% + {WSTH}{Black}{YellowGreen}{upper}{up} + \funcgroup{\ 53.7 (P)}{P}{White}{PineGreen}{upper}{up} + \funcgroup{\ 59.1 (Y); 60.9 (D); 62.2 (N)}% + {YDN}{Black}{SkyBlue}{upper}{up} + \funcgroup{\ 72.3 (E); 74.0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up} + \funcgroup{\ 93.8 (R)}{R}{White}{RedViolet}{upper}{up} + \funcgroup{110.3 (K)}{K}{White}{Black}{upper}{up} + \else + \funcgroup{\ 13.9 (C); Accessible sidechain area (\AA$^2$)}% + {CIV}{Black}{BrickRed}{upper}{up} + \funcgroup{\ 23.0 (I); 23.5 (V); 25.2 (G)}% + {IVG}{Black}{Orange}{upper}{up} + \funcgroup{\ 28.7 (F); 29.0 (L); 30.5 (M); 31.5 (A)}% + {FLMA}{Black}{Yellow}{upper}{up} + \funcgroup{\ 41.7 (W); 44.2 (S); 46.0 (T); 46.7 (H)}% + {WSTH}{Black}{YellowGreen}{upper}{up} + \funcgroup{\ 53.7 (P)}{P}{White}{PineGreen}{upper}{up} + \funcgroup{\ 59.1 (Y); 60.9 (D); 62.2 (N)}% + {YDN}{Black}{SkyBlue}{upper}{up} + \funcgroup{\ 72.3 (E); 74.0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up} + \funcgroup{\ 93.8 (R)}{R}{White}{RedViolet}{upper}{up} + \funcgroup{110.3 (K)}{K}{White}{Black}{upper}{up} + \fi + \fi + \else \message{} + \fi\fi\fi\fi\fi\fi +} +\def\shadeallresidues{\all@fshadetrue} +\def\get@fromstack#1;#2;#3;#4;#5@{% + \xdef\first@{#1} \xdef\second@{#2} + \xdef\third@{#3} \xdef\fourth@{#4} \xdef\last@{#5@} +} +\def\getregion@fromstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@reg\temp@\endcsname} + \expandafter\get@fromstack\first@ + \expandafter\xdef\csname style\temp@\endcsname{\first@} + \expandafter\xdef\csname start\temp@\endcsname{\second@} + \expandafter\xdef\csname stop\temp@\endcsname{\third@} + \expandafter\xdef\csname all\temp@\endcsname{\fourth@} + \expandafter\xdef\csname stack@reg\temp@\endcsname{\last@} +} +\def\sort@stack{% + \expandafter\get@fromstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;&;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;% + \first@;\second@;\third@;\fourth@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@stack + \fi\fi +} +\def\get@regions#1..#2,#3@{% + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@reg\seq@\endcsname} + \xdef\tmpstack{} + \sort@stack + \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack} +} +\def\get@fromemphstack#1;#2;#3;#4@{% + \xdef\first@{#1} \xdef\second@{#2} + \xdef\third@{#3} \xdef\last@{#4@} +} +\def\getregion@fromemphstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@emphreg\temp@\endcsname} + \expandafter\get@fromemphstack\first@ + \expandafter\xdef\csname emphstart\temp@\endcsname{\first@} + \expandafter\xdef\csname emphstop\temp@\endcsname{\second@} + \expandafter\xdef\csname emphall\temp@\endcsname{\third@} + \expandafter\xdef\csname stack@emphreg\temp@\endcsname{\last@} +} +\def\sort@emphstack{% + \expandafter\get@fromemphstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@emphstack + \fi\fi +} +\def\get@emphregions#1..#2,#3@{% + \regionalemphtrue + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@emphreg\seq@\endcsname} + \xdef\tmpstack{} + \sort@emphstack + \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack} +} +\def\getregion@fromtintstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@tintreg\temp@\endcsname} + \expandafter\get@fromemphstack\first@ + \expandafter\xdef\csname tintstart\temp@\endcsname{\first@} + \expandafter\xdef\csname tintstop\temp@\endcsname{\second@} + \expandafter\xdef\csname tintall\temp@\endcsname{\third@} + \expandafter\xdef\csname stack@tintreg\temp@\endcsname{\last@} +} +\def\sort@tintstack{% + \expandafter\get@fromemphstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@tintstack + \fi\fi +} +\def\get@tintregions#1..#2,#3@{% + \regionaltinttrue + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@tintreg\seq@\endcsname} + \xdef\tmpstack{} + \sort@tintstack + \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} +} +\def\getregion@fromframestack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@framereg\temp@\endcsname} + \expandafter\get@fromemphstack\first@ + \expandafter\xdef\csname framestart\temp@\endcsname{\first@} + \expandafter\xdef\csname framestop\temp@\endcsname{\second@} + \expandafter\xdef\csname framestyle\temp@\endcsname{\third@} + \expandafter\xdef\csname stack@framereg\temp@\endcsname{\last@} +} +\def\get@frameregions#1..#2,#3@{% + \frame@true + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} + \xdef\last@{\csname stack@framereg\seq@\endcsname} + \xdef\tmpstack{} + \sort@emphstack + \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack} +} +\def\getregion@fromfstack#1{% + \xdef\temp@{#1} + \xdef\first@{\csname stack@\bottop@\temp@\endcsname} + \expandafter\get@fromstack\first@ + \expandafter\xdef\csname text\bottop@\temp@\endcsname{\first@} + \expandafter\xdef\csname start\bottop@\temp@\endcsname{\second@} + \expandafter\xdef\csname stop\bottop@\temp@\endcsname{\third@} + \ifx\fourth@\ampers@nd \xdef\fourth@{///} \fi + \expandafter\xdef\csname style\bottop@\temp@\endcsname{\fourth@} + \expandafter\xdef\csname stack@\bottop@\temp@\endcsname{\last@} +} +\def\sort@fstack{% + \expandafter\get@fromstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\f@text@;\st@rt;\st@p;\style@;&;&;&;&;@} + \else + \ifnum\st@rt<\second@ + \xdef\tmpstack{\tmpstack\f@text@;\st@rt;\st@p;\style@;% + \first@;\second@;\third@;\fourth@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} + \sort@fstack + \fi\fi +} +\def\get@fregions#1..#2,#3@{% + \xdef\st@rt{#1} + \ifx\temp@\y@ + \xdef\st@p{#1} + \else + \xdef\st@p{#2} + \fi + \xdef\list@{#3} + \xdef\last@{\csname stack@\bottop@\seq@\endcsname} + \xdef\tmpstack{} + \sort@fstack + \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack} +} +\def\getarrow@shape#1#2#3#4&{% + \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3} + \if\first@@ v + \if\second@@ = + \else \xdef\style@{\first@@ v\third@@#4} \fi + \else + \if\first@@ v + \if\second@@ = + \else \xdef\style@{\first@@ v\third@@#4} \fi + \else + \if\third@@ v + \if\second@@ = + \else \xdef\style@{\first@@ v\third@@#4} \fi + \else + \if\third@@ v + \if\second@@ = + \else \xdef\style@{\first@@ v\third@@#4} \fi + \fi\fi\fi\fi +} +\def\get@shape#1#2#3{% + \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}% + \if\second@@ v \xdef\second@@{arrow}% + \fi% + \if\second@@ = \xdef\second@@{doublearrow}% + \fi% +} +\def\getstyle@left#1#2#3#4@{% + \ifstop@ + \xdef\style@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \else + \xdef\style@@{#2} + \xdef\temp@{-} + \ifx\style@@\temp@ \xdef\style@@{#1#2-#4} + \else + \xdef\temp@{v} + \ifx\style@@\temp@ \xdef\style@@{#1#2-#4} + \else + \xdef\temp@{=} + \ifx\style@@\temp@ \xdef\style@@{#1#2=#4} + \else + \xdef\style@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \fi\fi\fi\fi +} +\def\getstyle@right#1#2#3#4@{% + \xdef\style@@{#2} + \xdef\temp@{-} + \ifx\style@@\temp@ + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{-#2#3#4} + \fi + \xdef\temp@{v} + \ifx\style@@\temp@ + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{-#2#3#4} + \fi + \xdef\temp@{=} + \ifx\style@@\temp@ + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{=#2#3#4} + \fi +} +\def\opt@color#1[#2]#3&{\xdef\fourth@{#1}\xdef\f@color{#2}} +\def\graph@opt@color#1[#2]:#3[#4][#5]#6&{% + \xdef\fourth@{#1} + \xdef\f@color{#2} + \xdef\ffourth@{#3} + \xdef\ff@color{#4} + \xdef\fffourth@{#5}} +\def\arrow@col@width#1[#2][#3]#4&{\xdef\fourth@{#1}\xdef\f@color{#2}\xdef\rule@@thick{#3}} +\def\second@color#1,&{\xdef\back@color{#1}} +\def\two@opt@color#1,#2@{% + \xdef\sixth@{#1}% + \xdef\seventh@{#2}% + \ifx\first@\ampers@nd% + \else% + \xdef\frame@color{#1}% + \ifx\seventh@\ampers@nd% + \xdef\back@color{#1}% + \else% + \expandafter\second@color\seventh@% + \fi% + \fi% +} +\def\test@fill#1:#2:#3&{% + \xdef\last@{#1[,][,]&}\expandafter\arrow@col@width\last@% + \xdef\second@@{\fourth@}% + \xdef\last@{///}% + \ifx\fourth@\last@% + \xdef\second@@{empty}% + \else + \xdef\last@{translate}% + \ifx\fourth@\last@% + \xdef\second@@{translate}% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{fill}% + \ifx\fourth@\last@ + \xdef\second@@{fill}% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{bar}% + \ifx\fourth@\last@ + \xdef\second@@{bar}% + \xdef\b@r{bar}% + \ifx\f@color\comm@ + \xdef\g@min{,}\xdef\g@max{,}% + \else + \xdef\f@color{\f@color @}% + \expandafter\get@item\f@color% + \xdef\g@min{\fourth@} \xdef\g@max{\first@@}% + \xdef\pm@shift{\fourth@}% + \fi% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi% + \xdef\fill@char{\fourth@}% + \xdef\box@color{\f@color,&@}% + \expandafter\two@opt@color\box@color% + \else + \xdef\last@{color}% + \ifx\fourth@\last@ + \xdef\second@@{color}% + \ifx\f@color\comm@ + \xdef\g@min{,}\xdef\g@max{,}% + \else + \xdef\f@color{\f@color @}% + \expandafter\get@item\f@color% + \xdef\g@min{\fourth@} \xdef\g@max{\first@@}% + \fi% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{box}% + \ifx\fourth@\last@% + \xdef\second@@{box}% + \ifx\f@color\comm@\xdef\f@color{White}\fi% + \xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@% + \ifnumber% + \ifx\rule@@thick\comm@% + \xdef\rule@@thick{\f@color}% + \xdef\box@color{White,&@}% + \else% + \xdef\seventh@{\rule@@thick}% + \xdef\rule@@thick{\f@color}% + \xdef\box@color{\seventh@,&@}% + \fi% + \else% + \xdef\box@color{\f@color,&@}% + \fi% + \expandafter\two@opt@color\box@color% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{plotcolor}% + \ifx\fourth@\last@% + \xdef\second@@{plotcolor}% + \ifx\f@color\comm@% + \xdef\pm@shift{0}% + \else% + \xdef\pm@shift{\f@color}% + \fi% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \xdef\fill@char{\fourth@}% + \else + \xdef\last@{plotbar}% + \ifx\fourth@\last@% + \xdef\second@@{plotbar}% + \xdef\b@r{bar}% + \ifx\f@color\comm@ + \xdef\pm@shift{0}% + \else + \xdef\pm@shift{\f@color}% + \fi% + \xdef\fill@char{#2[,]&}% + \expandafter\opt@color\fill@char% + \ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi% + \xdef\fill@char{\fourth@}% + \xdef\box@color{\f@color,&@}% + \expandafter\two@opt@color\box@color% + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@% + \ifnumber% + \ifx\rule@@thick\comm@% + \xdef\rule@@thick{\f@color}% + \xdef\f@color{Black}% + \else% + \xdef\seventh@{\rule@@thick}% + \xdef\rule@@thick{\f@color}% + \xdef\f@color{\seventh@}% + \fi% + \fi% + \ifx\rule@@thick\comm@\xdef\rule@@thick{\the\rule@thick}\fi% + \ifx\f@color\comm@\xdef\f@color{Black}\fi} +\def\clear@groups{% + \expandafter\xdef\csname \prfx grpA\endcsname{ -1} + \expandafter\xdef\csname \prfx grpB\endcsname{ -2} + \expandafter\xdef\csname \prfx grpC\endcsname{ -3} + \expandafter\xdef\csname \prfx grpD\endcsname{ -4} + \expandafter\xdef\csname \prfx grpE\endcsname{ -5} + \expandafter\xdef\csname \prfx grpF\endcsname{ -6} + \expandafter\xdef\csname \prfx grpG\endcsname{ -7} + \expandafter\xdef\csname \prfx grpH\endcsname{ -8} + \expandafter\xdef\csname \prfx grpI\endcsname{ -9} + \expandafter\xdef\csname \prfx grpJ\endcsname{-10} + \expandafter\xdef\csname \prfx grpK\endcsname{-11} + \expandafter\xdef\csname \prfx grpL\endcsname{-12} + \expandafter\xdef\csname \prfx grpM\endcsname{-13} + \expandafter\xdef\csname \prfx grpN\endcsname{-14} + \expandafter\xdef\csname \prfx grpO\endcsname{-15} + \expandafter\xdef\csname \prfx grpP\endcsname{-16} + \expandafter\xdef\csname \prfx grpQ\endcsname{-17} + \expandafter\xdef\csname \prfx grpR\endcsname{-18} + \expandafter\xdef\csname \prfx grpS\endcsname{-19} + \expandafter\xdef\csname \prfx grpT\endcsname{-20} + \expandafter\xdef\csname \prfx grpU\endcsname{-21} + \expandafter\xdef\csname \prfx grpV\endcsname{-22} + \expandafter\xdef\csname \prfx grpW\endcsname{-23} + \expandafter\xdef\csname \prfx grpX\endcsname{-24} + \expandafter\xdef\csname \prfx grpY\endcsname{-25} + \expandafter\xdef\csname \prfx grpZ\endcsname{-26} + \expandafter\xdef\csname \prfx grp-\endcsname{-999} + \expandafter\xdef\csname \prfx grp.\endcsname{-999} +} +\def\inactivate@chars{% + \catcode`\#=12 + \catcode`\"=12 + \catcode`\~=12 + \catcode`\^=12 + \catcode`\_=12 + } +\def\numcount{\the\loopcount} +\def\Alphacount{\@Alph\loopcount} +\def\alphacount{\@alph\loopcount} +\def\romancount{\@roman\loopcount} +\def\Romancount{\@Roman\loopcount} +\def\cut@name#1.#2@{\global\xdef\file@n@me{#1}} +\def\struc@get#1 #2 #3 #4 #5 #6 #7 #8 #9@{% + \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\fourth@{#4} + \xdef\fifth@{#5} \xdef\sixth@{#6} \xdef\seventh@{#7}\xdef\eighth@{#8}} +\def\get@PHD#1|#2|#3@{\xdef\PHD@line{\PHD@line #2}} +\def\write@PHDsec{% + \expandafter\get@sim\last@ + \ifx\sim@char\c@mp + \def\end@{\the\innerloopcount} + \advance\innerloopcount by 1 + \else + \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi + \if\c@mp . + \else + \if\c@mp L + \else + \if\c@mp H + \ifx\show@Hsec\yes + \loopcount=\first@ + \advance\loopcount by 1 + \xdef\first@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Hsec}{\begin@..\end@}% + {\label@Hsec}{\text@Hsec}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Hsec}{\st@rt}{\begin@..\end@}% + {\label@Hsec}{\text@Hsec}}\fi + \fi + \else + \if\c@mp E + \ifx\show@Esec\yes + \loopcount=\second@ + \advance\loopcount by 1 + \xdef\second@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Esec}{\begin@..\end@}% + {\label@Esec}{\text@Esec}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Esec}{\st@rt}{\begin@..\end@}% + {\label@Esec}{\text@Esec}}\fi + \fi + \fi\fi\fi\fi + \xdef\c@mp{\sim@char} + \advance\innerloopcount by 1 + \xdef\begin@{\the\innerloopcount} + \fi + \ifx\sim@char\ampers@nd\else\write@PHDsec\fi +} +\def\write@PHDtopo{% + \expandafter\get@sim\last@ + \ifx\sim@char\c@mp + \def\end@{\the\innerloopcount} + \advance\innerloopcount by 1 + \else + \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi + \if\c@mp . + \else + \if\c@mp L + \else + \if\c@mp T + \ifx\show@TMtop\yes + \loopcount=\first@ + \advance\loopcount by 1 + \xdef\first@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@TMtop}{\begin@..\end@}% + {\label@TMtop}{\text@TMtop}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@TMtop}{\st@rt}{\begin@..\end@}% + {\label@TMtop}{\text@TMtop}}\fi + \fi + \else + \if\c@mp i + \ifx\show@itop\yes + \loopcount=\second@ + \advance\loopcount by 1 + \xdef\second@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@itop}{\begin@..\end@}% + {\label@itop}{\text@itop}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@itop}{\st@rt}{\begin@..\end@}% + {\label@itop}{\text@itop}}\fi + \fi + \else + \if\c@mp o + \ifx\show@etop\yes + \loopcount=\second@ + \advance\loopcount by 1 + \xdef\second@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@etop}{\begin@..\end@}% + {\label@etop}{\text@etop}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@etop}{\st@rt}{\begin@..\end@}% + {\label@etop}{\text@etop}}\fi + \fi + \fi\fi\fi\fi\fi + \xdef\c@mp{\sim@char} + \advance\innerloopcount by 1 + \xdef\begin@{\the\innerloopcount} + \fi + \ifx\sim@char\ampers@nd\else\write@PHDtopo\fi +} +\def\include@DSSP{% + \xdef\first@{\csname optiondssp\the\loopcount\endcsname} + \xdef\bottop@{\csname bottopdssp\the\loopcount\endcsname} + \xdef\st@rt{\csname doseqdssp\the\loopcount\endcsname} + \xdef\structurefilename{\csname filenamedssp\the\loopcount\endcsname} + \bgroup + \xdef\file@n@me{\structurefilename .@} + \expandafter\cut@name\file@n@me + \xdef\file@n@me{\file@n@me.sec} + \ifx\first@\file@n@me + \else + \immediate\openin\alignfile = \file@n@me\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \fi + \xdef\temp@{make new} + \ifx\first@\temp@ + \def\par{} + \inactivate@chars + \immediate\openin\structurefile = \structurefilename\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\structurefilename' not found} + {\MessageBreak + The `DSSP' file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No labels for secondary structures will be displayed. \MessageBreak + Type to proceed. \MessageBreak + Type X to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \message{[\structurefilename] ->} + \xdef\second@{} \xdef\temp@{RESIDUE} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\second@\temp@ \xdef\temp@{AA}\fi + \ifx\third@\temp@ \else\repeat + \immediate\openout\featurefile = \file@n@me + \xdef\c@mp{+} + \xdef\begin@{\csname seq@start\st@rt\endcsname} + \xdef\end@{\csname seq@start\st@rt\endcsname} + \xdef\st@rt@{\begin@} + \expandafter\innerloopcount=\csname seq@start\st@rt\endcsname + \advance\innerloopcount by -1 + \xdef\first@@{0} \xdef\second@@{0} \xdef\third@@{0} + \xdef\fourth@@{0} \xdef\fifth@@{0} \xdef\sixth@@{0} + \xdef\seventh@@{0} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \if\c@mp + \xdef\c@mp{\fifth@}\fi + \ifx\fifth@\c@mp + \ifx\fc@DSSP\y@ + \temp@count=\first@ + \else + \temp@count=\second@ + \fi + \advance\temp@count by \st@rt@ + \advance\temp@count by -1 + \xdef\end@{\the\temp@count} + \else + \ifnum\begin@>0 + \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi + \if\c@mp C + \else + \if\c@mp H + \ifx\show@Hdssp\yes + \loopcount=\first@@ + \advance\loopcount by 1 + \xdef\first@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Hdssp}{\begin@..\end@}% + {\label@Hdssp}{\text@Hdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Hdssp}{\st@rt}{\begin@..\end@}% + {\label@Hdssp}{\text@Hdssp}}\fi + \fi + \else + \if\c@mp G + \ifx\show@Gdssp\yes + \loopcount=\second@@ + \advance\loopcount by 1 + \xdef\second@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Gdssp}{\begin@..\end@}% + {\label@Gdssp}{\text@Gdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Gdssp}{\st@rt}{\begin@..\end@}% + {\label@Gdssp}{\text@Gdssp}}\fi + \fi + \else + \if\c@mp I + \ifx\show@Idssp\yes + \loopcount=\third@@ + \advance\loopcount by 1 + \xdef\third@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Idssp}{\begin@..\end@}% + {\label@Idssp}{\text@Idssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Idssp}{\st@rt}{\begin@..\end@}% + {\label@Idssp}{\text@Idssp}}\fi + \fi + \else + \if\c@mp E + \ifx\show@Edssp\yes + \loopcount=\fourth@@ + \advance\loopcount by 1 + \xdef\fourth@@{\the\loopcount} + \advance\innerloopcount by 1 + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Edssp}{\begin@..\end@}% + {\label@Edssp}{\text@Edssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Edssp}{\st@rt}{\begin@..\end@}% + {\label@Edssp}{\text@Edssp}}\fi + \fi + \else + \if\c@mp B + \ifx\show@Bdssp\yes + \loopcount=\fifth@@ + \advance\loopcount by 1 + \xdef\fifth@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Bdssp}{\begin@..\end@}% + {\label@Bdssp}{\text@Bdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Bdssp}{\st@rt}{\begin@..\end@}% + {\label@Bdssp}{\text@Bdssp}}\fi + \fi + \else + \if\c@mp T + \ifx\show@Tdssp\yes + \loopcount=\sixth@@ + \advance\loopcount by 1 + \xdef\sixth@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Tdssp}{\begin@..\end@}% + {\label@Tdssp}{\text@Tdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Tdssp}{\st@rt}{\begin@..\end@}% + {\label@Tdssp}{\text@Tdssp}}\fi + \fi + \else + \if\c@mp S + \ifx\show@Sdssp\yes + \loopcount=\seventh@@ + \advance\loopcount by 1 + \xdef\seventh@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Sdssp}{\begin@..\end@}% + {\label@Sdssp}{\text@Sdssp}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Sdssp}{\st@rt}{\begin@..\end@}% + {\label@Sdssp}{\text@Sdssp}}\fi + \fi + \fi\fi\fi\fi\fi\fi\fi\fi + \fi + \xdef\c@mp{\fifth@} + \ifx\fc@DSSP\y@ + \temp@count=\first@ + \else + \temp@count=\second@ + \fi + \advance\temp@count by \st@rt@ + \advance\temp@count by -1 + \xdef\begin@{\the\temp@count} + \fi + \fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \immediate\closeout\featurefile + \egroup + \input{\file@n@me} + \fi + \else + \egroup + \message{using existing file:} + \input{\file@n@me} + \fi + } + +\def\include@HMMTOP{% + \def\get@HMMTOP@TMs##1-##2 ##3@{% + \xdef\temp@@{\temp@@\fourth@@##1\fourth@@##2} + \xdef\structureline{##3 @} + } + \def\get@HMMTOP{% + \ifnum\temp@count<\fifth@ + \advance\temp@count by 1 + \expandafter\get@HMMTOP@TMs\structureline + \get@HMMTOP + \fi + } + \def\rem@ve@TM@info Transmembrane helices: ##1@{% + \xdef\structureline{##1 @} + \temp@count=0 + \get@HMMTOP + } + \xdef\bottop@{\csname bottopHMMTOP\the\loopcount\endcsname} + \xdef\st@rt{\csname doseqHMMTOP\the\loopcount\endcsname} + \xdef\first@{\csname optionHMMTOP\the\loopcount\endcsname} + \xdef\structurefilename{\csname filenameHMMTOP\the\loopcount\endcsname} + \bgroup + \xdef\file@n@me{\structurefilename .@} + \expandafter\cut@name\file@n@me + \xdef\file@n@me{\file@n@me.top} + \ifx\first@\file@n@me + \else + \immediate\openin\alignfile = \file@n@me\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \fi + \xdef\temp@{make new} + \ifx\first@\temp@ + \def\par{} + \inactivate@chars + \immediate\openin\structurefile = \structurefilename\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\structurefilename' not found} + {\MessageBreak + The `HMMTOP' file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No labels for secondary structures will be displayed. \MessageBreak + Type to proceed. \MessageBreak + Type X to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \message{[\structurefilename] ->} + \immediate\openout\featurefile = \file@n@me + + \xdef\first@{\csname fileseqHMMTOP\the\loopcount\endcsname @} + \expandafter\check@letter\first@ + \ifletter + \xdef\st@p{\csname fileseqHMMTOP\the\loopcount\endcsname} + \else + \xdef\first@{\csname fileseqHMMTOP\the\loopcount\endcsname} + \ifnum\first@=0 + \xdef\st@p{0} + \else + \xdef\st@p{\csname fileseqHMMTOP\the\loopcount\endcsname} + \fi + \fi + \xdef\temp@{yes} \innerloopcount=0 + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\@HP + \ifx\temp@\yes \xdef\temp@{\readline} \fi + \ifletter + \ifx\st@p\third@ \xdef\temp@{\readline} \fi + \else + \ifnum\st@p=0 + \expandafter\ifx\csname seqname\st@rt\endcsname\third@ + \xdef\temp@{\readline} \xdef\st@p{-1} + \else + \expandafter\ifx\csname newseqname\st@rt\endcsname\third@ + \xdef\temp@{\readline} \xdef\st@p{-1} + \fi + \fi + \else + \advance\innerloopcount by 1 + \ifnum\st@p=\innerloopcount \xdef\temp@{\readline} \fi + \fi + \fi + \else + \xdef\first@@{Protein:} + \ifx\first@\first@@ + \xdef\second@@{\second@} + \xdef\temp@@{>HP:} \xdef\fourth@@{ } + \read\structurefile to \readline + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \xdef\temp@@{\temp@@\fourth@@\second@\fourth@@\second@@} + \read\structurefile to \readline + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \xdef\temp@@{\temp@@\fourth@@\second@} + \read\structurefile to \readline + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \xdef\temp@@{\temp@@\fourth@@\fifth@} + \read\structurefile to \readline + \xdef\structureline{\readline @} + \expandafter\rem@ve@TM@info\structureline + \xdef\temp@@{\temp@@\fourth@@} + \ifx\temp@\yes \xdef\temp@{\temp@@} \fi + \ifletter + \ifx\st@p\third@ \xdef\temp@{\temp@@} \fi + \else + \ifnum\st@p=0 + \expandafter\ifx\csname seqname\st@rt\endcsname\second@@ + \xdef\temp@{\temp@@} + \else + \expandafter\ifx\csname newseqname\st@rt\endcsname\second@@ + \xdef\temp@{\temp@@} + \fi + \fi + \else + \advance\innerloopcount by 1 + \ifnum\st@p=\innerloopcount \xdef\temp@{\temp@@} \fi + \fi + \fi + \fi + \fi + \fi + \ifeof\structurefile \else\repeat + \xdef\seq@line{\temp@ @} + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \expandafter\seq@get\seq@line + \xdef\seq@line{\seq@line @} + \ifnum\innerloopcount=4 \xdef\c@mp{\first@} \fi + \ifnum\innerloopcount=5 \xdef\st@p{\first@} \else \repeat + \xdef\first@{IN} + \ifx\c@mp\first@ \xdef\c@mp{i} \else \xdef\c@mp{e} \fi + \xdef\begin@{1} \xdef\first@@{0} \xdef\second@@{0} + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \expandafter\seq@get\seq@line + \xdef\seq@line{\seq@line @} + \temp@count=\first@ + \advance\temp@count by -1 + \xdef\end@{\the\temp@count} + \loopcount=\second@@ + \advance\loopcount by 1 + \xdef\second@@{\the\loopcount} + \if\c@mp i + \ifx\show@i@HMMTOP\yes + \immediate\write\featurefile{% + \string\feature{\bottop@i@HMMTOP}{\st@rt}{\begin@..\end@}% + {\label@i@HMMTOP}{\text@i@HMMTOP}}\fi + \xdef\c@mp{e} + \else + \ifx\show@e@HMMTOP\yes + \immediate\write\featurefile{% + \string\feature{\bottop@e@HMMTOP}{\st@rt}{\begin@..\end@}% + {\label@e@HMMTOP}{\text@e@HMMTOP}}\fi + \xdef\c@mp{i} + \fi + \advance\temp@count by 1 + \xdef\begin@{\the\temp@count} + \expandafter\seq@get\seq@line + \xdef\seq@line{\seq@line @} + \xdef\end@{\first@} + \loopcount=\first@@ + \advance\loopcount by 1 + \xdef\first@@{\the\loopcount} + \ifx\show@TM@HMMTOP\yes + \immediate\write\featurefile{% + \string\feature{\bottop@TM@HMMTOP}{\st@rt}{\begin@..\end@}% + {\label@TM@HMMTOP}{\text@TM@HMMTOP}}\fi + \temp@count=\end@ \advance\temp@count by 1 \xdef\begin@{\the\temp@count} + \ifnum\innerloopcount=\st@p\else\repeat + \closein\structurefile + \immediate\closeout\featurefile + \egroup + + \input{\file@n@me} + \fi + \else + \egroup + \message{using existing file:} + \input{\file@n@me} + \fi + } + +\def\include@stride{% + \xdef\first@{\csname optionstride\the\loopcount\endcsname} + \xdef\bottop@{\csname bottopstride\the\loopcount\endcsname} + \xdef\st@rt{\csname doseqstride\the\loopcount\endcsname} + \xdef\structurefilename{\csname filenamestride\the\loopcount\endcsname} + \bgroup + \xdef\file@n@me{\structurefilename .@} + \expandafter\cut@name\file@n@me + \xdef\file@n@me{\file@n@me.sec} + \ifx\first@\file@n@me + \else + \immediate\openin\alignfile = \file@n@me\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \fi + \xdef\temp@{make new} + \ifx\first@\temp@ + \def\par{} + \inactivate@chars + \immediate\openin\structurefile = \structurefilename\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\structurefilename' not found} + {\MessageBreak + The `STRIDE' file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No labels for secondary structures will be displayed. \MessageBreak + Type to proceed. \MessageBreak + Type X to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \message{[\structurefilename] ->} + \immediate\openout\featurefile = \file@n@me + \xdef\c@mp{+} + \xdef\begin@{\csname seq@start\st@rt\endcsname} + \xdef\end@{\csname seq@start\st@rt\endcsname} + \xdef\st@rt@{\begin@} + \expandafter\innerloopcount=\csname seq@start\st@rt\endcsname + \advance\innerloopcount by -1 + \xdef\first@@{0} \xdef\second@@{0} \xdef\third@@{0} + \xdef\fourth@@{0} \xdef\fifth@@{0} \xdef\sixth@@{0} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \ifx\first@\@asg + \if\c@mp + \xdef\c@mp{\sixth@}\fi + \ifx\sixth@\c@mp + \temp@count=\fifth@ + \advance\temp@count by \st@rt@ + \advance\temp@count by -1 + \xdef\end@{\the\temp@count} + \else + \ifnum\begin@>0 + \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi + \if\c@mp C + \else + \if\c@mp H + \ifx\show@Hstride\yes + \loopcount=\first@@ + \advance\loopcount by 1 + \xdef\first@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Hstride}{\begin@..\end@}% + {\label@Hstride}{\text@Hstride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Hstride}{\st@rt}{\begin@..\end@}% + {\label@Hstride}{\text@Hstride}}\fi + \fi + \else + \if\c@mp G + \ifx\show@Gstride\yes + \loopcount=\second@@ + \advance\loopcount by 1 + \xdef\second@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Gstride}{\begin@..\end@}% + {\label@Gstride}{\text@Gstride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Gstride}{\st@rt}{\begin@..\end@}% + {\label@Gstride}{\text@Gstride}}\fi + \fi + \else + \if\c@mp I + \ifx\show@Istride\yes + \loopcount=\third@@ + \advance\loopcount by 1 + \xdef\third@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Istride}{\begin@..\end@}% + {\label@Istride}{\text@Istride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Istride}{\st@rt}{\begin@..\end@}% + {\label@Istride}{\text@Istride}}\fi + \fi + \else + \if\c@mp E + \ifx\show@Estride\yes + \loopcount=\fourth@@ + \advance\loopcount by 1 + \xdef\fourth@@{\the\loopcount} + \advance\innerloopcount by 1 + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Estride}{\begin@..\end@}% + {\label@Estride}{\text@Estride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Estride}{\st@rt}{\begin@..\end@}% + {\label@Estride}{\text@Estride}}\fi + \fi + \else + \if\c@mp B + \ifx\show@Bstride\yes + \loopcount=\fifth@@ + \advance\loopcount by 1 + \xdef\fifth@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Bstride}{\begin@..\end@}% + {\label@Bstride}{\text@Bstride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Bstride}{\st@rt}{\begin@..\end@}% + {\label@Bstride}{\text@Bstride}}\fi + \fi + \else + \if\c@mp T + \ifx\show@Tstride\yes + \loopcount=\sixth@@ + \advance\loopcount by 1 + \xdef\sixth@@{\the\loopcount} + \ifx\m@p\yes + \immediate\write\featurefile{% + \string\feature{\bottop@Tstride}{\begin@..\end@}% + {\label@Tstride}{\text@Tstride}} + \else + \immediate\write\featurefile{% + \string\feature{\bottop@Tstride}{\st@rt}{\begin@..\end@}% + {\label@Tstride}{\text@Tstride}}\fi + \fi + \fi\fi\fi\fi\fi\fi\fi + \fi + \xdef\c@mp{\sixth@} + \temp@count=\fifth@ + \advance\temp@count by \st@rt@ + \advance\temp@count by -1 + \xdef\begin@{\the\temp@count} + \fi + \fi + \fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \immediate\closeout\featurefile + \egroup + \input{\file@n@me} + \fi + \else + \egroup + \message{using existing file:} + \input{\file@n@me} + \fi + } +\def\include@PHD{% + \xdef\first@{\csname optionphd\the\loopcount\endcsname} + \xdef\bottop@{\csname bottopphd\the\loopcount\endcsname} + \xdef\st@rt{\csname doseqphd\the\loopcount\endcsname} + \xdef\m@de{\csname modephd\the\loopcount\endcsname} + \xdef\structurefilename{\csname filenamephd\the\loopcount\endcsname} + \bgroup + \xdef\file@n@me{\structurefilename .@} + \expandafter\cut@name\file@n@me + \xdef\temp@{structure} + \ifx\m@de\temp@ + \xdef\temp@{\file@n@me .sec} + \immediate\openin\alignfile = \temp@\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \else + \xdef\temp@{topology} + \ifx\m@de\temp@ + \xdef\temp@{\file@n@me .top} + \immediate\openin\alignfile = \temp@\relax + \ifeof\alignfile \xdef\first@{make new} \fi + \immediate\closein\alignfile + \else + \message{} + \xdef\first@{ignore} + \fi\fi + \xdef\temp@{make new} + \ifx\first@\temp@ + \def\par{} + \xdef\PHD@line{} + \inactivate@chars + \immediate\openin\structurefile=\structurefilename\relax + \ifeof\structurefile + \PackageError{TeXshade}% + {File `\structurefilename' not found}% + {\MessageBreak + The `PHD' file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No labels for secondary structures will be displayed. \MessageBreak + Type to proceed. \MessageBreak + Type X to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \message{[\structurefilename] ->} + \loop + \read\structurefile to \readline + \xdef\structureline{\readline & & & & & & & & &@} + \expandafter\struc@get\structureline + \xdef\temp@{structure} + \ifx\m@de\temp@ + \xdef\temp@{SUB} + \ifx\temp@\first@ + \xdef\temp@{sec} + \ifx\temp@\second@ + \xdef\third@{\third@ @} + \expandafter\get@PHD\third@ + \fi + \else + \ifx\temp@\second@ + \xdef\temp@{sec} + \ifx\temp@\third@ + \xdef\fourth@{\fourth@ @} + \expandafter\get@PHD\fourth@ + \fi + \fi + \fi + \else + \xdef\temp@{topology} + \ifx\m@de\temp@ + \xdef\temp@{PHDThtm} + \ifx\temp@\first@ + \xdef\second@{\second@ @} + \expandafter\get@PHD\second@ + \fi + \fi\fi + \ifeof\structurefile \else\repeat + \closein\structurefile + \xdef\c@mp{+} + \xdef\begin@{\csname seq@start\st@rt\endcsname} + \xdef\end@{\csname seq@start\st@rt\endcsname} + \expandafter\innerloopcount=\csname seq@start\st@rt\endcsname + \advance\innerloopcount by -1 + \xdef\first@{0} \xdef\second@{0} \xdef\third@{0} + \xdef\fourth@{0} \xdef\fifth@{0} \xdef\sixth@{0} + \xdef\last@{\PHD@line &@} + \xdef\temp@{structure} + \ifx\temp@\m@de + \xdef\file@n@me{\file@n@me .sec} + \immediate\openout\featurefile = \file@n@me\relax + \write@PHDsec + \fi + \xdef\temp@{topology} + \ifx\temp@\m@de + \xdef\file@n@me{\file@n@me .top} + \immediate\openout\featurefile = \file@n@me\relax + \write@PHDtopo + \fi + \immediate\closeout\featurefile + \egroup + \input{\file@n@me} + \fi + \else + \egroup + \xdef\temp@{ignore} + \ifx\temp@\first@ + \else + \message{using existing file:} + \xdef\temp@{structure} + \ifx\temp@\m@de \xdef\file@n@me{\file@n@me .sec} \fi + \xdef\temp@{topology} + \ifx\temp@\m@de \xdef\file@n@me{\file@n@me .top} \fi + \input{\file@n@me} + \fi + \fi} +\def\show@DSSP{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{alpha} + \ifx\fourth@\temp@ \xdef\show@Hdssp{\second@}\fi + \xdef\temp@{3-10} + \ifx\fourth@\temp@ \xdef\show@Gdssp{\second@}\fi + \xdef\temp@{pi} + \ifx\fourth@\temp@ \xdef\show@Idssp{\second@}\fi + \xdef\temp@{beta} + \ifx\fourth@\temp@ \xdef\show@Edssp{\second@}\fi + \xdef\temp@{bridge} + \ifx\fourth@\temp@ \xdef\show@Bdssp{\second@}\fi + \xdef\temp@{turn} + \ifx\fourth@\temp@ \xdef\show@Tdssp{\second@}\fi + \xdef\temp@{bend} + \ifx\fourth@\temp@ \xdef\show@Sdssp{\second@}\fi + \show@DSSP + \fi} +\def\show@HMMTOP{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{internal} + \ifx\fourth@\temp@ \xdef\show@i@HMMTOP{\second@}\fi + \xdef\temp@{external} + \ifx\fourth@\temp@ \xdef\show@e@HMMTOP{\second@}\fi + \xdef\temp@{TM} + \ifx\fourth@\temp@ \xdef\show@TM@HMMTOP{\second@}\fi + \show@HMMTOP + \fi} +\def\show@STRIDE{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{alpha} + \ifx\fourth@\temp@ \xdef\show@Hstride{\second@}\fi + \xdef\temp@{3-10} + \ifx\fourth@\temp@ \xdef\show@Gstride{\second@}\fi + \xdef\temp@{pi} + \ifx\fourth@\temp@ \xdef\show@Istride{\second@}\fi + \xdef\temp@{beta} + \ifx\fourth@\temp@ \xdef\show@Estride{\second@}\fi + \xdef\temp@{bridge} + \ifx\fourth@\temp@ \xdef\show@Bstride{\second@}\fi + \xdef\temp@{turn} + \ifx\fourth@\temp@ \xdef\show@Tstride{\second@}\fi + \show@STRIDE + \fi} +\def\show@PHDtopo{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{internal} + \ifx\fourth@\temp@ \xdef\show@itop{\second@}\fi + \xdef\temp@{external} + \ifx\fourth@\temp@ \xdef\show@etop{\second@}\fi + \xdef\temp@{TM} + \ifx\fourth@\temp@ \xdef\show@TMtop{\second@}\fi + \show@PHDtopo + \fi} +\def\show@PHDsec{% + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\temp@{alpha} + \ifx\fourth@\temp@ \xdef\show@Hsec{\second@}\fi + \xdef\temp@{beta} + \ifx\fourth@\temp@ \xdef\show@Esec{\second@}\fi + \show@PHDsec + \fi} +\def\get@triplet#1,#2@{% + \xdef\third@{#1} + \ifx\third@\ampers@nd + \else + \expandafter\xdef\csname @\third@\endcsname{\first@} + \expandafter\xdef\csname rev@\first@\endcsname{\third@} + \xdef\fourth@{#2,&,@} + \expandafter\get@triplet\fourth@ + \fi} + +\def\get@name@number{% + \xdef\second@{n} + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\ifx\csname newseqname\the\loopcount\endcsname\first@ + \xdef\first@{\the\loopcount} \loopcount=\seq@count + \xdef\second@{y} + \fi + \ifnum\loopcount=\seq@count \else \repeat + \ifx\second@\n@ + \message{} + \xdef\first@{1} + \fi +} + +%%%%% Definition of user commands + +\def\clearfuncgroups{\xdef\prfx{func} \clear@groups \xdef\fgroup@num{0}} +\clearfuncgroups +\def\germanlanguage{\germ@ntrue \sp@nishfalse \def\cons@name{Konsensus}} +\def\spanishlanguage{\germ@nfalse \sp@nishtrue \def\cons@name{consenso}} +\def\englishlanguage{\germ@nfalse \sp@nishfalse \def\cons@name{consensus}} +\def\showlegend{\legend@true} +\def\hidelegend{\legend@false} +\def\movelegend#1#2{% + \setlength\hspace@legend{#1} + \setlength\vspace@legend{#2} +} +\newcommand{\showcaption}[2][bottom]{\def\cap@pos{#1}\def\c@p{#2}} +\def\shortcaption#1{\def\c@pshort{#1}} +\def\funcgroup#1#2#3#4#5#6{% + \xdef\first@{#1} + \loopcount=0 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifx\csname fgroup@name\the\loopcount\endcsname\first@ + \innerloopcount=\loopcount \loopcount=\fgroup@num + \fi + \ifnum\loopcount<\fgroup@num \repeat + \ifnum\innerloopcount=0 + \ifnum\fgroup@num<9 + \innerloopcount=\fgroup@num + \advance\innerloopcount by 1 \xdef\fgroup@num{\the\innerloopcount} + \else \message{} + \fi + \fi + \ifnum\innerloopcount>0 + \expandafter\xdef\csname fgroup@name\the\innerloopcount\endcsname{\first@} + \expandafter\xdef\csname fg@textcolor\the\innerloopcount\endcsname{#3} + \expandafter\xdef\csname fg@color\the\innerloopcount\endcsname{#4} + \expandafter\xdef\csname funcm@tch\the\innerloopcount\endcsname{#5} + \expandafter\def\csname func@style\the\innerloopcount\endcsname{% + \csname text#6\endcsname} + \xdef\prfx{func} + \xdef\third@{#2&,@} \loopcount=\innerloopcount + \expandafter\group@get\third@ + \fi} +\def\pepgroups#1{% + \xdef\prfx{pep} + \clear@groups + \xdef\third@{#1&,@} \loopcount=0 + \loop \expandafter\group@get\third@ \advance\loopcount by 1 + \ifnum\loopcount<10 \repeat} +\def\DNAgroups#1{% + \xdef\prfx{DNA} + \clear@groups + \xdef\third@{#1&,@} \loopcount=0 + \loop \expandafter\group@get\third@ \advance\loopcount by 1 + \ifnum\loopcount<10 \repeat} +\def\pepsims#1#2{\xdef\prfx{pep} + \def\sim@set{\expandafter\residue@get\second@ + \ifx\first@\ampers@nd + \else \advance\innerloopcount by 1 + \xdef\second@{\csname sequence\the\loopcount\endcsname} \sim@set + \fi} + \xdef\first@{#1} \make@upper \xdef\third@{\first@} + \xdef\last@{#2} \xdef\second@{#2 &@} \innerloopcount=0 \sim@set + \expandafter\xdef\csname \prfx sim\third@\endcsname{% + (\the\innerloopcount)\last@}} +\def\DNAsims#1#2{\xdef\prfx{DNA} + \def\sim@set{\expandafter\residue@get\second@ + \ifx\first@\ampers@nd + \else \advance\innerloopcount by 1 + \xdef\second@{\csname sequence\the\loopcount\endcsname} \sim@set + \fi} + \xdef\first@{#1} \make@upper \xdef\third@{\first@} + \xdef\last@{#2} \xdef\second@{#2 &@} \innerloopcount=0 \sim@set + \expandafter\xdef\csname \prfx sim\third@\endcsname{% + (\the\innerloopcount)\last@}} +\def\fingerprint#1{% + \ifnum #1 >0 + \residuesperline*{#1} + \def\finger@linenum{#1} + \shownames{left} + \hidenumbering + \rulersteps{100} + \nomatchresidues{}{Gray10}{}{} + \loopcount=0 + \loop + \advance\loopcount by 1 + \separationline{\the\loopcount} + \ifnum\loopcount<\seq@count\repeat + \fi} +\def\shaderegion#1#2#3#4{% + \regionalshadetrue + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{} + \else + \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi + \loopcount=\seq@regions + \advance\loopcount by 1 + \xdef\seq@regions{\the\loopcount} + \expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3} + \expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4} + \xdef\list@{#2,&} + \loop + \xdef\list@{\list@ @} + \expandafter\get@regions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi +} +\def\shadeblock#1#2#3#4{% + \xdef\seq@{#1} + \xdef\@ll{yes} + \shaderegion{#1}{#2}{#3}{#4} + \xdef\@ll{} +} +\def\tintregion#1#2{% + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{} + \else + \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi + \xdef\list@{#2,&} + \loop + \xdef\list@{\list@ @} + \expandafter\get@tintregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi +} +\def\tintblock#1#2{% + \xdef\seq@{#1} + \xdef\@ll{yes} + \tintregion{#1}{#2} + \xdef\@ll{} +} +\def\tintdefault#1{% + \xdef\first@{#1} + \xdef\second@{strong} + \ifx\first@\second@ + \xdef\light@{LightLightLight} + \else + \xdef\second@{medium} + \ifx\first@\second@ + \xdef\light@{LightLight} + \else + \xdef\second@{weak} + \ifx\first@\second@ + \xdef\light@{Light} + \else + \xdef\light@{LightLight} + \fi\fi\fi +} +\def\emphregion#1#2{% + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{} + \else + \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi + \xdef\list@{#2,&} + \loop + \xdef\list@{\list@ @} + \expandafter\get@emphregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi +} +\def\emphblock#1#2{% + \xdef\seq@{#1} + \xdef\@ll{yes} + \emphregion{#1}{#2} + \xdef\@ll{} +} +\def\emphdefault#1{\def\res@style{\csname text#1\endcsname}} +\def\frameblock#1#2#3{% + \xdef\seq@{#1} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{} + \else + \xdef\@ll{#3} + \xdef\list@{#2,&} + \loop + \xdef\list@{\list@ @} + \expandafter\get@frameregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi +} +\def\bargraphstretch#1{\def\b@r@stretch{#1}} +\def\colorscalestretch#1{\def\sc@le@stretch{#1}} +\def\rm@@measure#1#2@{% + \xdef\test@{#1} + \ifx\test@\ampers@nd + \else + \expandafter\check@char\test@ + \ifnumber\xdef\first@{\first@ #1} + \xdef\second@{#2 &@} + \expandafter\rm@@measure\second@ + \fi + \fi +} +\def\rm@measure#1.#2@{\xdef\first@{#1.}\xdef\second@{#2 @}\xdef\third@{#1}\expandafter\rm@@measure\second@} +\def\pm@calc{% + \temp@@length=100000sp + \temp@@length=\g@min\temp@@length + \innerloopcount=\temp@@length + \xdef\min@{\the\innerloopcount} + \arrow@height=\temp@@length + \temp@@length=100000sp + \temp@@length=\g@max\temp@@length + \advance\temp@@length by -\arrow@height + \innerloopcount=\temp@@length + \divide\innerloopcount by 100 + \ifnum\innerloopcount=0 \innerloopcount=1 \fi + \xdef\m@x{\the\innerloopcount} + \xdef\test@{\g@min pt} + \setlength\arrow@width{\test@} + \xdef\test@{\g@max pt} + \setlength\arrow@height{\test@} + \advance\arrow@height by -\arrow@width + \ifdim\arrow@width<0pt\temp@@length=-\arrow@width\xdef\test@{y}\else\temp@@length=\arrow@width\xdef\test@{n}\fi + \ifdim\arrow@height>0pt + \ifx\test@\n@ \xdef\test@{y} \else \xdef\test@{n} \fi + \ifdim\temp@@length<\arrow@height\temp@@length=\arrow@height\fi + \else + \ifdim\temp@@length>-\arrow@height\temp@@length=\arrow@height\fi + \fi + \ifdim\temp@@length<100pt\arrow@width=100\arrow@width\arrow@height=100\arrow@height\else + \ifdim\temp@@length<10pt\arrow@width=1000\arrow@width\arrow@height=1000\arrow@height\else + \ifdim\temp@@length<1pt\arrow@width=10000\arrow@width\arrow@height=10000\arrow@height\else + \ifdim\temp@@length<0.1pt\arrow@width=100000\arrow@width\arrow@height=100000\arrow@height\else + \ifdim\temp@@length<0.01pt\arrow@width=1000000\arrow@width \arrow@height=1000000\arrow@height\else + \ifdim\temp@@length<0.001pt\arrow@width=10000000\arrow@width \arrow@height=10000000\arrow@height\else + \ifdim\temp@@length<0.0001pt\arrow@width=100000000\arrow@width \arrow@height=100000000\arrow@height\else + \ifdim\temp@@length<0.00001pt\arrow@width=1000000000\arrow@width \arrow@height=1000000000\arrow@height + \fi\fi\fi\fi\fi\fi\fi\fi + \ifx\test@\y@ + \xdef\pm@{0} + \else + \xdef\test@{-\the\arrow@height @} + \expandafter\rm@measure\test@ + \divide\arrow@width by \third@ + \xdef\pm@{\the\arrow@width @} + \expandafter\rm@measure\pm@ + \xdef\pm@{\first@} + \fi +} +\def\read@graph{% + \bgroup + \immediate\openin\structurefile = \fill@char\relax + \ifeof\structurefile + \PackageError{TeXshade} + {File `\fill@char' not found} + {\MessageBreak + The file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + No feature graph will be displayed. \MessageBreak + Type to proceed. \MessageBreak + Type X to quit. \MessageBreak +} + \immediate\closein\structurefile\egroup + \else + \ifx\g@min\comm@ + \def\par@{} + \xdef\g@min{,} \xdef\g@max{,} + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\second@{\test@ @} + \expandafter\check@letter\second@ + \ifletter + \xdef\second@{\expandafter\string\readline} + \xdef\second@{\second@ @} + \expandafter\firstchar@get\second@ + \if\first@ - \numbertrue\fi + \fi + \ifnumber + \temp@@length=1pt + \temp@@length=\test@\temp@@length + \innerloopcount=\temp@@length + \ifx\g@min\comm@ \xdef\min@{\test@ pt} \xdef\g@min{\test@} + \else + \ifdim\temp@@length<\min@\relax \xdef\min@{\the\temp@@length} \xdef\g@min{\test@} \fi\fi% + \ifx\g@max\comm@ \xdef\m@x{\test@ pt} \xdef\g@max{\test@} + \else + \ifdim\temp@@length>\m@x\relax \xdef\m@x{\the\temp@@length} \xdef\g@max{\test@} \fi\fi% + \fi + \fi + \ifeof\structurefile\else\repeat + \fi + \immediate\closein\structurefile + \pm@calc + \expandafter\temp@count=\csname seq@start\seq@\endcsname + \advance\temp@count by -1 + \xdef\temp@@@{n} + \immediate\openin\structurefile = \fill@char\relax + \loop + \read\structurefile to \readline + \xdef\test@{\expandafter\string\readline} + \ifx\test@\par@ + \else + \xdef\second@{\test@ @} + \expandafter\check@letter\second@ + \ifletter + \xdef\second@{\expandafter\string\readline} + \xdef\second@{\second@ @} + \expandafter\firstchar@get\second@ + \if\first@ - \numbertrue + \else + \if\first@ N + \expandafter\firstchar@get\third@ + \if\first@ a + \expandafter\firstchar@get\third@ + \if\first@ N + \advance\temp@count by 1 + \ifnum\temp@count=0 \temp@count=1 \fi + \ifnum\temp@count<\st@rt + \else + \ifnum\temp@count>\st@p + \else + \ifx\temp@@@\n@ + \xdef\temp@@@{N} + \else + \xdef\temp@@@{\temp@@@,N} + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \ifnumber + \advance\temp@count by 1 + \ifnum\temp@count=0 \temp@count=1 \fi + \ifnum\temp@count<\st@rt + \else + \ifnum\temp@count>\st@p + \else + \temp@@length=100000sp + \temp@@length=\test@\temp@@length + \innerloopcount=\temp@@length + \advance\innerloopcount by 1 + \xdef\test@{\pm@ pt} + \ifdim\test@=0pt + \advance\innerloopcount by -\min@ + \else + \ifx\b@r\n@ + \advance\innerloopcount by -\min@ + \fi + \fi + \divide\innerloopcount by \m@x + \ifx\temp@@@\n@ + \xdef\temp@@@{\the\innerloopcount} + \else + \xdef\temp@@@{\temp@@@,\the\innerloopcount} + \fi + \fi + \fi + \fi + \fi + \ifeof\structurefile\else\repeat + \immediate\closein\structurefile + \xdef\temp@@@{\temp@@@,@} \xdef\temp@@{y} + \fi + \egroup +} +\def\sort@gstack{% + \expandafter\get@fromstack\last@ + \ifx\first@\ampers@nd + \xdef\tmpstack{\tmpstack\f@text@&;&;&;&;@} + \else + \ifnum\loopcount<\second@ + \xdef\tmpstack{\tmpstack\f@text@\first@;\second@;\third@;\fourth@;\last@} + \else + \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} + \sort@gstack + \fi\fi +} +\def\get@gregion#1..#2,#3&{% + \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} +} +\def\do@bargraph{% + \expandafter\get@gregion\list@ + \expandafter\ifnum\csname seq@start\seq@\endcsname>\st@rt + \else + \xdef\temp@@{n} + \xdef\b@r{y} + \xdef\pm@{0} + \xdef\temp@@@{\fill@char,@} + \expandafter\check@letter\temp@@@ + \ifletter + \read@graph + \else + \ifx\g@min\comm@ \xdef\g@min{0} \fi + \ifx\g@max\comm@ \xdef\g@max{100} \fi + \pm@calc + \xdef\temp@@@{\fill@char,@} + \xdef\temp@@{y} + \fi + \ifx\temp@@\y@ + \loopcount=\st@rt + \xdef\tmpstack{} + \loop + \expandafter\get@item\temp@@@ + \xdef\temp@@@{\first@} + \xdef\style@{bar[\pm@,0]:\fourth@[\f@color]} + \xdef\tmpstack{\tmpstack\f@text@;\the\loopcount;\the\loopcount;\style@;} + \advance\loopcount by 1 + \ifnum\loopcount=0 \loopcount=1 \fi + \ifnum\loopcount>\st@p + \else\repeat + \xdef\f@text@{\tmpstack} \xdef\tmpstack{} + \xdef\last@{\csname stack@\bottop@\seq@\endcsname} + \sort@gstack + \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack} + \fi + \fi + \xdef\list@{\list@ &} + \ifx\list@\ampers@nd\else\do@bargraph\fi +} +\def\do@colorgraph{% + \expandafter\get@gregion\list@ + \expandafter\ifnum\csname seq@start\seq@\endcsname>\st@rt + \else + \xdef\temp@@{n} + \xdef\b@r{n} + \xdef\pm@{0} + \xdef\temp@@@{\fill@char,@} + \expandafter\check@letter\temp@@@ + \ifletter + \read@graph + \else + \ifx\g@min\comm@ \xdef\g@min{0} \fi + \ifx\g@max\comm@ \xdef\g@max{100} \fi + \pm@calc + \xdef\temp@@@{\fill@char,@} + \xdef\temp@@{y} + \fi + \ifx\temp@@\y@ + \loopcount=\st@rt + \xdef\tmpstack{} + \loop + \xdef\last@{\csname stack@\bottop@\seq@\endcsname} + \expandafter\get@item\temp@@@ + \xdef\temp@@@{\first@} + \ifx\fourth@\N@ + \xdef\style@{color:50[White]} + \else + \ifnum\fourth@<1 \xdef\fourth@{1} \fi + \innerloopcount=\fourth@ + \advance\innerloopcount by 4 + \divide\innerloopcount by 5 + \multiply\innerloopcount by 5 + \ifnum\innerloopcount>100 \innerloopcount=100 \fi + \xdef\style@{color:50[\f@color\the\innerloopcount]} + \fi + \xdef\tmpstack{\tmpstack\f@text@;\the\loopcount;\the\loopcount;\style@;} + \advance\loopcount by 1 + \ifnum\loopcount=0 \loopcount=1 \fi + \ifnum\loopcount>\st@p + \else\repeat + \xdef\f@text@{\tmpstack} \xdef\tmpstack{} + \xdef\last@{\csname stack@\bottop@\seq@\endcsname} + \sort@gstack + \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack} + \fi + \fi + \xdef\list@{\list@ &} + \ifx\list@\ampers@nd\else\do@colorgraph\fi +} +\def\feature#1#2#3#4#5{% + \xdef\bottop@{#1} + \xdef\temp@{top} + \ifx\bottop@\temp@ \topfeaturetrue\fi + \xdef\temp@{ttop} + \ifx\bottop@\temp@ \ttopfeaturetrue\fi + \xdef\temp@{bottom} + \ifx\bottop@\temp@ \bottomfeaturetrue\fi + \xdef\temp@{bbottom} + \ifx\bottop@\temp@ \bbottomfeaturetrue\fi + \xdef\seq@{#2} + \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi + \xdef\first@{\seq@ @} \expandafter\check@letter\first@ + \xdef\first@{\seq@} + \ifletter \get@name@number \xdef\seq@{\first@} \fi + \ifnum\seq@>\seq@count + \message{} + \else + \ifnum\seq@>-1 + \xdef\temp@{#4::&}\expandafter\test@fill\temp@ + \xdef\last@{bar} + \ifx\second@@\last@ + \xdef\last@{hydrophobicity} + \ifx\last@\fourth@ + \xdef\second@@{bh} + \else + \xdef\last@{molweight} + \ifx\last@\fourth@ + \xdef\second@@{bm} + \else + \xdef\last@{charge} + \ifx\last@\fourth@ + \xdef\second@@{bc} + \else + \xdef\last@{conservation} + \ifx\last@\fourth@ + \xdef\second@@{bcons} + \fi + \fi + \fi + \fi + \fi + \xdef\last@{color} + \ifx\second@@\last@ + \xdef\last@{hydrophobicity} + \ifx\last@\fourth@ + \xdef\second@@{ch} + \else + \xdef\last@{molweight} + \ifx\last@\fourth@ + \xdef\second@@{cm} + \else + \xdef\last@{charge} + \ifx\last@\fourth@ + \xdef\second@@{cc} + \else + \xdef\last@{conservation} + \ifx\last@\fourth@ + \xdef\second@@{ccons} + \fi + \fi + \fi + \fi + \fi + \xdef\last@{bar} + \ifx\second@@\last@ + \xdef\list@{#3,&} + \xdef\style@{#4} + \xdef\f@text@{#5} + \do@bargraph + \xdef\temp@{bottom} + \ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi + \xdef\temp@{bbottom} + \ifx\bottop@\temp@ \xdef\bbottom@stretch{y}\fi + \else + \xdef\last@{color} + \ifx\second@@\last@ + \xdef\list@{#3,&} + \xdef\style@{#4} + \xdef\f@text@{#5} + \do@colorgraph + \else + \xdef\f@text@{#5} + \xdef\list@{#3,&} + \xdef\temp@{#4&} + \ifx\temp@\ampers@nd + \xdef\style@{&} + \else + \xdef\last@{restriction} + \ifx\second@@\last@ + \xdef\temp@{\bottop@ @} + \expandafter\firstchar@get\temp@ + \xdef\temp@{y} + \if\first@ t + \xdef\style@{fill:\kern0.9\box@width$\blacktriangledown$[\f@color]} + \else + \xdef\style@{fill:\kern0.9\box@width$\blacktriangle$[\f@color]} + \fi + \xdef\f@text@{\kern0.9\box@width#5} + \else + \xdef\last@{bh} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\style@{plot[bar]:Hydro[\f@color][-53]} + \else + \xdef\last@{bm} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\style@{plot[bar]:molw[\f@color][0]} + \else + \xdef\last@{bc} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\style@{plot[bar]:charge[\f@color][-50]} + \else + \xdef\last@{bcons} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi + \xdef\style@{cons[bar]:cons[\f@color][0]} + \else + \xdef\last@{ch} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{RedGreen}\fi + \xdef\style@{plot[color]:Hydro[\f@color][-53]} + \else + \xdef\last@{cm} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray}\fi + \xdef\style@{plot[color]:molw[\f@color][0]} + \else + \xdef\last@{cc} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{RedBlue}\fi + \xdef\style@{plot[color]:charge[\f@color][-50]} + \else + \xdef\last@{ccons} + \ifx\second@@\last@ + \ifx\f@color\gr@ydef@ult\xdef\f@color{ColdHot}\fi + \xdef\style@{cons[color]:cons[\f@color][0]} + \else + \xdef\style@{#4} \expandafter\getarrow@shape\temp@ + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \loop + \xdef\list@{\list@ @} + \expandafter\get@fregions\list@ + \ifx\list@\ampers@nd\else\repeat + \fi\fi\fi + \fi +} +\def\seqtype#1{\xdef\seq@type{#1} + \if\seq@type P \xdef\prefix@{pep} + \else \if\seq@type p \xdef\seq@type{P} \xdef\prefix@{pep} + \else \xdef\seq@type{N} \xdef\prefix@{DNA} \fi\fi} +\def\nameseq#1#2{% + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \expandafter\xdef\csname newseqname\first@\endcsname{#2} +} +\def\threshold#1{\xdef\thresh@ld{#1}} +\def\constosingleseq#1{% + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count + \message{} + \else + \ifnum\first@>0 \xdef\cons@num{\first@} \hideconsensus\fi\fi +} +\def\constoallseqs{\xdef\cons@num{0}} +\def\residuesperline{% + \def\@rplfix*##1{% + \res@perline=##1 + \ifnum\res@perline<1 \res@perline=1\fi \rpl@fixtrue} + \def\@rplvar ##1{% + \res@perline=##1 + \ifnum\res@perline<5 \res@perline=5\fi \rpl@fixfalse} + \def\decide@{\ifx\l@@k * \let\next\@rplfix \else \let\next\@rplvar \fi \next} + \futurelet\l@@k\decide@} +\def\numberingwidth#1{\def\num@width{#1}} +\def\charstretch#1{\def\char@stretch{#1}} +\def\linestretch#1{\def\line@stretch{#1}} +\def\noblockskip{\def\block@skip{\vspace{0pt}}} +\def\smallblockskip{\def\block@skip{\vspace{\baselineskip}}} +\def\medblockskip{\def\block@skip{\vspace{1.5\baselineskip}}} +\def\bigblockskip{\def\block@skip{\vspace{2\baselineskip}}} +\def\vblockspace#1{\def\block@skip{\vspace{#1}}} +\def\topspace#1{\def\t@sp@ce{#1}} +\def\ttopspace#1{\def\tt@sp@ce{#1}} +\def\bottomspace#1{\def\b@sp@ce{#1}} +\def\bbottomspace#1{\def\bb@sp@ce{#1}} +\def\fixblockspace{\fix@true} +\def\flexblockspace{\fix@false} +\def\nosepline{\def\seq@skip{\relax}} +\def\smallsepline{\def\seq@skip{\vspace{3pt}}\def\sep@space{3pt}} +\def\medsepline{\def\seq@skip{\vspace{6pt}}\def\sep@space{6pt}} +\def\bigsepline{\def\seq@skip{\vspace{12pt}}\def\sep@space{12pt}} +\def\vsepspace#1{\def\seq@skip{\vspace{#1}}\xdef\sep@space{#1}} +\def\separationline#1{% + \xdef\start@seq{#1} + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} + \ifletter \get@name@number \xdef\start@seq{\first@} \fi + \ifnum\start@seq>\seq@count \xdef\start@seq{1} + \else + \ifnum\start@seq<0 \xdef\start@seq{1} + \else + \expandafter\def\csname seq@gap\start@seq\endcsname{yes} + \loopcount=\seq@gap@num + \advance\loopcount by 1 + \xdef\seq@gap@num{\the\loopcount} + \fi + \fi} +\newcommand{\shadingmode}[2][1]{% + \xdef\last@{#2} + \xdef\first@{identical} + \all@shadefalse + \ifx\first@\last@ + \simmodefalse \funcmodefalse + \xdef\last@{#1} \xdef\second@{allmatchspecial} + \ifx\second@\last@ \all@shadetrue \fi + \else + \xdef\first@{similar} + \ifx\first@\last@ + \simmodetrue \funcmodefalse + \xdef\last@{#1} \xdef\second@{allmatchspecial} + \ifx\second@\last@ \all@shadetrue \fi + \else + \xdef\first@{functional} + \ifx\first@\last@ + \if\seq@type P \simmodefalse \funcmodetrue \func@shading{#1} + \else \message{} \fi + \else + \xdef\first@{diverse} + \ifx\first@\last@ + \xdef\last@{#1} + \ifnum\last@>\seq@count \xdef\last@{1}\fi + \ifnum\last@<1 \xdef\last@{1}\fi + \simmodetrue \funcmodefalse + \threshold{0} + \donotshade{\last@} \constosingleseq{\last@} + \nomatchresidues{Black}{White}{lower}{up} + \similarresidues{Black}{White}{lower}{up} + \conservedresidues{Black}{White}{{.}}{up} + \allmatchresidues{Black}{White}{{.}}{up} + \gapchar{-} + \hideconsensus + \else + \message{} + \simmodetrue \funcmodefalse + \fi\fi\fi\fi} +\def\allmatchspecial{\all@shadetrue} +\def\allmatchspecialoff{\all@shadefalse} +\def\gapchar#1{% + \xdef\first@{rule}\xdef\second@{#1} + \ifx\first@\second@\def\gap@char{o} + \else\def\gap@char{#1}\fi} +\def\gaprule#1{\def\gap@rulethick{#1}} +\def\setends#1#2{% + \xdef\start@seq{#1} + \xdef\temp@{consensus} + \ifx\start@seq\temp@ \xdef\start@seq{0} \fi + \xdef\first@{\start@seq @} \expandafter\check@letter\first@ + \xdef\first@{\start@seq} + \ifletter \get@name@number \xdef\start@seq{\first@} \fi + \ifnum\start@seq>\seq@count \xdef\start@seq{1} + \else + \ifnum\start@seq<0 \xdef\start@seq{1} + \else + \xdef\second@{#2@} \expandafter\get@nums\second@ + \xdef\start@num{\first@} \xdef\end@num{\second@} + \start@false + \fi + \fi} +\def\startnumber#1#2{% + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count \message{} + \else + \xdef\second@{#2} \ifnum\second@=0 \xdef\second@{1} \fi + \expandafter\xdef\csname seq@start\first@\endcsname{\second@} + \csname res@count\first@\endcsname=\second@ + \advance\csname res@count\first@\endcsname by -1 + \fi} +\def\seqlength#1#2{% + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count \message{} + \else + \xdef\second@{#2} \ifnum\second@<0 \xdef\second@{1} \fi + \expandafter\xdef\csname seq@len\first@\endcsname{\second@} + \fi} +\def\shownumbering#1{% + \xdef\first@{#1} \xdef\second@{right} + \ifx\first@\second@ \numbers@leftfalse \else \numbers@lefttrue \fi + \numbers@true} +\def\hidenumbering{\numbers@false} +\def\hidenumber#1{\xdef\first@{#1,&,@} \hidenumber@} +\def\shownames#1{% + \xdef\first@{#1} \xdef\second@{left} + \ifx\first@\second@ \names@rightfalse \else \names@righttrue \fi + \names@true} +\def\hidenames{\names@false} +\def\hidename#1{\xdef\first@{#1,&,@} \hidename@} +\def\hideresidues{\hidechartrue} +\def\showresidues{\hidecharfalse} +\def\alignment#1{% + \xdef\first@{#1} + \xdef\temp@{left} + \ifx\first@\temp@ \xdef\c@factor{0} + \else + \xdef\temp@{center} + \ifx\first@\temp@ \xdef\c@factor{0.5} + \else + \xdef\temp@{right} + \ifx\first@\temp@ \xdef\c@factor{1} + \fi\fi\fi} +\def\donotshade#1{% + \xdef\temp@{consensus} + \xdef\first@{#1} + \ifx\first@\temp@ + \consensuscolors{Black}{White}{Black}{White}{Black}{White} + \else + \xdef\first@{#1,&,@} \donot@shade + \fi} +\def\hideseq#1{\xdef\first@{#1,&,@} \hideseq@} +\def\killseq#1{\xdef\first@{#1,&,@} \killseq@} +\newcommand\showconsensus[2][n]{% + \xdef\text@scale{n} + \xdef\box@scale{n} + \xdef\first@{#1} + \ifx\first@\n@ + \xdef\collect@cons@colors{no} + \else + \xdef\first@{#1,&,@} + \expandafter\get@item\first@ + \xdef\c@nsc@l{\fourth@} + \xdef\first@@{Gray} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{RedBlue} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{BlueRed} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{RedGreen} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{GreenRed} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{ColdHot} + \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else + \xdef\first@@{HotCold} + \ifx\c@nsc@l\first@@\xdef\text@scale{y} + \fi\fi\fi\fi\fi\fi\fi + \expandafter\get@item\first@ + \ifx\fourth@\ampers@nd + \xdef\c@nssc@le{White} + \else + \xdef\c@nssc@le{\fourth@} + \xdef\first@{Gray} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{RedBlue} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{BlueRed} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{RedGreen} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{GreenRed} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{ColdHot} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \xdef\first@{HotCold} + \ifx\c@nssc@le\first@\xdef\box@scale{y}\else + \fi\fi\fi\fi\fi\fi\fi + \fi + \xdef\collect@cons@colors{y} + \fi + \xdef\first@{#2} \xdef\last@{top} + \ifx\first@\last@\xdef\cons@top{0}\else\xdef\cons@top{1}\fi + \show@construe} +\def\consensuscolors#1#2#3#4#5#6{% + \xdef\last@{\ampers@nd} + \xdef\first@{#1&}\xdef\second@{#2&} + \ifx\first@\last@\else\def\ConsTextNomatch{#1}\fi + \ifx\second@\last@\else\def\ConsNomatch{#2}\fi + \xdef\first@{#3&}\xdef\second@{#4&} + \ifx\first@\last@\else\def\ConsTextMatch{#3}\fi + \ifx\second@\last@\else\def\ConsMatch{#4}\fi + \xdef\first@{#5&}\xdef\second@{#6&} + \ifx\first@\last@\else\def\ConsTextAllmatch{#5}\fi + \ifx\second@\last@\else\def\ConsAllmatch{#6}\fi +} +\def\defconsensus#1#2#3{% + \xdef\second@{#1&} + \ifx\second@\ampers@nd \else \def\n@m@tch{#1}\fi + \xdef\second@{#2&} + \ifx\second@\ampers@nd \else \def\m@tch{#2}\fi + \xdef\second@{#3&} + \ifx\second@\ampers@nd \else \def\@llm@tch{#3}\fi} +\def\hideconsensus{\show@consfalse} +\def\nameconsensus#1{\def\cons@name{#1}} +\def\hideleadinggaps{\sh@wg@psfalse} +\def\showleadinggaps{\sh@wg@pstrue} +\def\showruler#1#2{% + \xdef\first@{consensus} \xdef\second@{#2} + \xdef\third@{bottom} \xdef\fourth@{#1} + \ifx\third@\fourth@ \xdef\rule@top{1}\else\xdef\rule@top{0}\fi + \ifx\first@\second@ \xdef\rule@num{0} + \else + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \ifnum\first@>\seq@count + \else + \ifnum\first@>0 + \xdef\rule@num{\first@} + \fi + \fi + \fi + \xdef\ruler@{}} +\def\hideruler{\xdef\rule@num{-1}} +\def\rulersteps#1{\xdef\ruler@step{#1}} +\def\featurerule#1{\setlength\rule@thick{#1}} +\def\orderseqs#1{% + \def\order@loop{% + \expandafter\check@letter\first@ + \ifletter + \expandafter\get@item\first@ + \xdef\first@{\fourth@} + \get@name@number + \xdef\seq@order{\seq@order,\first@} + \xdef\first@{\first@@ @} + \order@loop + \else + \expandafter\get@digit\first@ + \ifx\fourth@\ampers@nd + \else + \xdef\seq@order{\seq@order,\fourth@} + \order@loop + \fi + \fi} + \xdef\first@{#1,&,@} + \xdef\seq@order{} + \order@loop + \xdef\seq@order{\seq@order @} + \expandafter\get@item\seq@order + \xdef\seq@order{\first@@,@} +} +\def\setfamily#1#2{% + \xdef\second@{#2&} + \ifx\second@\ampers@nd + \else + \xdef\first@{#1} + \xdef\second@{#2} + \xdef\temp@{rm} + \ifx\second@\temp@ + \xdef\third@{\rmdefault} + \else + \xdef\temp@{sf} + \ifx\second@\temp@ + \xdef\third@{\sfdefault} + \else + \xdef\temp@{tt} + \ifx\second@\temp@ + \xdef\third@{\ttdefault} + \else + \xdef\third@{\second@} + \fi\fi\fi + \xdef\temp@{features} + \ifx\first@\temp@ \xdef\featuretext@family{\third@} + \else + \xdef\temp@{featurestyles} + \ifx\first@\temp@ \xdef\featurestyles@family{\third@} + \else + \xdef\temp@{numbering} + \ifx\first@\temp@ \xdef\numbertext@family{\third@} + \else + \xdef\temp@{names} + \ifx\first@\temp@ \xdef\namestext@family{\third@} + \else + \xdef\temp@{residues} + \ifx\first@\temp@ \xdef\residues@family{\third@} + \else + \xdef\temp@{legend} + \ifx\first@\temp@ \xdef\legend@family{\third@} + \else + \xdef\temp@{labels} + \ifx\first@\temp@ \xdef\label@family{\third@} + \else + \xdef\temp@{all} + \ifx\first@\temp@ + \xdef\featuretext@family{\third@} + \xdef\featurestyles@family{\third@} + \xdef\numbertext@family{\third@} + \xdef\namestext@family{\third@} + \xdef\residues@family{\third@} + \xdef\legend@family{\third@} + \xdef\label@family{\third@} + \fi\fi\fi\fi\fi\fi\fi\fi + \fi +} +\def\setseries#1#2{% + \xdef\second@{#2&} + \ifx\second@\ampers@nd + \else + \xdef\first@{#1} + \xdef\second@{#2} + \xdef\temp@{bf} + \ifx\second@\temp@ + \xdef\third@{\bfdefault} + \else + \xdef\temp@{md} + \ifx\second@\temp@ + \xdef\third@{\mddefault} + \else + \xdef\third@{\second@} + \fi\fi + \xdef\temp@{features} + \ifx\first@\temp@ \xdef\featuretext@series{\third@} + \else + \xdef\temp@{featurestyles} + \ifx\first@\temp@ \xdef\featurestyles@series{\third@} + \else + \xdef\temp@{numbering} + \ifx\first@\temp@ \xdef\numbertext@series{\third@} + \else + \xdef\temp@{names} + \ifx\first@\temp@ \xdef\namestext@series{\third@} + \else + \xdef\temp@{residues} + \ifx\first@\temp@ \xdef\residues@series{\third@} + \else + \xdef\temp@{legend} + \ifx\first@\temp@ \xdef\legend@series{\third@} + \else + \xdef\temp@{labels} + \ifx\first@\temp@ \xdef\label@series{\third@} + \else + \xdef\temp@{all} + \ifx\first@\temp@ + \xdef\featuretext@series{\third@} + \xdef\featurestyles@series{\third@} + \xdef\numbertext@series{\third@} + \xdef\namestext@series{\third@} + \xdef\residues@series{\third@} + \xdef\legend@series{\third@} + \xdef\label@series{\third@} + \fi\fi\fi\fi\fi\fi\fi\fi + \fi +} +\def\setshape#1#2{% + \xdef\second@{#2&} + \ifx\second@\ampers@nd + \else + \xdef\first@{#1} + \xdef\second@{#2} + \xdef\temp@{it} + \ifx\second@\temp@ + \xdef\third@{\itdefault} + \else + \xdef\temp@{sl} + \ifx\second@\temp@ + \xdef\third@{\sldefault} + \else + \xdef\temp@{sc} + \ifx\second@\temp@ + \xdef\third@{\scdefault} + \else + \xdef\temp@{up} + \ifx\second@\temp@ + \xdef\third@{\updefault} + \else + \xdef\third@{\second@} + \fi\fi\fi\fi + \xdef\temp@{features} + \ifx\first@\temp@ \xdef\featuretext@shape{\third@} + \else + \xdef\temp@{featurestyles} + \ifx\first@\temp@ \xdef\featurestyles@shape{\third@} + \else + \xdef\temp@{numbering} + \ifx\first@\temp@ \xdef\numbertext@shape{\third@} + \else + \xdef\temp@{names} + \ifx\first@\temp@ \xdef\namestext@shape{\third@} + \else + \xdef\temp@{residues} + \ifx\first@\temp@ \xdef\residues@shape{\third@} + \else + \xdef\temp@{legend} + \ifx\first@\temp@ \xdef\legend@shape{\third@} + \else + \xdef\temp@{labels} + \ifx\first@\temp@ \xdef\label@shape{\third@} + \else + \xdef\temp@{all} + \ifx\first@\temp@ + \xdef\featuretext@shape{\third@} + \xdef\featurestyles@shape{\third@} + \xdef\numbertext@shape{\third@} + \xdef\namestext@shape{\third@} + \xdef\residues@shape{\third@} + \xdef\legend@shape{\third@} + \xdef\label@shape{\third@} + \fi\fi\fi\fi\fi\fi\fi\fi + \fi +} +\def\setsize#1#2{% + \xdef\second@{#2&} + \ifx\second@\ampers@nd + \else + \xdef\first@{#1} + \xdef\temp@{features} + \ifx\first@\temp@ + \def\featuretext@size{\csname #2\endcsname} + \else + \xdef\temp@{featurestyles} + \ifx\first@\temp@ + \def\featurestyles@size{\csname #2\endcsname} + \else + \xdef\temp@{numbering} + \ifx\first@\temp@ + \def\numbertext@size{\csname #2\endcsname} + \else + \xdef\temp@{names} + \ifx\first@\temp@ + \def\namestext@size{\csname #2\endcsname} + \else + \xdef\temp@{legend} + \ifx\first@\temp@ + \def\legend@size{\csname #2\endcsname} + \else + \xdef\temp@{labels} + \ifx\first@\temp@ + \def\label@size{\csname #2\endcsname} + \else + \xdef\temp@{residues} + \ifx\first@\temp@ + \def\residues@size{\csname #2\endcsname} + \xdef\res@size{#2} + \else + \xdef\temp@{all} + \ifx\first@\temp@ + \def\featuretext@size{\csname #2\endcsname} + \def\featurestyles@size{\csname #2\endcsname} + \def\numbertext@size{\csname #2\endcsname} + \def\namestext@size{\csname #2\endcsname} + \def\legend@size{\csname #2\endcsname} + \def\label@size{\csname #2\endcsname} + \def\residues@size{\csname #2\endcsname} + \xdef\res@size{#2} + \fi\fi\fi\fi\fi\fi\fi\fi + \xdef\temp@{Huge} + \ifx\temp@\res@size + \def\bottomruler@size{\csname Large\endcsname} + \else + \xdef\temp@{huge} + \ifx\temp@\res@size + \def\bottomruler@size{\csname large\endcsname} + \else + \xdef\temp@{LARGE} + \ifx\temp@\res@size + \def\bottomruler@size{\csname normalsize\endcsname} + \else + \xdef\temp@{Large} + \ifx\temp@\res@size + \def\bottomruler@size{\csname small\endcsname} + \else + \xdef\temp@{large} + \ifx\temp@\res@size + \def\bottomruler@size{\csname footnotesize\endcsname} + \else + \xdef\temp@{normalsize} + \ifx\temp@\res@size + \def\bottomruler@size{\csname scriptsize\endcsname} + \else + \def\bottomruler@size{\csname tiny\endcsname} + \fi\fi\fi\fi\fi\fi + \fi +} +\def\setfont#1#2#3#4#5{% + \setfamily{#1}{#2}\setseries{#1}{#3} + \setshape{#1}{#4}\setsize{#1}{#5}} +\def\featuresrm{\setfamily{features}{rm}} +\def\featuressf{\setfamily{features}{sf}} +\def\featurestt{\setfamily{features}{tt}} +\def\featuresmd{\setseries{features}{md}} +\def\featuresbf{\setseries{features}{bf}} +\def\featuresup{\setshape {features}{up}} +\def\featuresit{\setshape {features}{it}} +\def\featuressl{\setshape {features}{sl}} +\def\featuressc{\setshape {features}{sc}} +\def\featurestiny {\setsize{features}{tiny}} +\def\featuresscriptsize {\setsize{features}{scriptsize}} +\def\featuresfootnotesize{\setsize{features}{footnotesize}} +\def\featuressmall {\setsize{features}{small}} +\def\featuresnormalsize {\setsize{features}{normalsize}} +\def\featureslarge {\setsize{features}{large}} +\def\featuresLarge {\setsize{features}{Large}} +\def\featuresLARGE {\setsize{features}{LARGE}} +\def\featureshuge {\setsize{features}{huge}} +\def\featuresHuge {\setsize{features}{Huge}} +\def\featurestylesrm{\setfamily{featurestyles}{rm}} +\def\featurestylessf{\setfamily{featurestyles}{sf}} +\def\featurestylestt{\setfamily{featurestyles}{tt}} +\def\featurestylesmd{\setseries{featurestyles}{md}} +\def\featurestylesbf{\setseries{featurestyles}{bf}} +\def\featurestylesup{\setshape {featurestyles}{up}} +\def\featurestylesit{\setshape {featurestyles}{it}} +\def\featurestylessl{\setshape {featurestyles}{sl}} +\def\featurestylessc{\setshape {featurestyles}{sc}} +\def\featurestylestiny {\setsize{featurestyles}{tiny}} +\def\featurestylesscriptsize {\setsize{featurestyles}{scriptsize}} +\def\featurestylesfootnotesize{\setsize{featurestyles}{footnotesize}} +\def\featurestylessmall {\setsize{featurestyles}{small}} +\def\featurestylesnormalsize {\setsize{featurestyles}{normalsize}} +\def\featurestyleslarge {\setsize{featurestyles}{large}} +\def\featurestylesLarge {\setsize{featurestyles}{Large}} +\def\featurestylesLARGE {\setsize{featurestyles}{LARGE}} +\def\featurestyleshuge {\setsize{featurestyles}{huge}} +\def\featurestylesHuge {\setsize{featurestyles}{Huge}} +\def\numberingrm{\setfamily{numbering}{rm}} +\def\numberingsf{\setfamily{numbering}{sf}} +\def\numberingtt{\setfamily{numbering}{tt}} +\def\numberingmd{\setseries{numbering}{md}} +\def\numberingbf{\setseries{numbering}{bf}} +\def\numberingup{\setshape {numbering}{up}} +\def\numberingit{\setshape {numbering}{it}} +\def\numberingsl{\setshape {numbering}{sl}} +\def\numberingsc{\setshape {numbering}{sc}} +\def\numberingtiny {\setsize{numbering}{tiny}} +\def\numberingscriptsize {\setsize{numbering}{scriptsize}} +\def\numberingfootnotesize{\setsize{numbering}{footnotesize}} +\def\numberingsmall {\setsize{numbering}{small}} +\def\numberingnormalsize {\setsize{numbering}{normalsize}} +\def\numberinglarge {\setsize{numbering}{large}} +\def\numberingLarge {\setsize{numbering}{Large}} +\def\numberingLARGE {\setsize{numbering}{LARGE}} +\def\numberinghuge {\setsize{numbering}{huge}} +\def\numberingHuge {\setsize{numbering}{Huge}} +\def\namesrm{\setfamily{names}{rm}} +\def\namessf{\setfamily{names}{sf}} +\def\namestt{\setfamily{names}{tt}} +\def\namesmd{\setseries{names}{md}} +\def\namesbf{\setseries{names}{bf}} +\def\namesup{\setshape {names}{up}} +\def\namesit{\setshape {names}{it}} +\def\namessl{\setshape {names}{sl}} +\def\namessc{\setshape {names}{sc}} +\def\namestiny {\setsize{names}{tiny}} +\def\namesscriptsize {\setsize{names}{scriptsize}} +\def\namesfootnotesize{\setsize{names}{footnotesize}} +\def\namessmall {\setsize{names}{small}} +\def\namesnormalsize {\setsize{names}{normalsize}} +\def\nameslarge {\setsize{names}{large}} +\def\namesLarge {\setsize{names}{Large}} +\def\namesLARGE {\setsize{names}{LARGE}} +\def\nameshuge {\setsize{names}{huge}} +\def\namesHuge {\setsize{names}{Huge}} +\def\residuesrm{\setfamily{residues}{rm}} +\def\residuessf{\setfamily{residues}{sf}} +\def\residuestt{\setfamily{residues}{tt}} +\def\residuesmd{\setseries{residues}{md}} +\def\residuesbf{\setseries{residues}{bf}} +\def\residuesup{\setshape {residues}{up}} +\def\residuesit{\setshape {residues}{it}} +\def\residuessl{\setshape {residues}{sl}} +\def\residuessc{\setshape {residues}{sc}} +\def\residuestiny {\setsize{residues}{tiny}} +\def\residuesscriptsize {\setsize{residues}{scriptsize}} +\def\residuesfootnotesize{\setsize{residues}{footnotesize}} +\def\residuessmall {\setsize{residues}{small}} +\def\residuesnormalsize {\setsize{residues}{normalsize}} +\def\residueslarge {\setsize{residues}{large}} +\def\residuesLarge {\setsize{residues}{Large}} +\def\residuesLARGE {\setsize{residues}{LARGE}} +\def\residueshuge {\setsize{residues}{huge}} +\def\residuesHuge {\setsize{residues}{Huge}} +\def\legendrm{\setfamily{legend}{rm}} +\def\legendsf{\setfamily{legend}{sf}} +\def\legendtt{\setfamily{legend}{tt}} +\def\legendmd{\setseries{legend}{md}} +\def\legendbf{\setseries{legend}{bf}} +\def\legendup{\setshape {legend}{up}} +\def\legendit{\setshape {legend}{it}} +\def\legendsl{\setshape {legend}{sl}} +\def\legendsc{\setshape {legend}{sc}} +\def\legendtiny {\setsize{legend}{tiny}} +\def\legendscriptsize {\setsize{legend}{scriptsize}} +\def\legendfootnotesize{\setsize{legend}{footnotesize}} +\def\legendsmall {\setsize{legend}{small}} +\def\legendnormalsize {\setsize{legend}{normalsize}} +\def\legendlarge {\setsize{legend}{large}} +\def\legendLarge {\setsize{legend}{Large}} +\def\legendLARGE {\setsize{legend}{LARGE}} +\def\legendhuge {\setsize{legend}{huge}} +\def\legendHuge {\setsize{legend}{Huge}} +\def\funcshadingstyle#1#2#3#4#5{% + \xdef\temp@{nomatch} \xdef\first@{#1} + \ifx\temp@\first@ + \xdef\first@{0} + \else + \xdef\first@{\csname funcgrp#1\endcsname} + \fi + \ifnum\first@>-1 + \expandafter\xdef\csname fg@textcolor\first@\endcsname{#2} + \expandafter\xdef\csname fg@color\first@\endcsname{#3} + \expandafter\xdef\csname funcm@tch\first@\endcsname{#4} + \expandafter\def\csname func@style\first@\endcsname{\csname text#5\endcsname} + \fi} +\def\shadingcolors#1{% + \gapcolors{Black}{White} + \nomatchresidues{Black}{White}{upper}{up} + \xdef\first@{#1} \xdef\second@{blues} + \ifx\first@\second@ + \similarresidues{Black}{Magenta}{upper}{up} + \conservedresidues{White}{RoyalBlue}{upper}{up} + \allmatchresidues{Goldenrod}{RoyalPurple}{upper}{up} + \else \xdef\second@{greens} + \ifx\first@\second@ + \similarresidues{Black}{GreenYellow}{upper}{up} + \conservedresidues{White}{PineGreen}{upper}{up} + \allmatchresidues{YellowOrange}{OliveGreen}{upper}{up} + \else \xdef\second@{reds} + \ifx\first@\second@ + \similarresidues{Black}{YellowOrange}{upper}{up} + \conservedresidues{White}{BrickRed}{upper}{up} + \allmatchresidues{YellowGreen}{Mahagony}{upper}{up} + \else \xdef\second@{black} + \ifx\first@\second@ + \similarresidues{Black}{White}{upper}{sl} + \conservedresidues{White}{Black}{upper}{up} + \allmatchresidues{White}{Black}{upper}{sl} + \else \xdef\second@{grays} + \ifx\first@\second@ + \else \message{} \xdef\first@{grays}\fi + \ifx\first@\second@ + \similarresidues{Black}{LightGray}{upper}{up} + \conservedresidues{White}{DarkGray}{upper}{up} + \allmatchresidues{White}{Black}{upper}{up} + \fi\fi\fi\fi\fi} +\def\nomatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\TextNomatch{#1} + \expandafter\def\csname fg@textcolor0\endcsname{#1} + \fi + \ifx\second@\last@\else\gdef\Nomatch{#2} + \expandafter\def\csname fg@color0\endcsname{#2} + \fi + \ifx\third@\last@\else\def\resn@m@tch{#3} + \fi + \xdef\first@{#4&} + \ifx\first@\last@\else + \def\no@style{\csname text#4\endcsname} + \expandafter\def\csname func@style0\endcsname% + {\csname text#4\endcsname}\fi} +\def\similarresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\TextSimilar{#1}\fi + \ifx\second@\last@\else\gdef\Similar{#2}\fi + \ifx\third@\last@\else\def\ressimm@tch{#3}\fi + \xdef\first@{#4&} + \ifx\first@\last@\else + \def\sim@style{\csname text#4\endcsname}\fi} +\def\conservedresidues#1#2#3#4{\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\TextIdentical{#1}\fi + \ifx\second@\last@\else\gdef\Identical{#2}\fi + \ifx\third@\last@\else\def\resm@tch{#3}\fi + \xdef\first@{#4&} + \ifx\first@\last@\else + \def\id@style{\csname text#4\endcsname}\fi} +\def\allmatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\TextAllmatch{#1}\fi + \ifx\second@\last@\else\gdef\Allmatch{#2}\fi + \ifx\third@\last@\else\def\res@llm@tch{#3}\fi + \xdef\first@{#4&} + \ifx\first@\last@\else + \def\all@style{\csname text#4\endcsname}\fi} +\def\gapcolors#1#2 {\xdef\first@{#1&}\xdef\second@{#2&} + \xdef\last@{\ampers@nd} + \ifx\first@\last@\else\def\gap@fg{#1} + \expandafter\def\csname fg@textcolor*\endcsname{#1}\fi + \ifx\second@\last@\else\def\gap@bg{#2} + \expandafter\def\csname fg@color*\endcsname{#2}\fi} +\def\shadebox#1{% + \xdef\first@{White}% + \xdef\third@{#1}% + \xdef\second@{nomatch}% + \ifx\second@\third@ + \ifx\Nomatch\first@\white@box\else\textcolor{\Nomatch}{\box@rule}\fi% + \else + \xdef\second@{similar}% + \ifx\second@\third@ + \ifx\Similar\first@\white@box\else\textcolor{\Similar}{\box@rule}\fi% + \else + \xdef\second@{conserved}% + \ifx\second@\third@ + \ifx\Identical\first@\white@box\else\textcolor{\Identical}{\box@rule}\fi% + \else + \xdef\second@{allmatch}% + \ifx\second@\third@ + \ifx\Allmatch\first@\white@box\else\textcolor{\Allmatch}{\box@rule}\fi% + \else + \ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi + \fi\fi\fi\fi} +\def\namescolor#1{\xdef\names@fg{#1}} +\def\namecolor#1#2{% + \xdef\first@{consensus} \xdef\second@{#1} + \ifx\first@\second@ + \expandafter\xdef\csname name@col0\endcsname{#2} + \else + \xdef\first@{#1,&,@} \xdef\third@{#2} \namecolor@ + \fi +} +\def\numberingcolor#1{\xdef\numbering@fg{#1}} +\def\numbercolor#1#2{% + \xdef\first@{consensus} \xdef\second@{#1} + \ifx\first@\second@ + \expandafter\xdef\csname number@col0\endcsname{#2} + \else + \xdef\first@{#1,&,@} \xdef\third@{#2} \numbercolor@ + \fi +} +\def\legendcolor#1{\xdef\legend@fg{#1}} +\def\rulercolor#1{\xdef\ruler@fg{#1}} +\def\molweight#1#2{% + \xdef\temp@{Da}% + \xdef\second@{#2}% + \ifx\second@\temp@\xdef\third@{Da}\else\xdef\third@{kDa}\fi% + \xdef\first@{#1 @} \expandafter\check@letter\first@ + \xdef\first@{#1} \ifletter \get@name@number \fi + \xdef\first@{\csname @rd\first@\endcsname}% + \loopcount=\csname mol@weight\first@\endcsname% + \divide\loopcount by 10\relax% + \innerloopcount=\loopcount% + \hbox{% + \ifnum\loopcount>1000% + \divide\loopcount by 1000\relax% + \pos@count=\loopcount% + \multiply\loopcount by 1000\relax% + \advance\innerloopcount by -\loopcount% + \loopcount=\innerloopcount% + \ifnum\loopcount>949\advance\pos@count by 1\relax\fi% + \the\pos@count% + \ifx\temp@\second@\ifgerm@n .\else {,}\fi\fi% + \else% + \ifx\second@\temp@ \else 0\fi% + \fi% + \ifx\second@\temp@% + \the\loopcount% + \loopcount=\csname mol@weight\first@\endcsname% + \innerloopcount=\loopcount% + \divide\loopcount by 10\relax% + \multiply\loopcount by 10\relax% + \advance\innerloopcount by -\loopcount\relax% + \else% + \divide\innerloopcount by 10\relax% + \advance\innerloopcount by 5\relax% + \divide\innerloopcount by 10\relax% + \fi% + \ifnum\innerloopcount>9\relax\innerloopcount=0\relax\fi% + \ifgerm@n {,}\else .\fi% + \the\innerloopcount~\third@}} +\newcommand\charge[2][o]{% + \xdef\temp@{pep}% + \ifx\prefix@\temp@% + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \xdef\second@{\csname @rd\first@\endcsname}% + \loopcount=\csname ch@rge\second@\endcsname% + \xdef\first@{#1}\make@lower% + \if\first@ i\fi% + \if\first@ o\advance\loopcount by \chargeNterm% + \advance\loopcount by \chargeCterm\fi% + \if\first@ n\advance\loopcount by \chargeNterm\fi% + \if\first@ c\advance\loopcount by \chargeCterm\fi% + \hbox{\ensuremath{% + \ifnum\loopcount>0 +% + \else\ifnum\loopcount=0 \pm% + \else -\multiply\loopcount by -1\relax% + \fi\fi% + \innerloopcount=\loopcount% + \divide\loopcount by 1000\relax% + \the\loopcount% + \multiply\loopcount by 1000\relax% + \advance\innerloopcount by -\loopcount\relax% + \divide\innerloopcount by 10\relax% + \ifnum\innerloopcount=0% + \else% + \ifgerm@n {,}\else .\fi% + \ifnum\innerloopcount<10 0\fi% + \the\innerloopcount% + \fi}}% + \fi} +\def\TeXshade{% + \setbox1=\hbox{\texttt{H}}% + \def\logo@rule{\vrule depth0.25\ht1 height1.25\ht1 width\wd1}% + \TeX% + \logo@rule\kern-\wd1\textcolor{White}{\texttt{s}}% + \logo@rule\kern-\wd1\textcolor{White}{\texttt{h}}% + \texttt{a}% + \logo@rule\kern-\wd1\textcolor{White}{\texttt{d}}% + \texttt{e}} + +\def\firstcolumnDSSP{\xdef\fc@DSSP{y}} +\def\secondcolumnDSSP{\xdef\fc@DSSP{n}} + +\newcommand{\includeDSSP}[3][existing]{% + \temp@count=\dssp@num + \advance\temp@count by 1 + \xdef\dssp@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optiondssp\the\temp@count\endcsname{\first@} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqdssp\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname filenamedssp\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqdssp\the\temp@count\endcsname>\seq@count + \message{} + \advance\temp@count by -1 + \xdef\dssp@num{\the\temp@count} + \fi +} + +\newcommand{\includeHMMTOP}[3][existing]{% + \temp@count=\HMMTOP@num + \advance\temp@count by 1 + \xdef\HMMTOP@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optionHMMTOP\the\temp@count\endcsname{\first@} + \xdef\first@{#2[,]&}\expandafter\opt@color\first@ + \ifx\f@color\comm@ + \expandafter\xdef\csname fileseqHMMTOP\the\temp@count\endcsname{0} + \else + \expandafter\xdef\csname fileseqHMMTOP\the\temp@count\endcsname{\f@color} + \fi + \xdef\first@{\fourth@ @} \expandafter\check@letter\first@ + \xdef\first@{\fourth@} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqHMMTOP\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname filenameHMMTOP\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqHMMTOP\the\temp@count\endcsname>\seq@count + \message{} + \advance\temp@count by -1 + \xdef\HMMTOP@num{\the\temp@count} + \fi +} + +\newcommand{\includeSTRIDE}[3][existing]{% + \temp@count=\stride@num + \advance\temp@count by 1 + \xdef\stride@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optionstride\the\temp@count\endcsname{\first@} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqstride\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname filenamestride\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqstride\the\temp@count\endcsname>\seq@count + \message{} + \advance\temp@count by -1 + \xdef\stride@num{\the\temp@count} + \fi +} +\newcommand{\includePHDsec}[3][existing]{% + \temp@count=\PHD@num + \advance\temp@count by 1 + \xdef\PHD@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optionphd\the\temp@count\endcsname{\first@} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqphd\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname modephd\the\temp@count\endcsname{structure} + \expandafter\xdef\csname filenamephd\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqphd\the\temp@count\endcsname>\seq@count + \message{} + \advance\temp@count by -1 + \xdef\PHD@num{\the\temp@count} + \fi +} +\newcommand{\includePHDtopo}[3][existing]{% + \temp@count=\PHD@num + \advance\temp@count by 1 + \xdef\PHD@num{\the\temp@count} + \xdef\first@{#1} \xdef\temp@{existing} + \ifx\first@\temp@ \else\xdef\first@{make new}\fi + \expandafter\xdef\csname optionphd\the\temp@count\endcsname{\first@} + \xdef\first@{#2 @} \expandafter\check@letter\first@ + \xdef\first@{#2} \ifletter \get@name@number \fi + \expandafter\xdef\csname doseqphd\the\temp@count\endcsname{\first@} + \expandafter\xdef\csname modephd\the\temp@count\endcsname{topology} + \expandafter\xdef\csname filenamephd\the\temp@count\endcsname{#3} + \expandafter\ifnum\csname doseqphd\the\temp@count\endcsname>\seq@count + \message{} + \advance\temp@count by -1 + \xdef\PHD@num{\the\temp@count} + \fi +} +\def\appearance#1#2#3#4#5{% + \xdef\first@{#1} \xdef\second@{#2} + \xdef\temp@{PHDsec} + \ifx\temp@\first@ + \xdef\temp@{alpha} + \ifx\second@\temp@ + \def\bottop@Hsec{#3} + \def\label@Hsec{#4} + \def\text@Hsec{#5} + \else + \xdef\temp@{beta} + \ifx\second@\temp@ + \def\bottop@Esec{#3} + \def\label@Esec{#4} + \def\text@Esec{#5} + \fi\fi + \else + \xdef\temp@{PHDtopo} + \ifx\temp@\first@ + \xdef\temp@{internal} + \ifx\second@\temp@ + \def\bottop@itop{#3} + \def\label@itop{#4} + \def\text@itop{#5} + \else + \xdef\temp@{external} + \ifx\second@\temp@ + \def\bottop@etop{#3} + \def\label@etop{#4} + \def\text@etop{#5} + \else + \xdef\temp@{TM} + \ifx\second@\temp@ + \def\bottop@TMtop{#3} + \def\label@TMtop{#4} + \def\text@TMtop{#5} + \fi\fi\fi + \else + \xdef\temp@{STRIDE} + \ifx\temp@\first@ + \xdef\temp@{alpha} + \ifx\second@\temp@ + \def\bottop@Hstride{#3} + \def\label@Hstride{#4} + \def\text@Hstride{#5} + \else + \xdef\temp@{3-10} + \ifx\second@\temp@ + \def\bottop@Gstride{#3} + \def\label@Gstride{#4} + \def\text@Gstride{#5} + \else + \xdef\temp@{pi} + \ifx\second@\temp@ + \def\bottop@Istride{#3} + \def\label@Istride{#4} + \def\text@Istride{#5} + \else + \xdef\temp@{beta} + \ifx\second@\temp@ + \def\bottop@Estride{#3} + \def\label@Estride{#4} + \def\text@Estride{#5} + \else + \xdef\temp@{bridge} + \ifx\second@\temp@ + \def\bottop@Bstride{#3} + \def\label@Bstride{#4} + \def\text@Bstride{#5} + \else + \xdef\temp@{turn} + \ifx\second@\temp@ + \def\bottop@Tstride{#3} + \def\label@Tstride{#4} + \def\text@Tstride{#5} + \fi\fi\fi\fi\fi\fi + \else + \xdef\temp@{DSSP} + \ifx\temp@\first@ + \xdef\temp@{alpha} + \ifx\second@\temp@ + \def\bottop@Hdssp{#3} + \def\label@Hdssp{#4} + \def\text@Hdssp{#5} + \else + \xdef\temp@{3-10} + \ifx\second@\temp@ + \def\bottop@Gdssp{#3} + \def\label@Gdssp{#4} + \def\text@Gdssp{#5} + \else + \xdef\temp@{pi} + \ifx\second@\temp@ + \def\bottop@Idssp{#3} + \def\label@Idssp{#4} + \def\text@Idssp{#5} + \else + \xdef\temp@{beta} + \ifx\second@\temp@ + \def\bottop@Edssp{#3} + \def\label@Edssp{#4} + \def\text@Edssp{#5} + \else + \xdef\temp@{bridge} + \ifx\second@\temp@ + \def\bottop@Bdssp{#3} + \def\label@Bdssp{#4} + \def\text@Bdssp{#5} + \else + \xdef\temp@{turn} + \ifx\second@\temp@ + \def\bottop@Tdssp{#3} + \def\label@Tdssp{#4} + \def\text@Tdssp{#5} + \else + \xdef\temp@{bend} + \ifx\second@\temp@ + \def\bottop@Sdssp{#3} + \def\label@Sdssp{#4} + \def\text@Sdssp{#5} + \fi\fi\fi\fi\fi\fi\fi + \else + \xdef\temp@{HMMTOP} + \ifx\temp@\first@ + \xdef\temp@{internal} + \ifx\second@\temp@ + \def\bottop@i@HMMTOP{#3} + \def\label@i@HMMTOP{#4} + \def\text@i@HMMTOP{#5} + \else + \xdef\temp@{external} + \ifx\second@\temp@ + \def\bottop@e@HMMTOP{#3} + \def\label@e@HMMTOP{#4} + \def\text@e@HMMTOP{#5} + \else + \xdef\temp@{TM} + \ifx\second@\temp@ + \def\bottop@TM@HMMTOP{#3} + \def\label@TM@HMMTOP{#4} + \def\text@TM@HMMTOP{#5} + \fi\fi\fi + \fi\fi\fi\fi\fi +} + +\def\showonDSSP#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@DSSP} +\def\hideonDSSP#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@DSSP} + +\def\showonSTRIDE#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@STRIDE} +\def\hideonSTRIDE#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@STRIDE} + +\def\showonPHDtopo#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@PHDtopo} +\def\hideonPHDtopo#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@PHDtopo} + +\def\showonPHDsec#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@PHDsec} +\def\hideonPHDsec#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@PHDsec} + +\def\showonHMMTOP#1{% + \xdef\first@{#1,&,@} \xdef\second@{yes} \show@HMMTOP} +\def\hideonHMMTOP#1{% + \xdef\first@{#1,&,@} \xdef\second@{no} \show@HMMTOP} + +\def\codon#1#2{% + \xdef\first@{#1} + \xdef\second@{#2,&,@} + \expandafter\get@triplet\second@} +\def\geneticcode#1{% + \xdef\first@{#1} + \xdef\temp@{standard} + \ifx\first@\temp@ + \c@d@ns + \else + \input{#1.cod} + \fi} +\newcommand{\backtranslabel}[2][tiny]{% + \def\trans@size{\csname #1\endcsname} + \xdef\first@{#2} + \xdef\temp@{horizontal} + \ifx\temp@\first@ \xdef\tr@nsstyle{0}\fi + \xdef\temp@{zigzag} + \ifx\temp@\first@ \xdef\tr@nsstyle{1}\fi + \xdef\temp@{alternating} + \ifx\temp@\first@ \xdef\tr@nsstyle{2}\fi + \xdef\temp@{oblique} + \ifx\temp@\first@ \xdef\tr@nsstyle{3}\fi + \xdef\temp@{vertical} + \ifx\temp@\first@ \xdef\tr@nsstyle{4}\fi +} +\newcommand{\backtranstext}[2][tiny]{% + \def\transtext@size{\csname #1\endcsname} + \xdef\first@{#2} + \xdef\temp@{horizontal} + \ifx\temp@\first@ \xdef\tr@nstextstyle{0}\fi + \xdef\temp@{zigzag} + \ifx\temp@\first@ \xdef\tr@nstextstyle{1}\fi + \xdef\temp@{alternating} + \ifx\temp@\first@ \xdef\tr@nstextstyle{2}\fi + \xdef\temp@{oblique} + \ifx\temp@\first@ \xdef\tr@nstextstyle{3}\fi + \xdef\temp@{vertical} + \ifx\temp@\first@ \xdef\tr@nstextstyle{4}\fi +} + +%%%%% Calculate consensus + +\def\check@sim{% + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\first@{\csname \prefix@ grp\first@\endcsname} + \newrestrue + \ifnum\first@<0 \newresfalse + \else + \innerloopcount=\loopcount + \ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count + \loop + \advance\innerloopcount by 1 + \xdef\second@{\csname res\the\innerloopcount\endcsname} + \expandafter\ifx\csname \prefix@ grp\second@\endcsname\first@ + \newresfalse \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count \repeat + \fi + \fi + + \ifnewres + \expandafter\csname pos\the\loopcount\endcsname=0 + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \xdef\second@{\csname res\the\innerloopcount\endcsname} + \expandafter\ifx\csname \prefix@ grp\second@\endcsname\first@ + \expandafter\advance\csname pos\the\loopcount\endcsname by 1 \fi + \ifnum\innerloopcount<\seq@count \repeat + + \expandafter\multiply\csname pos\the\loopcount\endcsname by \seq@percent + \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld + \else + \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x + \xdef\m@x{\the\csname pos\the\loopcount\endcsname} + \xdef\cons@seq{\the\loopcount} \xdef\match@case{\c@se} + \xdef\simgroup@{\first@} + \else + \expandafter\ifnum\csname pos\the\loopcount\endcsname=\m@x + \xdef\match@case{0} + \fi + \fi + \fi + \fi + + \ifnum\loopcount=\cons@num \loopcount=1 \fi + \advance\loopcount by -1 + \ifnum\loopcount>0 \check@sim \fi} + +\def\check@ident{% + \xdef\first@{\csname res\the\loopcount\endcsname} + \newrestrue \expandafter\check@char\first@ + \ifletter + \innerloopcount=\loopcount + \ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count + \loop + \advance\innerloopcount by 1 + \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ + \newresfalse \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count \repeat + \fi + \else + \newresfalse + \expandafter\xdef\csname res\the\loopcount\endcsname{\d@t} + \fi + + \ifnewres + \expandafter\csname pos\the\loopcount\endcsname=0 + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ + \expandafter\advance\csname pos\the\loopcount\endcsname by 1 \fi + \ifnum\innerloopcount<\seq@count \repeat + + \expandafter\ifnum\csname pos\the\loopcount\endcsname=\seq@count + \xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \loopcount=1 + \else + \expandafter\multiply\csname pos\the\loopcount\endcsname by \seq@percent + \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld + \else + \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x + \xdef\m@x{\the\csname pos\the\loopcount\endcsname} + \xdef\cons@seq{\the\loopcount} \xdef\match@case{1} + \else + \expandafter\ifnum\csname pos\the\loopcount\endcsname=\m@x + \xdef\match@case{0} + \fi + \fi + \fi + \fi + \fi + + \ifnum\loopcount=\cons@num \loopcount=1 \fi + \advance\loopcount by -1 + \ifnum\loopcount>0 \check@ident \fi} + +\def\get@simchar{% + \xdef\first@{\csname res\the\loopcount\endcsname} + \newrestrue \expandafter\check@char\first@ + \ifletter + \innerloopcount=\loopcount + \ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count + \loop + \advance\innerloopcount by 1 + \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ + \newresfalse \innerloopcount=\seq@count \fi + \ifnum\innerloopcount<\seq@count \repeat + \fi + \else + \newresfalse + \fi + + \ifnewres + \expandafter\csname pos\the\loopcount\endcsname=0 + \innerloopcount=0 + \loop + \advance\innerloopcount by 1 + \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ + \xdef\second@{\csname res\the\innerloopcount\endcsname} + \expandafter\ifx\csname \prefix@ grp\second@\endcsname\simgroup@ + \expandafter\advance\csname pos\the\loopcount\endcsname by 1 \fi + \fi + \ifnum\innerloopcount<\seq@count \repeat + + \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x + \xdef\m@x{\the\csname pos\the\loopcount\endcsname} + \xdef\cons@seq{\the\loopcount} + \fi + \fi + + \ifnum\loopcount=\cons@num \loopcount=1 \fi + \advance\loopcount by -1 + \ifnum\loopcount>0 \get@simchar \fi} + +\def\unc@nserved{% + \ifsimmode + \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi + \xdef\match@case{0} \xdef\m@x{1} \check@sim + \ifnum\match@case=0 + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \expandafter\ifx\csname res\the\loopcount\endcsname\d@t + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname3\gap@char} + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 3\csname res\the\loopcount\endcsname} + \fi + \else + \xdef\first@{\csname res\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\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\gap@char} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname3\first@} + \fi + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else + \xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }} + \else \xdef\first@{\n@m@tch} \fi\fi + \expandafter\ifx\csname 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\consensus{\consensus 4\first@} + \expandafter\ifx\csname res\cons@num\endcsname\d@t + \else\xdef\constopo{\constopo 0}\fi + \else + \ifnum\cons@num>0 + \xdef\tmp@{\csname res\cons@num\endcsname} + \else + \xdef\m@x{0} \loopcount=\seq@count \get@simchar + \xdef\tmp@{\csname res\cons@seq\endcsname} + \fi + \xdef\second@{\csname \prefix@ grp\tmp@\endcsname} + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\d@t\def\first@{\gap@char}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 3\first@} + \else + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\last@{\csname res\the\loopcount\endcsname} + \expandafter\ifnum\csname \prefix@ grp\last@\endcsname=\second@ + \xdef\third@{2} + \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\ressimm@tch\low@up + \else \xdef\first@{\ressimm@tch} \fi\fi + \else + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\gap@char} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \else + \xdef\third@{3} + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi + \fi + \fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\first@{\tmp@} + \xdef\low@up{lower} \ifx\m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\m@tch\low@up + \else \xdef\first@{\m@tch} \fi\fi + \expandafter\ifx\csname 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\consensus{\consensus5\first@} + \xdef\constopo{\constopo 1} + \fi + \else + \iffuncmode + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{\csname res\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\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\gap@char}\def\third@{*} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \fi + \fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname0\first@} + \fi + \ifnum\loopcount<\seq@count \repeat + \else + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\d@t\def\first@{\gap@char}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 3\first@} + \else + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\gap@char} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname3\first@} + \fi + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else + \xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }} + \else \xdef\first@{\n@m@tch} \fi\fi + \expandafter\ifx\csname 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\consensus{\consensus 4\first@} + \xdef\constopo{\constopo 0} + \fi\fi} + +\def\c@nserved{% + \xdef\tmp@{\csname res\cons@seq\endcsname} + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\d@t\def\first@{\gap@char}\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 3\first@} + \else + \xdef\second@{\csname res\the\loopcount\endcsname} + \ifx\tmp@\second@ + \xdef\third@{1} + \else + \xdef\third@{3} + \ifsimmode + \xdef\last@{\csname \prefix@ sim\tmp@\endcsname &@} + \expandafter\get@count\last@ + \innerloopcount=0 \getsim@char + \fi + \fi + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifcase\third@ \or + \xdef\low@up{lower} \ifx\resm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resm@tch\low@up + \else \xdef\first@{\resm@tch} \fi\fi + \or + \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\ressimm@tch\low@up + \else \xdef\first@{\ressimm@tch} \fi\fi + \else + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi + \fi + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\third@{7}\def\first@{\gap@char} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{7} + \else + \def\first@{{}} \def\third@{8} + \fi + \fi + \fi + \fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\first@{\csname res\cons@seq\endcsname} + \xdef\second@{lower} \ifx\m@tch\second@ \make@lower \else + \xdef\second@{upper} \ifx\m@tch\second@ + \else \xdef\first@{\m@tch} \fi\fi + \expandafter\ifx\csname 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\consensus{\consensus 5\first@} + \xdef\constopo{\constopo 2}} + +\def\allm@tch{% + \ifall@shade \xdef\third@{0} \else \xdef\third@{1} \fi + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 3\first@} + \else + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\res@llm@tch\low@up + \else \xdef\first@{\res@llm@tch} \fi\fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat + \xdef\first@{\csname res\cons@seq\endcsname} + \xdef\second@{lower} \ifx\@llm@tch\second@ \make@lower \else + \xdef\second@{upper} \ifx\@llm@tch\second@ + \else \xdef\first@{\@llm@tch} \fi\fi + \expandafter\ifx\csname 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\consensus{\consensus 6\first@} + \xdef\constopo{\constopo 3}} + +\def\functi@nal{% + \ifnum\cons@num>0 + \xdef\first@{\csname res\cons@num\endcsname} + \else + \xdef\first@{\csname res\cons@seq\endcsname} + \fi + \xdef\second@{\csname funcgrp\first@\endcsname} + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\third@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ + \xdef\first@{\csname res\the\loopcount\endcsname} + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 0\first@} + \else + \xdef\first@{\csname res\the\loopcount\endcsname} + \ifx\first@\d@t + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@start\the\loopcount\endcsname + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \else + \expandafter\ifnum\csname res@count\the\loopcount\endcsname% + <\csname seq@len\the\loopcount\endcsname + \def\first@{\gap@char}\def\third@{*} + \else + \ifsh@wg@ps + \def\first@{\gap@char}\def\third@{*} + \else + \def\first@{{}} \def\third@{/} + \fi + \fi + \fi + \else + \expandafter\ifnum\csname funcgrp\first@\endcsname=\second@ + \xdef\low@up{lower} + \expandafter\ifx\csname funcm@tch\second@\endcsname\low@up + \make@lower \fi + \xdef\third@{\second@} + \else \xdef\third@{0} + \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else + \xdef\low@up{upper} \ifx\resn@m@tch\low@up + \else \xdef\first@{\resn@m@tch} \fi\fi + \fi + \fi + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname\third@\first@} + \fi + \ifnum\loopcount<\seq@count \repeat} + +\def\all@funcshade{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\first@{\csname res\the\loopcount\endcsname} + \xdef\second@{\csname funcgrp\first@\endcsname} + \ifnum\second@<0 \xdef\second@{0} \fi + \ifx\first@\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\low@up{lower} + \expandafter\ifx\csname funcm@tch\second@\endcsname\low@up + \make@lower \fi + \xdef\third@{noshade} + \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \xdef\first@{=\first@}\fi + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \xdef\first@{,\first@}\fi + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + 0\first@} + \else + \expandafter\ifx\csname 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 + \else + \expandafter\ifnum\csname stop\the\loopcount\endcsname<\first@@ + \getregion@fromstack@first + \else + \expandafter\ifx\csname all\the\loopcount\endcsname\y@ + \innerloopcount=\csname style\the\loopcount\endcsname + \fi + \expandafter\xdef\csname shade@style\the\loopcount\endcsname{% + \csname style\the\loopcount\endcsname} + \fi + \fi +} + +\def\calc@regshade{% + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname shade@style\the\loopcount\endcsname{y} + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\the\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname stop\the\loopcount\endcsname<\first@@ + \getregion@fromstack@first + \else + \expandafter\ifx\csname all\the\loopcount\endcsname\y@ + \innerloopcount=\csname style\the\loopcount\endcsname + \fi + \expandafter\xdef\csname shade@style\the\loopcount\endcsname{% + \csname style\the\loopcount\endcsname} + \expandafter\ifnum\csname stop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromstack{\the\loopcount} + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat + \loopcount=0 + \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@ + \else + \xdef\consensus{\consensus&\csname shade@style\the\loopcount\endcsname)} + \fi + \loop + \advance\loopcount by 1 + \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@ + \ifnum\innerloopcount>0 + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + &\the\innerloopcount)} + \fi + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + &\csname shade@style\the\loopcount\endcsname)} + \fi + \ifnum\loopcount<\seq@count \repeat +} + +\def\getregion@fromemphstack@first{% + \expandafter\getregion@fromemphstack{\the\loopcount} + \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname emphstop\the\loopcount\endcsname<\first@@ + \getregion@fromemphstack@first + \else + \expandafter\ifx\csname emphall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} + \fi + \fi +} + +\def\calc@regemph{% + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\the\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname emphstop\the\loopcount\endcsname<\first@@ + \getregion@fromemphstack@first + \else + \expandafter\ifx\csname emphall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} + \expandafter\ifnum\csname emphstop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromemphstack{\the\loopcount} + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat + \loopcount=0 + \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} + \fi + \ifnum\innerloopcount>0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} + \ifnum\loopcount<\seq@count \repeat + \fi +} + +\def\getregion@fromtintstack@first{% + \expandafter\getregion@fromtintstack{\the\loopcount} + \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname tintstop\the\loopcount\endcsname<\first@@ + \getregion@fromtintstack@first + \else + \expandafter\ifx\csname tintall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} + \fi + \fi +} + +\def\calc@regtint{% + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\the\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname tintstop\the\loopcount\endcsname<\first@@ + \getregion@fromtintstack@first + \else + \expandafter\ifx\csname tintall\the\loopcount\endcsname\y@ + \innerloopcount=1 + \fi + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} + \expandafter\ifnum\csname tintstop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromtintstack{\the\loopcount} + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat + \loopcount=0 + \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} + \fi + \ifnum\innerloopcount>0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} + \ifnum\loopcount<\seq@count \repeat + \fi +} + +\def\getregion@fromframestack@first{% + \expandafter\getregion@fromframestack{\the\loopcount} + \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname framestop\the\loopcount\endcsname<\first@@ + \getregion@fromframestack@first + \else + \ifnum\frame@on=0 + \xdef\frame@on{1} + \xdef\frame@{1} + \expandafter\xdef\csname fr@style\the\loopcount\endcsname{% + \csname framestyle\the\loopcount\endcsname} + \innerloopcount=\pos@count + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;&;} + \xdef\frame@pos{\the\pos@count} + \fi + \expandafter\ifnum\csname framestop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromframestack{\the\loopcount} + \ifnum\frame@on=1 + \xdef\frame@on{0} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \ifnum\pos@count=\res@perline + \ifnum\frame@on=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=\end@num\relax + \ifnum\frame@on=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \fi + \fi +} + +\def\calc@frame{% + \advance\pos@count by -1 + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\the\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname framestart\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname framestop\the\loopcount\endcsname<\first@@ + \getregion@fromframestack@first + \else + \ifnum\frame@on=0 + \xdef\frame@on{1} + \xdef\frame@{1} + \expandafter\xdef\csname fr@style\the\loopcount\endcsname{% + \csname framestyle\the\loopcount\endcsname} + \innerloopcount=\pos@count + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;&;} + \xdef\frame@pos{\the\pos@count} + \fi + \expandafter\ifnum\csname framestop\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromframestack{\the\loopcount} + \ifnum\frame@on=1 + \xdef\frame@on{0} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \ifnum\pos@count=\res@perline + \ifnum\frame@on=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=\end@num\relax + \ifnum\frame@on=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\frame@pos + \xdef\styleframe{\styleframe&\the\innerloopcount;% + \csname fr@style\the\loopcount\endcsname;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \xdef\frame@pos{\the\innerloopcount} + \fi + \fi + \fi + \fi\fi + \ifnum\loopcount<\seq@count \repeat + \advance\pos@count by 1 +} + +\def\get@nextres#1#2:{% + \xdef\first@{#1} + \xdef\temp@{#2:} + \ifnum`#1>96 \make@upper \fi + \ifx\first@\gap@char \expandafter\get@nextres\temp@ + \else + \if\first@ @ + \xdef\temp@{} + \else + \xdef\temp@{+\first@} + \expandafter\xdef\csname last@res\bottop@\endcsname{} + \fi + \fi} +\def\get@@nextres#1#2:{% + \xdef\first@{#1} + \xdef\temp@@{#2:} + \ifnum`#1>96 \make@upper \fi + \ifx\first@\gap@char \expandafter\get@@nextres\temp@@ + \else + \if\first@ @ + \xdef\temp@@{} + \else + \xdef\temp@@{+\first@} + \expandafter\xdef\csname last@res\bottop@\endcsname{} + \fi + \fi} + +\def\char@get#1#2@{\xdef\first@{#1} \xdef\tr@nsl@ted{#2@}} +\def\trans@now#1#2@{% + \xdef\first@{#1} + \xdef\tr@nsl@ted{#2@} + \ifx\first@\ampers@nd + \else + \expandafter\check@char\first@ + \ifletter + \xdef\triplet@{\triplet@\first@} + \advance\triple@count by 1 + \ifnum\triple@count=1 + \xdef\out@{\out@{-}} + \fi + \ifnum\triple@count=3 + \expandafter\ifx\csname @\triplet@\endcsname\relax + \expandafter\xdef\csname @\triplet@\endcsname{?} \fi + \xdef\out@{\out@\csname @\triplet@\endcsname\out@@{-}} + \triple@count=0 + \xdef\triplet@{} + \xdef\out@@{} + \fi + \fi + \if\first@ - + \ifnum\triple@count<2 + \xdef\out@{\out@{-}} + \else + \xdef\out@@{\out@@{-}} + \fi + \fi + \if\first@ + + \expandafter\char@get\tr@nsl@ted + \xdef\triplet@{\triplet@\first@} + \advance\triple@count by 1 + \ifnum\triple@count=3 + \expandafter\ifx\csname @\triplet@\endcsname\relax + \expandafter\xdef\csname @\triplet@\endcsname{?} \fi + \xdef\out@{\out@\csname @\triplet@\endcsname\out@@} + \triple@count=0 + \xdef\triplet@{} + \xdef\out@@{} + \fi + \fi + \if\first@ 2 + \loop + \expandafter\char@get\tr@nsl@ted + \ifx\first@\ampers@nd + \lettertrue + \xdef\tr@nsl@ted{&@} + \else + \expandafter\check@char\first@ + \fi + \ifletter\else\xdef\out@{\out@{-}}\repeat + \xdef\out@{\out@{-}} + \fi + \expandafter\trans@now\tr@nsl@ted + \fi +} + +\def\do@translation{% + \xdef\triplet@{} + \xdef\out@{} + \xdef\out@@{} + \xdef\tr@nsl@ted{\tr@nsl@ted &@} + \triple@count=0 + \expandafter\trans@now\tr@nsl@ted + \xdef\tr@nsl@ted{\out@} +} + +\def\trans@pep#1#2@{% + \xdef\first@{#1} + \xdef\tr@nsl@ted{#2@} + \ifx\first@\ampers@nd + \else + \expandafter\check@char\first@ + \ifletter + \xdef\out@{\out@\csname rev@\first@\endcsname} + \else + \xdef\out@{\out@{-}{-}{-}} + \fi + \expandafter\trans@pep\tr@nsl@ted + \fi +} + +\def\rev@translation{% + \xdef\out@{} + \xdef\tr@nsl@ted{\tr@nsl@ted &@} + \expandafter\trans@pep\tr@nsl@ted + \xdef\tr@nsl@ted{\out@} +} + +\def\sum@up{% + \advance\innerloopcount by 1 + \xdef\second@@@{\csname res\the\innerloopcount\endcsname} + \xdef\third@@@{\csname cons\first@@@\second@@@\endcsname} + \advance\temp@count by \third@@@ + \ifnum\innerloopcount<\seq@count\sum@up\fi +} + +\def\sum@up@cons{% + \innerloopcount=\outerloopcount + \xdef\first@@@{\csname res\the\outerloopcount\endcsname} + \sum@up + \advance\outerloopcount by 1\relax + \ifnum\outerloopcount<\seq@count + \sum@up@cons + \else + \innerloopcount=\seq@count + \advance\innerloopcount by -1 + \multiply\innerloopcount by \seq@count + \multiply\temp@count by 2 + \divide\temp@count by \innerloopcount + \xdef\cons@val{\the\temp@count} + \fi +} + +\def\collect@cons@res{% + \xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname} + \advance\innerloopcount by 1 + \ifnum\innerloopcount>\seq@count\relax + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \else + \collect@cons@res + \fi +} + +\def\calc@feature{% + \advance\pos@count by -1 + \loopcount=-1 \innerloopcount=0 + \loop + \advance\loopcount by 1 + \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} + \else \xdef\first@@{\the\csname res@count\the\loopcount\endcsname} \fi + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>\first@@ + \else + \expandafter\ifnum\csname stop\bottop@\the\loopcount\endcsname<\first@@ + \expandafter\getregion@fromfstack{\the\loopcount} + \else + \innerloopcount=\loopcount + \expandafter\ifnum\csname featureon\bottop@\endcsname=0 + \expandafter\xdef\csname featureon\bottop@\endcsname{1} + \expandafter\xdef\csname feature@\bottop@\endcsname{1} + \expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{% + \csname text\bottop@\the\loopcount\endcsname} + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{% + \csname style\bottop@\the\loopcount\endcsname} + \innerloopcount=\pos@count + \advance\innerloopcount by -\csname featurepos\bottop@\endcsname + \expandafter\xdef\csname textfeature\bottop@\endcsname{% + \csname textfeature\bottop@\endcsname% + &\the\innerloopcount;{};} + \expandafter\xdef\csname stylefeature\bottop@\endcsname{% + \csname stylefeature\bottop@\endcsname% + &\the\innerloopcount;&;} + \expandafter\xdef\csname featurepos\bottop@\endcsname{\the\pos@count} + \xdef\temp@@@{n} + \xdef\fourth@{} + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi + \xdef\fourth@{} + \xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi + \ifx\temp@@@\y@ + \ifnum\loopcount=0 + \message{} + \expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{% + No consensus translations!} + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{% + ///} + \else + \if\seq@type P + \expandafter\xdef\csname collect@res\bottop@\endcsname{yes} + \expandafter\xdef\csname tr@nsseq\bottop@\endcsname{\the\loopcount} + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + \csname res\the\loopcount\endcsname} + \else + \expandafter\xdef\csname collect@res\bottop@\endcsname{yes} + \expandafter\xdef\csname tr@nsseq\bottop@\endcsname{\the\loopcount} + \expandafter\ifx\csname res\the\loopcount\endcsname\gap@char + \expandafter\xdef\csname triple@count\bottop@\endcsname{0} + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{-} + \else + \expandafter\xdef\csname triple@count\bottop@\endcsname{1} + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + \csname res\the\loopcount\endcsname} + \expandafter\xdef\csname last@@res\bottop@\endcsname{% + \csname res\the\loopcount\endcsname} + \fi + \fi + \fi + \fi + \xdef\temp@{plot} + \ifx\temp@\fourth@ + \ifnum\loopcount=0 + \message{} + \expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{} + \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{% + ///} + \else + \expandafter\xdef\csname collect@val\bottop@\endcsname{yes} + \expandafter\xdef\csname v@lseq\bottop@\endcsname{\the\loopcount} + \expandafter\xdef\csname ffourth@\bottop@\endcsname{\ffourth@} + \xdef\temp@{\ffourth@\csname res\the\loopcount\endcsname} + \expandafter\xdef\csname v@l\bottop@\endcsname{\csname \temp@\endcsname} + \fi + \fi + \xdef\temp@{cons} + \ifx\temp@\fourth@ + \expandafter\xdef\csname collect@cons@graph\bottop@\endcsname{yes} + \expandafter\xdef\csname v@lseq\bottop@\endcsname{\the\loopcount} + \expandafter\xdef\csname ffourth@\bottop@\endcsname{\ffourth@} + \innerloopcount=1 + \collect@cons@res + \expandafter\xdef\csname v@l\bottop@\endcsname{\cons@val} + \fi + \else + \ifnum\pos@count=1\relax + \xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname @} + \expandafter\getstyle@right\temp@ + \xdef\temp@@@{n} + \xdef\fourth@{} + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi + \xdef\fourth@{} + \xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi + \ifx\temp@@@\y@ + \if\seq@type P + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + \csname res\the\loopcount\endcsname} + \else + \expandafter\ifnum\csname triple@count\bottop@\endcsname=2 + \expandafter\ifx\csname res\the\loopcount\endcsname\gap@char + \else + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + +\csname last@res\bottop@\endcsname% + \csname tr@nslate\bottop@\endcsname} + \fi + \fi + \expandafter\ifnum\csname triple@count\bottop@\endcsname=1 + \expandafter\xdef\csname last@res\bottop@\endcsname{% + \csname last@@res\bottop@\endcsname} + \expandafter\ifx\csname res\the\loopcount\endcsname\gap@char + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{% + +\csname last@res\bottop@\endcsname% + \csname tr@nslate\bottop@\endcsname} + \fi + \fi + \fi + \fi + \xdef\temp@{plot} + \ifx\temp@\fourth@ + \expandafter\ifx\csname res\the\loopcount\endcsname\gap@char + \expandafter\xdef\csname v@l\bottop@\endcsname{N} + \else + \xdef\temp@{\ffourth@\csname res\the\loopcount\endcsname} + \expandafter\xdef\csname v@l\bottop@\endcsname{% + \csname \temp@\endcsname} + \fi + \fi + \xdef\temp@{cons} + \ifx\temp@\fourth@ + \innerloopcount=1 + \collect@cons@res + \expandafter\xdef\csname v@l\bottop@\endcsname{\cons@val} + \fi + \fi + \fi + \expandafter\ifnum\csname stop\bottop@\the\loopcount\endcsname=\first@@ + \expandafter\getregion@fromfstack{\the\loopcount} + \xdef\temp@@@{n} + \xdef\fourth@{} + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns + \ifx\f@color\comm@ + \xdef\f@color{} \else \xdef\f@color{[\f@color]} + \fi + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \if\seq@type N \do@translation \else \rev@translation \fi + \xdef\temp@{translate:\tr@nsl@ted\f@color} + \xdef\temp@@@{y} + \else + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \fi + \xdef\fourth@{} + \xdef\temp@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \xdef\temp@@{\temp@@[,]:[,][]&}\expandafter\graph@opt@color\temp@@ + \ifx\fourth@\tr@ns + \ifx\f@color\comm@ + \xdef\f@color{} \else \xdef\f@color{[\f@color]} + \fi + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \if\seq@type N \do@translation \else \rev@translation \fi + \xdef\temp@@{translate:\tr@nsl@ted\f@color} + \xdef\temp@@@{y} + \else + \xdef\temp@@{plot} + \ifx\temp@@\fourth@ + \xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]} + \expandafter\xdef\csname collect@val\bottop@\endcsname{no} + \expandafter\xdef\csname v@l\bottop@\endcsname{} + \else + \xdef\temp@@{cons} + \ifx\temp@@\fourth@ + \xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]} + \expandafter\xdef\csname collect@cons@graph\bottop@\endcsname{no} + \expandafter\xdef\csname v@l\bottop@\endcsname{} + \else + \xdef\temp@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \fi + \fi + \fi + \ifx\temp@@@\y@ + \expandafter\xdef\csname collect@res\bottop@\endcsname{no} + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{} + \fi + \expandafter\ifnum\csname featureon\bottop@\endcsname=1 + \expandafter\xdef\csname featureon\bottop@\endcsname{0} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \advance\innerloopcount by -\csname featurepos\bottop@\endcsname + \expandafter\xdef\csname textfeature\bottop@\endcsname{% + \csname textfeature\bottop@\endcsname% + &\the\innerloopcount;\temp@;} + \expandafter\xdef\csname stylefeature\bottop@\endcsname{% + \csname stylefeature\bottop@\endcsname% + &\the\innerloopcount;\temp@@;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \expandafter\xdef\csname % + featurepos\bottop@\endcsname{\the\innerloopcount} + \fi + \fi + \ifnum\pos@count=\res@perline + \expandafter\ifnum\csname featureon\bottop@\endcsname=1 + \innerloopcount=\pos@count + \advance\innerloopcount by 1 + \advance\innerloopcount by -\csname featurepos\bottop@\endcsname + \xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname @} + \expandafter\getstyle@left\temp@ + \xdef\temp@@@{n} + \xdef\fourth@{} + \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ + \ifx\fourth@\tr@ns + \ifx\f@color\comm@ + \xdef\f@color{} \else \xdef\f@color{[\f@color]} + \fi + \expandafter\ifnum\csname triple@count\bottop@\endcsname=2 + \if\seq@type N + \xdef\temp@{\csname sequence\the\loopcount\endcsname:} + \expandafter\get@nextres\temp@ + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname\temp@} + \do@translation + \xdef\temp@@@{2} + \else + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \rev@translation + \xdef\temp@@@{} + \fi + \xdef\temp@{translate:\tr@nsl@ted\f@color} + \else + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \if\seq@type N \do@translation \else \rev@translation \fi + \xdef\temp@{translate:\tr@nsl@ted\f@color} + \xdef\temp@@@{} + \fi + \else \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} + \fi + \xdef\fourth@{} + \xdef\temp@@{\csname fstyle\bottop@\the\loopcount\endcsname} + \xdef\temp@@{\temp@@[,]:[,][]&}\expandafter\graph@opt@color\temp@@ + \ifx\fourth@\tr@ns + \ifx\f@color\comm@ + \xdef\f@color{} \else \xdef\f@color{[\f@color]} + \fi + \expandafter\ifnum\csname triple@count\bottop@\endcsname=2 + \if\seq@type N + \xdef\temp@@{\csname sequence\the\loopcount\endcsname:} + \expandafter\get@@nextres\temp@@ + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname\temp@@} + \do@translation + \xdef\temp@@@{2} + \else + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \rev@translation + \xdef\temp@@@{} + \fi + \xdef\temp@@{translate:\tr@nsl@ted\f@color} + \else + \xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname} + \if\seq@type N \do@translation \else \rev@translation \fi + \xdef\temp@@{translate:\tr@nsl@ted\f@color} + \xdef\temp@@@{} + \fi + \else + \xdef\temp@@{plot} + \ifx\temp@@\fourth@ + \xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]} + \else + \xdef\temp@@{cons} + \ifx\temp@@\fourth@ + \xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]} + \else + \xdef\temp@@{\style@@} + \fi + \fi + \fi + \ifx\temp@@@\n@ + \else + \expandafter\xdef\csname tr@nslate\bottop@\endcsname{\temp@@@} + \fi + \expandafter\xdef\csname textfeature\bottop@\endcsname{% + \csname textfeature\bottop@\endcsname% + &\the\innerloopcount;\temp@;} + \expandafter\xdef\csname stylefeature\bottop@\endcsname{% + \csname stylefeature\bottop@\endcsname% + &\the\innerloopcount;\temp@@;} + \innerloopcount=\pos@count \advance\innerloopcount by 1 + \expandafter\xdef\csname % + featurepos\bottop@\endcsname{\the\innerloopcount} + \fi + \fi + \fi + \fi + \fi + \ifnum\loopcount<\seq@count \repeat + \advance\pos@count by 1 +} + +\def\c@nsensus{% + \ifnum\pos@count>\res@perline + \else + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\seq@line{\csname sequence\the\loopcount\endcsname} + \expandafter\residue@get\seq@line + \xdef\first@{\csname res\the\loopcount\endcsname} + \expandafter\check@char\first@ + \ifletter + \global\advance\csname res@count\the\loopcount\endcsname by 1 + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=0 + \global\advance\csname res@count\the\loopcount\endcsname by 1 + \fi + \ifnum\loopcount=\rule@num\relax + \expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens + \xdef\ruler@{\ruler@ !<\rule@tens>} + \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step + \ifnum\innerloopcount=0 \innerloopcount=1 \fi + \advance\innerloopcount by -1 + \ifnum\innerloopcount=\ruler@step + \else \advance\innerloopcount by 1 \fi + \xdef\rule@tens{\the\innerloopcount} + \else + \xdef\ruler@{\ruler@ -} + \fi + \fi + \ifx\collect@valtop\yes + \ifnum\v@lseqtop=\loopcount + \xdef\v@ltop{\v@ltop,\csname \ffourth@top\first@\endcsname} + \fi\fi + \ifx\collect@valttop\yes + \ifnum\v@lseqttop=\loopcount + \xdef\v@lttop{\v@lttop,\csname \ffourth@ttop\first@\endcsname} + \fi\fi + \ifx\collect@valbottom\yes + \ifnum\v@lseqbottom=\loopcount + \xdef\v@lbottom{\v@lbottom,\csname \ffourth@bottom\first@\endcsname} + \fi\fi + \ifx\collect@valbbottom\yes + \ifnum\v@lseqbbottom=\loopcount + \xdef\v@lbbottom{\v@lbbottom,\csname \ffourth@bbottom\first@\endcsname} + \fi\fi + \ifx\collect@restop\yes + \ifnum\tr@nsseqtop=\loopcount + \xdef\last@restop{\last@@restop} + \xdef\tr@nslatetop{\tr@nslatetop\first@} + \xdef\last@@restop{\first@} + \innerloopcount=\triple@counttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@counttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resttop\yes + \ifnum\tr@nsseqttop=\loopcount + \xdef\last@resttop{\last@@resttop} + \xdef\tr@nslatettop{\tr@nslatettop\first@} + \xdef\last@@resttop{\first@} + \innerloopcount=\triple@countttop + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countttop{\the\innerloopcount} + \fi\fi + \ifx\collect@resbottom\yes + \ifnum\tr@nsseqbottom=\loopcount + \xdef\last@resbottom{\last@@resbottom} + \xdef\tr@nslatebottom{\tr@nslatebottom\first@} + \xdef\last@@resbottom{\first@} + \innerloopcount=\triple@countbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbottom{\the\innerloopcount} + \fi\fi + \ifx\collect@resbbottom\yes + \ifnum\tr@nsseqbbottom=\loopcount + \xdef\last@resbbottom{\last@@resbbottom} + \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@} + \xdef\last@@resbbottom{\first@} + \innerloopcount=\triple@countbbottom + \advance\innerloopcount by 1 + \ifnum\innerloopcount>3 \innerloopcount=1 \fi + \xdef\triple@countbbottom{\the\innerloopcount} + \fi\fi + \innerloopcount=\csname mol@weight\the\loopcount\endcsname + \advance\innerloopcount by \csname \prefix@ mw\first@\endcsname + \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{% + \the\innerloopcount} + \innerloopcount=\csname ch@rge\the\loopcount\endcsname + \advance\innerloopcount by \csname pepcharge\first@\endcsname + \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{% + \the\innerloopcount} + \else + \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi + \ifx\collect@valtop\yes + \ifnum\v@lseqtop=\loopcount + \xdef\v@ltop{\v@ltop,N} + \fi\fi + \ifx\collect@valttop\yes + \ifnum\v@lseqttop=\loopcount + \xdef\v@lttop{\v@lttop,N} + \fi\fi + \ifx\collect@valbottom\yes + \ifnum\v@lseqbottom=\loopcount + \xdef\v@lbottom{\v@lbottom,N} + \fi\fi + \ifx\collect@valbbottom\yes + \ifnum\v@lseqbbottom=\loopcount + \xdef\v@lbbottom{\v@lbbottom,N} + \fi\fi + \ifx\collect@restop\yes + \ifnum\tr@nsseqtop=\loopcount + \xdef\tr@nslatetop{\tr@nslatetop -} + \fi\fi + \ifx\collect@resttop\yes + \ifnum\tr@nsseqttop=\loopcount + \xdef\tr@nslatettop{\tr@nslatettop -} + \fi\fi + \ifx\collect@resbottom\yes + \ifnum\tr@nsseqbottom=\loopcount + \xdef\tr@nslatebottom{\tr@nslatebottom -} + \fi\fi + \ifx\collect@resbbottom\yes + \ifnum\tr@nsseqbbottom=\loopcount + \xdef\tr@nslatebbottom{\tr@nslatebbottom -} + \fi\fi + \fi + \ifnum\loopcount<\seq@count \repeat + \ifx\collect@cons@graphtop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@ltop{\v@ltop,\cons@val} + \fi + \ifx\collect@cons@graphttop\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lttop{\v@lttop,\cons@val} + \fi + \ifx\collect@cons@graphbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbottom{\v@lbottom,\cons@val} + \fi + \ifx\collect@cons@graphbbottom\yes + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \xdef\v@lbbottom{\v@lbbottom,\cons@val} + \fi + \ifx\collect@cons@colors\y@ + \outerloopcount=1\relax + \temp@count=0\relax + \sum@up@cons + \outerloopcount=\cons@val + \advance\outerloopcount by 4 + \divide\outerloopcount by 5 + \multiply\outerloopcount by 5 + \ifnum\outerloopcount<5\relax\outerloopcount=5\fi + \xdef\c@nscol{\c@nscol\the\outerloopcount,} + \fi + + \global\advance\cons@count by 1\relax + \global\csname res@count0\endcsname=\cons@count + \ifnum\rule@num=0 + \ifnum\cons@count=\rule@tens + \xdef\ruler@{\ruler@ !<\rule@tens>} + \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step + \ifnum\innerloopcount=0 \innerloopcount=1 \fi + \advance\innerloopcount by -1 + \ifnum\innerloopcount=\ruler@step + \else \advance\innerloopcount by 1 \fi + \xdef\rule@tens{\the\innerloopcount} + \else + \xdef\ruler@{\ruler@ -} + \fi + \fi + \advance\pos@count by 1 + \ifregionalshadenow \calc@regshade \fi + \ifregionaltintnow \calc@regtint \fi + \ifregionalemphnow \calc@regemph \fi + \ifframenow \calc@frame \fi + \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi + \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi + \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi + \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 + \fi + \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax + \c@nsensus + \else + \global\stop@true + \loopcount=\pos@count \advance\loopcount by -1 \relax + \res@perline=\loopcount + \iftopfeature \xdef\bottop@{top} \calc@feature \fi + \ifttopfeature \xdef\bottop@{ttop} \calc@feature \fi + \ifbottomfeature \xdef\bottop@{bottom} \calc@feature \fi + \ifbbottomfeature \xdef\bottop@{bbottom} \calc@feature \fi + \pos@count=0 + \fi + \fi} + +\def\c@unt{% + \advance\loopcount by 1 + \xdef\seq@line{\csname sequence\the\loopcount\endcsname} + \expandafter\residue@get\seq@line + \xdef\first@{\csname res\the\loopcount\endcsname} + \expandafter\check@char\first@ + \ifletter + \global\advance\csname res@count\the\loopcount\endcsname by 1 + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=0 + \global\advance\csname res@count\the\loopcount\endcsname by 1 + \fi + \ifnum\rule@num=\loopcount + \temp@count=\csname res@count\the\loopcount\endcsname + \divide\temp@count by \ruler@step + \multiply\temp@count by \ruler@step + \ifnum\temp@count<0 \else \advance\temp@count by \ruler@step \fi + \xdef\rule@tens{\the\temp@count} + \fi + \fi + \ifnum\loopcount<\seq@count \c@unt\fi} +\def\count@first{% + \advance\end@count by 1 + \ifnum\end@count<\start@number + \loopcount=0 + \c@unt + \count@first + \fi} +\def\findc@nsensus{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname sequence\the\loopcount\endcsname{% + \csname sequence\the\loopcount\endcsname @} + \ifnum\loopcount<\seq@count \repeat + \end@count=0 \count@first \end@count=0 \xdef\start@number{0} + \regionalshadenowfalse \regionalemphnowfalse \regionaltintnowfalse + \framenowfalse + \topfeaturenowfalse \bottomfeaturenowfalse + \ttopfeaturenowfalse \bbottomfeaturenowfalse + \innerloopcount=\cons@count + \advance\innerloopcount by \res@perline \advance\innerloopcount by 1 + \loopcount=0 + \ifregionalshade + \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\the\loopcount\endcsname>% + \innerloopcount + \else + \regionalshadenowtrue + \fi + \fi + \fi + \ifregionaltint + \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionaltintnowtrue + \fi + \fi + \fi + \ifregionalemph + \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionalemphnowtrue + \fi + \fi + \fi + \ifframe@ + \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname framestart\the\loopcount\endcsname>% + \innerloopcount + \else + \framenowtrue + \fi + \fi + \fi + \iftopfeature + \xdef\bottop@{top} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \topfeaturenowtrue + \fi + \fi + \fi + \ifttopfeature + \xdef\bottop@{ttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttopfeaturenowtrue + \fi + \fi + \fi + \ifbottomfeature + \xdef\bottop@{bottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bottomfeaturenowtrue + \fi + \fi + \fi + \ifbbottomfeature + \xdef\bottop@{bbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbottomfeaturenowtrue + \fi + \fi + \fi +\loop + \advance\loopcount by 1 + \ifnumbers@left + \innerloopcount=\csname seq@len\the\loopcount\endcsname + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=% + \innerloopcount + \else + \global\advance\csname res@count\the\loopcount\endcsname by 1 + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=0 + \global\advance\csname res@count\the\loopcount\endcsname by 1 + \fi + \fi + \ifnames@right + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \the\csname res@count\the\loopcount\endcsname)} + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + <\csname newseqname\the\loopcount\endcsname> + \the\csname res@count\the\loopcount\endcsname)} + \fi + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=% + \innerloopcount + \else + \global\advance\csname res@count\the\loopcount\endcsname by -1 + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=0 + \global\advance\csname res@count\the\loopcount\endcsname by -1 + \fi + \fi + \else + \ifnames@right + \expandafter\xdef\csname seq\the\loopcount\endcsname{} + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + <\csname newseqname\the\loopcount\endcsname>} + \fi + \fi + \innerloopcount=\csname res@count\the\loopcount\endcsname + \advance\innerloopcount by \res@perline \advance\innerloopcount by 1 + \ifregionalshade + \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\the\loopcount\endcsname>% + \innerloopcount + \else + \regionalshadenowtrue + \fi + \fi + \fi + \ifregionaltint + \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionaltintnowtrue + \fi + \fi + \fi + \ifregionalemph + \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>% + \innerloopcount + \else + \regionalemphnowtrue + \fi + \fi + \fi + \ifframe@ + \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname framestart\the\loopcount\endcsname>% + \innerloopcount + \else + \framenowtrue + \fi + \fi + \fi + \iftopfeature + \xdef\bottop@{top} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \topfeaturenowtrue + \fi + \fi + \fi + \ifttopfeature + \xdef\bottop@{ttop} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \ttopfeaturenowtrue + \fi + \fi + \fi + \ifbottomfeature + \xdef\bottop@{bottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bottomfeaturenowtrue + \fi + \fi + \fi + \ifbbottomfeature + \xdef\bottop@{bbottom} + \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd + \else + \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% + \innerloopcount + \else + \bbottomfeaturenowtrue + \fi + \fi + \fi +\ifnum\loopcount<\seq@count \repeat + \c@nsensus} + +%%%%% Output routines + +\def\white@box{% + \bgroup + \fboxsep-0.5pt\fboxrule0.5pt + \fcolorbox{Black}{White}{\box@hstrut\box@wstrut}\egroup} +\def\box@rule{\vrule depth\box@depth height\box@height width\box@width} +\def\box@hstrut{\vrule depth\box@depth height\box@height width 0pt} +\def\box@wstrut{\vrule depth 0pt height 0pt width\box@width} +\def\do@legend{% + \baselineskip=1.2\baselineskip + \xdef\first@{White} + \fontfamily{\legend@family}% + \fontseries{\legend@series}% + \fontshape{\legend@shape}% + \iffuncmode + \ifnum\fgroup@num>0 + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\third@{\csname fg@color\the\loopcount\endcsname}% + \noindent% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi% + \xdef\third@{\csname fg@textcolor\the\loopcount\endcsname}% + \def\res@@style{\csname func@style\the\loopcount\endcsname}% + \def\temp@{X}\xdef\low@up{lower}% + \expandafter\ifx\csname funcm@tch\the\loopcount\endcsname\low@up% + \def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\third@}{\hbox to \box@width{% + \res@@style{\hss\temp@\hss}}}% + \kern2ex\textcolor{\legend@fg}{% + \legend@size{\csname fgroup@name\the\loopcount\endcsname}} + \newline\hbox{}% + \ifnum\loopcount<\fgroup@num \repeat + \fi + \else + \noindent + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi% + \hbox to \hspace@legend{\hss}% + \ifx\Nomatch\first@\white@box\else\textcolor{\Nomatch}{\box@rule}\fi% + \def\res@@style{\csname no@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}\ifx\resn@m@tch\low@up\def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\TextNomatch}{\hbox to \box@width{% + \res@@style{\hss\temp@\hss}}}% + \textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{nicht konserviert}% + \else\ifsp@nish\kern2ex\legend@size{no conservado}% + \else\kern2ex\legend@size{non conserved}\fi\fi} + \newline\hbox{}\noindent% + \ifsimmode% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi + \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi + \hbox to \hspace@legend{\hss}% + \ifx\Similar\first@\white@box\else\textcolor{\Similar}{\box@rule}\fi + \def\res@@style{\csname sim@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}\ifx\ressimm@tch\low@up\def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\TextSimilar}{\hbox to \box@width{% + \res@@style{\hss\temp@\hss}}}% + \textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{\"ahnlich}% + \else\ifsp@nish\kern2ex\legend@size{similar}% + \else\kern2ex\legend@size{similar}\fi\fi} + \newline\hbox{}\noindent% + \fi% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi + \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi + \hbox to \hspace@legend{\hss}% + \ifx\Identical\first@\white@box\else\textcolor{\Identical}{\box@rule}\fi + \def\res@@style{\csname id@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}\ifx\resm@tch\low@up\def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\TextIdentical}{\hbox to \box@width{% + \res@@style{\hss\temp@\hss}}}% + \textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{konserviert}% + \else\ifsp@nish\kern2ex\legend@size{conservado}% + \else\kern2ex\legend@size{conserved}\fi\fi} + \newline\hbox{}\noindent% + \ifall@shade% + \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi + \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi + \hbox to \hspace@legend{\hss}% + \ifx\Allmatch\first@\white@box\else\textcolor{\Allmatch}{\box@rule}\fi + \def\res@@style{\csname all@style\endcsname}% + \def\temp@{X}\xdef\low@up{lower}\ifx\res@llm@tch\low@up\def\temp@{x}\fi% + \ifhidechar\xdef\temp@{}\fi% + \kern-\box@width\textcolor{\TextAllmatch}{\hbox to \box@width{% + \res@@style{\hss\temp@\hss}}}% + \textcolor{\legend@fg}{% + \ifgerm@n\kern2ex\legend@size{alle identisch}% + \else\ifsp@nish\kern2ex\legend@size{todos id\'enticos}% + \else\kern2ex\legend@size{all match}\fi\fi} + \newline\hbox{}\noindent + \fi + \fi +} +\def\put@name<#1>#2@{% + \ifnames@% + \expandafter\ifx\csname hide@name\the\loopcount\endcsname\yes% + \xdef\temp@{}\else\xdef\temp@{#1}\fi% + \expandafter\ifx\csname name@col\the\loopcount\endcsname\yes% + \def\second@{\names@fg}% + \else\def\second@{\csname name@col\the\loopcount\endcsname}\fi% + \fontfamily{\namestext@family}% + \fontseries{\namestext@series}% + \fontshape{\namestext@shape}% + \selectfont% + \textcolor{\second@}{% + \hbox to \name@width{\@kern\namestext@size{\temp@}\hss}}\fi% + \xdef\first@{#2@}% +} +\def\put@number#1)#2@{% + \ifnumbers@% + \expandafter\ifx\csname hide@number\the\loopcount\endcsname\yes% + \xdef\temp@{}\else\xdef\temp@{#1}\fi% + \expandafter\ifx\csname number@col\the\loopcount\endcsname\yes% + \def\second@{\numbering@fg}% + \else\def\second@{\csname number@col\the\loopcount\endcsname}\fi% + \fontfamily{\numbertext@family}% + \fontseries{\numbertext@series}% + \fontshape{\numbertext@shape}% + \selectfont% + \textcolor{\second@}{% + \hbox to \number@width{\hss\numbertext@size{\temp@}\@kern}}\fi% + \xdef\first@{#2@}% +} +\def\special@shade#1)#2#3#4@{% + \xdef\second@{\second@#1}% + \xdef\boxc@l@r{\csname bgseqregion\second@\endcsname}% + \xdef\textc@l@r{\csname fgseqregion\second@\endcsname}% + \xdef\first@{#4@}% + \xdef\second@{#3}% + \def\res@@style{\csname relax\endcsname}% +} +\def\get@second@#1#2@{\xdef\second@{#1}\xdef\first@{#2@}} +\def\next@char#1#2#3@{% + \xdef\first@{#3@}% + \xdef\second@{#2}% + \xdef\last@{#1}% + \xdef\temp@@{}% + \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% + \else% + \iffuncmode% + \xdef\boxc@l@r{\csname fg@color#1\endcsname}% + \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% + \def\res@@style{\csname func@style#1\endcsname}% + \if\last@ *\def\last@{0}\fi + \if\last@ /\def\last@{10}\fi + \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}% + \def\res@@style{\id@style}% + \or\xdef\boxc@l@r{\Similar}\xdef\textc@l@r{\TextSimilar}% + \def\res@@style{\sim@style}% + \or\xdef\boxc@l@r{\Nomatch}\xdef\textc@l@r{\TextNomatch}% + \def\res@@style{\no@style}% + \or\xdef\boxc@l@r{\ConsNomatch}\xdef\textc@l@r{\ConsTextNomatch}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\ConsMatch}\xdef\textc@l@r{\ConsTextMatch}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\ConsAllmatch}\xdef\textc@l@r{\ConsTextAllmatch}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}% + \def\res@@style{\csname relax\endcsname}% + \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \def\res@@style{\csname relax\endcsname}% + \fi\fi\fi% + \ifx\second@\comm@% + \def\temp@{\res@style}% + \expandafter\get@second@\first@% + \else% + \def\temp@{\csname relax\endcsname}% + \fi% + \ifx\second@\equ@l% + \xdef\temp@@{\light@}% + \expandafter\get@second@\first@% + \fi% + \textcolor{\temp@@\boxc@l@r}{\box@rule}% + \ifhidechar% + \ifx\second@\o@% + \def\second@{\gap@rule}% + \hbox to -\box@width{\hss\textcolor{\temp@@\textc@l@r}% + {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% + \kern\box@width% + \fi% + \else% + \ifx\second@\o@\def\second@{\gap@rule}\fi% + \hbox to -\box@width{\hss\textcolor{\temp@@\textc@l@r}% + {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% + \kern\box@width\fi% +} +\def\put@char{% + \ifnum\innerloopcount>\res@perline + \else + \expandafter\next@char\first@ + \advance\innerloopcount by 1 + \put@char% + \fi} +\def\next@cons#1#2#3@{% + \xdef\last@{#1}% + \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% + \else% + \ifx\collect@cons@colors\y@% + \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}% + \fi% + \ifx\text@scale\y@% + \xdef\textc@l@r{\c@nsc@l\fourth@}% + \else% + \xdef\textc@l@r{\c@nsc@l}% + \fi% + \def\res@@style{\csname relax\endcsname}% + \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}% + \def\res@@style{\id@style}% + \or\xdef\boxc@l@r{\Similar}\xdef\textc@l@r{\TextSimilar}% + \def\res@@style{\sim@style}% + \or\xdef\boxc@l@r{\Nomatch}\xdef\textc@l@r{\TextNomatch}% + \def\res@@style{\no@style}% + \or\xdef\boxc@l@r{\ConsNomatch}\xdef\textc@l@r{\ConsTextNomatch}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\ConsMatch}\xdef\textc@l@r{\ConsTextMatch}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\ConsAllmatch}\xdef\textc@l@r{\ConsTextAllmatch}% + \def\res@@style{\csname relax\endcsname}% + \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}% + \def\res@@style{\csname relax\endcsname}% + \else\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% + \def\res@@style{\csname relax\endcsname}% + \fi\fi\fi% + \xdef\first@{#3@}% + \xdef\second@{#2}% + \ifx\second@\comm@% + \def\temp@{\res@style}% + \expandafter\get@second@\first@% + \else% + \def\temp@{\csname relax\endcsname}% + \fi% + \textcolor{\boxc@l@r}{\box@rule}% + \ifhidechar% + \ifx\second@\o@% + \def\second@{\gap@rule}% + \hbox to -\box@width{\hss\textcolor{\textc@l@r}% + {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% + \kern\box@width% + \fi% + \else% + \ifx\second@\o@\def\second@{\gap@rule}\fi% + \hbox to -\box@width{\hss\textcolor{\textc@l@r}% + {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% + \kern\box@width\fi% +} +\def\put@cons{% + \ifnum\innerloopcount>\res@perline + \else + \expandafter\next@cons\first@ + \advance\innerloopcount by 1 + \put@cons% + \fi} +\def\put@line{% + \ifnames@right\else\def\@kern{\kern0em}\expandafter\put@name\first@\fi + \ifnumbers@left\def\@kern{\kern1em}\expandafter\put@number\first@\fi + \fontfamily{\residues@family}% + \fontseries{\residues@series}% + \fontshape{\residues@shape}% + \selectfont% + \ifx\cons@now\y@% + \innerloopcount=1\relax\put@cons% + \else + \innerloopcount=1\relax\put@char% + \fi + \ifnumbers@left\else\def\@kern{\kern0em}\expandafter\put@number\first@\fi + \ifnames@right\def\@kern{\kern1em}\expandafter\put@name\first@\fi + \newline\hbox{}% +} + +\def\set@consensus{% + \ifnames@right + \ifnumbers@left + \xdef\consensus{)\consensus<\cons@name>}% + \else + \xdef\consensus{\consensus)<\cons@name>}% + \fi + \else + \ifnumbers@left + \xdef\consensus{<\cons@name>)\consensus}% + \else + \xdef\consensus{<\cons@name>\consensus)}% + \fi + \fi} + +\def\get@rulenum<#1>#2@{% + \xdef\first@{#2@}% + \ifcase\rule@top + \def\third@{\ensuremath{\,\stackrel{\mathtt{#1}}{.}}}% + \else + \def\third@{\bottomruler@size\ensuremath{\,\stackrel{.}{\mathtt{#1}}}}% + \fi} + +\def\next@rulechar#1#2@{% + \xdef\third@{#1}% + \xdef\first@{#2@}% + \xdef\second@{!}% + \ifx\third@\second@ \expandafter\get@rulenum\first@% + \else \xdef\third@{}\fi + \hbox to \box@width{\hss\third@\hss}% + } + +\def\put@rulechar{% + \ifnum\innerloopcount>\res@perline + \else + \expandafter\next@rulechar\first@ + \advance\innerloopcount by 1 + \put@rulechar% + \fi} + +\def\put@ruler{% + \ifnames@right + \ifnumbers@left \xdef\ruler@{)\ruler@<>}\else\xdef\ruler@{\ruler@)<>}\fi + \else + \ifnumbers@left \xdef\ruler@{<>)\ruler@}\else\xdef\ruler@{<>\ruler@)}\fi + \fi + \xdef\first@{\ruler@ @}% + \ifnames@right\else\def\@kern{\kern0em}\expandafter\put@name\first@\fi + \ifnumbers@left\def\@kern{\kern1em}\expandafter\put@number\first@\fi + \vspace{-0.25\baselineskip}% + \innerloopcount=1\relax\textcolor{\ruler@fg}{\put@rulechar}% + \newline\hbox{}% +} +\def\get@firstfill#1#2&{\xdef\second@@{#1}\xdef\fill@char{#2&}} +\def\get@firstv@l#1,#2&{\xdef\second@@{#1}\xdef\fill@char{#2&}} +\def\get@tripletfill#1#2#3#4&{% + \multiply\temp@count by -1% + \def\second@@{#1}\def\second@@@{#2}\def\second@@@@{#3}\def\fill@char{#4&}} +\def\putfeature@style#1{% + \residues@size% + \setbox1=\hbox{\ensuremath{\overrightarrow{\hbox{}}}}% + \arrow@height=\ht1% + \arrow@width=\wd1% + \xdef\second@@{#1}% + \xdef\last@{\second@@::&}\expandafter\test@fill\last@% + \xdef\last@{empty}% + \ifx\second@@\last@% + \hbox to \second@\box@width{\hss}% + \else% + \xdef\last@{translate}% + \ifx\second@@\last@% + \fontfamily{\featurestyles@family}% + \fontseries{\featurestyles@series}% + \fontshape{\featurestyles@shape}% + \selectfont% + \xdef\fill@char{\fill@char &}% + \if\seq@type N% + \loop% + \expandafter\get@firstfill\fill@char% + \if\second@@ -\def\second@@{\hss}\fi% + \hbox to \box@width{\hss\textcolor{\f@color}{\featurestyles@size{\second@@}}\hss}% + \ifx\fill@char\ampers@nd\else\repeat% + \else% + \temp@count=1% + \loop% + \expandafter\get@tripletfill\fill@char% + \if\second@@ -\ifnum\tr@nsstyle>0\hbox to \box@width{\hss}\fi% + \else% + \ifcase\tr@nsstyle% + \hbox{\trans@size\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\,\hss}}% + \or% + \ifnum\temp@count=1% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% + \else% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}}% + \fi% + \or% + \ifnum\temp@count=1% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss}}}% + \else% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\hss}}% + \hbox to \box@width{\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\hss}}}% + \fi% + \or% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% + \or% + \vbox{\trans@size% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@\hss}}}% + \fi% + \fi% + \ifx\fill@char\ampers@nd\else\repeat% + \fi% + \else% + \xdef\last@{brace}% + \ifx\second@@\last@% + \xdef\last@{top}% + \textcolor{\f@color}{% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \xdef\last@{ttop}% + \ifx\bottop@\last@% + \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% + \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \raisebox{1.75\arrow@height}{\ensuremath{\underbrace{\hbox to % + \second@\box@width{}}}}% + \fi\fi}% + \else% + \xdef\last@{fill}% + \ifx\second@@\last@% + \fontfamily{\featurestyles@family}% + \fontseries{\featurestyles@series}% + \fontshape{\featurestyles@shape}% + \selectfont% + \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi% + \kern0.15\box@width% + \loopcount=0\relax% + \loop% + \advance\loopcount by 1\relax% + \raisebox{\last@\arrow@height}{% + \hbox to \box@width{\hss{\textcolor{\f@color}{\featurestyles@size\fill@char}}\hss}}% + \ifnum\loopcount<\second@ \repeat% + \else% + \xdef\last@{bar}% + \ifx\second@@\last@% + \setlength\arrow@width{\pm@shift\box@height}% + \setlength\arrow@width{\b@r@stretch\arrow@width}% + \ifx\fill@char\N@% + \raisebox{\pm@shift\box@height}{\vrule width\box@width}% + \else% + \kern-0.6\box@width% + \ifx\frame@color\back@color% + \else% + \setlength\arrow@height{\box@height}% + \advance\arrow@height by -\pm@shift\box@height% + \setlength\arrow@height{\b@r@stretch\arrow@height}% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\back@color}{\vrule depth\arrow@width% + height\arrow@height width\box@width}}\hss}}% + \kern-\box@width% + \fi% + \setlength\arrow@height{\fill@char\box@height}% + \setlength\arrow@height{\b@r@stretch\arrow@height}% + \divide\arrow@height by 100\relax% + \ifdim\arrow@height<0pt% + \arrow@height=-\arrow@height% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\frame@color}{\vrule depth\arrow@height width0.8\box@width}}\hss}}% + \else% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\frame@color}{\vrule height\arrow@height width0.8\box@width}}\hss}}\fi% + \kern-\box@width% + \raisebox{\arrow@width}{\textcolor{Black}{\vrule height0.25pt depth0.25pt width\box@width}}% + \fi% + \else% + \xdef\last@{color}% + \ifx\second@@\last@% + \setlength\arrow@height{\fill@char\box@height}% + \setlength\arrow@height{\sc@le@stretch\arrow@height}% + \divide\arrow@height by 100\relax% + \raisebox{0.2\box@height}{% + \hbox to \box@width{\hss{\textcolor{\f@color}{\vrule height\arrow@height width\box@width}}\hss}}% + \else% + \xdef\last@{plotcolor}% + \ifx\second@@\last@% + \xdef\fill@char{\fill@char,&}% + \loop% + \expandafter\get@firstv@l\fill@char% + \ifx\second@@\N@\hbox to \box@width{\hss}% + \else + \loopcount=\second@@% + \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% + \setlength\arrow@height{50\box@height}% + \divide\arrow@height by 100\relax% + \setlength\arrow@height{\sc@le@stretch\arrow@height}% + \raisebox{0.2\box@height}{% + \hbox to \box@width{\hss{\textcolor{\f@color\the\loopcount}{\vrule height\arrow@height width\box@width}}\hss}}% + \fi + \ifx\fill@char\ampers@nd\else\repeat% + \else% + \xdef\last@{plotbar}% + \ifx\second@@\last@% + \xdef\fill@char{\fill@char,&}% + \ifnum\pm@shift>0% + \setlength\arrow@width{0pt}% + \else + \setlength\arrow@width{-\pm@shift\box@height}% + \divide\arrow@width by 100% + \setlength\arrow@width{\b@r@stretch\arrow@width}% + \fi% + \loop% + \expandafter\get@firstv@l\fill@char% + \ifx\second@@\N@\hbox to \box@width{\hss}% + \else\relax% + \ifx\frame@color\back@color% + \else% + \setlength\arrow@height{\b@r@stretch\box@height}% + \hbox to \box@width{\hss{\textcolor{\back@color}% + {\vrule height\arrow@height width\box@width}}\hss}% + \kern-\box@width% + \fi% + \setlength\arrow@height{\second@@\box@height}% + \divide\arrow@height by 100\relax% + \setlength\arrow@height{\b@r@stretch\arrow@height}% + \ifdim\arrow@height<0pt% + \arrow@height=-\arrow@height% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\frame@color}% + {\vrule depth\arrow@height width0.8\box@width}}\hss}}% + \else% + \raisebox{\arrow@width}{% + \hbox to \box@width{\hss{\textcolor{\frame@color}% + {\vrule height\arrow@height width0.8\box@width}}\hss}}\fi% + \kern-\box@width% + \raisebox{\arrow@width}{\textcolor{Black}% + {\vrule height0.25pt depth0.25pt width\box@width}}% + \fi + \ifx\fill@char\ampers@nd\else\repeat% + \else% + \xdef\last@{helix}% + \ifx\second@@\last@% + \fontfamily{\rmdefault}% + \fontseries{\mddefault}% + \fontshape{\itdefault}% + \selectfont% + \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi% + \kern0.15\box@width% + \setbox1=\hbox{\ensuremath{\smile}\kern-1.13exo\kern-1.02ex}% + \arrow@width=\second@\box@width% + \divide\arrow@width by \wd1% + \arrow@width=2\wd1% + \loop% + \textcolor{\f@color}{\raisebox{-0.25ex}{\ensuremath{\smile}}% + \kern-1.13ex\raisebox{0.3ex}{o}}\kern-1.02ex% + \advance\arrow@width by \wd1\relax% + \ifdim\arrow@width<\second@\box@width \repeat% + \textcolor{\f@color}{\raisebox{-0.25ex}{\ensuremath{\smile}}}% + \else% + \xdef\last@{box}% + \ifx\second@@\last@% + \fontfamily{\featurestyles@family}% + \fontseries{\featurestyles@series}% + \fontshape{\featurestyles@shape}% + \selectfont% + \kern-\second@\box@width% + \bgroup% + \textcolor{\back@color}{% + \vrule width\second@\box@width height\box@height depth\box@depth}% + \kern-\second@\box@width% + \fboxsep-\rule@@thick\fboxrule\rule@@thick% + \textcolor{\frame@color}{% + \fbox{\makebox[\second@\box@width]% + {\vrule\@height\box@height\@depth\box@depth \@width\z@}}}% + \egroup% + \setbox1=\hbox{\residues@size{\fill@char}}% + \temp@count=\wd1 \xdef\wd@{\the\temp@count}% + \width@tmp=\second@\box@width% + \temp@count=\width@tmp% + \xdef\sb@{\the\temp@count}% + \ifnum\wd@>\sb@ \xdef\fill@char{}\fi% + \hbox to -\second@\box@width{\hss\textcolor{\f@color}% + {\residues@size{\fill@char}}\hss}% + \else% + \expandafter\get@shape\second@@% + \xdef\last@{arrow}% + \ifx\second@@\last@% + \kern-0.75\box@width% + \ifx\bottop@\temp@ \xdef\last@{0.35}\else\xdef\last@{-0.55}\fi% + \textcolor{\f@color}{% + \raisebox{\last@\arrow@height}{% + \if\first@@ ,% + \rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height% + \else% + \if\first@@ |% + \rule{0.1\arrow@height}{2\arrow@height}\kern-0.35\arrow@height% + \else% + \if\first@@ `\xdef\first@@{'}\fi% + \if\first@@ '% + \rule[\arrow@height]% + {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height% + \else% + \if\first@@ -% + \rule{0pt}{0pt}\kern-0.35\arrow@height% + \fi% + \fi% + \fi% + \fi% + \if\third@@ v% + \if\first@@ v% + \ensuremath{\overleftarrow{\hbox to % + \second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% + \kern-\arrow@width% + \ensuremath{\overrightarrow{\hbox% + {\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% + \else% + \ensuremath{\overrightarrow{\hbox to % + \second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% + \fi% + \else% + \if\first@@ v% + \ensuremath{\overleftarrow{\hbox to % + \second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% + \else + \kern0.35\arrow@height% + \rule[0.9\arrow@height]{\second@\box@width}{0.1\arrow@height}% + \kern0.35\arrow@height% + \fi + \if\third@@ ,% + \kern-0.4\arrow@height\rule{0.1\arrow@height}{\arrow@height}% + \else% + \if\third@@ |% + \kern-0.4\arrow@height\rule{0.1\arrow@height}{2\arrow@height}% + \else% + \if\third@@ `\xdef\third@@{'}\fi% + \if\third@@ '% + \kern-0.4\arrow@height% + \rule[\arrow@height]{0.1\arrow@height}{\arrow@height}% + \fi% + \fi% + \fi% + \fi}}% + \else% + \xdef\last@{doublearrow}% + \ifx\second@@\last@% + \setbox1=\hbox{\ensuremath{\Rightarrow}}% + \arrow@height=\ht1% + \arrow@width=\wd1% + \setbox1=\hbox to \second@\box@width{}% + \width@tmp=\wd1% + \kern-0.75\box@width% + \xdef\temp@{top}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\temp@{ttop}% + \ifx\bottop@\temp@ \xdef\last@{0.25}% + \else% + \xdef\last@{-0.25}\fi\fi% + \textcolor{\f@color}{% + \raisebox{\last@\arrow@height}{% + \if\first@@ ,% + \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% + \kern-0.1\arrow@height% + \else% + \if\first@@ |% + \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}% + \kern-0.1\arrow@height% + \else% + \if\first@@ `\xdef\first@@{'}\fi% + \if\first@@ '% + \rule[0.4\arrow@height]% + {0.1\arrow@height}{1.5\arrow@height}% + \kern-0.1\arrow@height% + \else% + \if\first@@ <% + \ensuremath{\Leftarrow}\kern-0.5\arrow@width% + \advance\width@tmp by -0.5\arrow@width + \else + \rule{0pt}{0pt}% + \fi% + \fi% + \fi% + \fi% + \if\third@@ >% + \advance\width@tmp by -0.5\arrow@width% + \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}% + \kern-\width@tmp% + \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}% + \kern-0.5\arrow@width\ensuremath{\Rightarrow}% + \else% + \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}% + \kern-\width@tmp% + \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}% + \if\third@@ ,% + \kern-0.05\arrow@height% + \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% + \else% + \if\third@@ |% + \kern-0.05\arrow@height% + \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}% + \else% + \if\third@@ `\xdef\third@@{'}\fi% + \if\third@@ '% + \kern-0.05\arrow@height% + \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% + \fi% + \fi% + \fi% + \fi}}% + \else + \loopcount=0\relax% + \width@tmp=\arrow@height% + \temp@@length=\rule@@thick% + \advance\width@tmp by -0.5\temp@@length% + \if\first@@ o\xdef\first@@{O}\fi% + \if\third@@ o\xdef\third@@{O}\fi% + \ifx\bottop@\temp@ \else \advance\width@tmp by -0.4\arrow@height\fi% + \textcolor{\f@color}{% + \if\first@@ ,% + \rule{\temp@@length}{\arrow@height}\kern-\temp@@length% + \else% + \if\first@@ |% + \rule{\temp@@length}{2\arrow@height}\kern-\temp@@length% + \else% + \if\first@@ O% + \raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex% + \rule[\width@tmp]{0.65ex}{\temp@@length}% + \else% + \if\first@@ <% + \raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex% + \else + \if\first@@ `\xdef\first@@{'}\fi% + \if\first@@ '% + \advance\width@tmp by 0.5\temp@@length% + \rule[\width@tmp]{\temp@@length}{\arrow@height}\kern-\temp@@length% + \advance\width@tmp by -0.5\temp@@length% + \fi% + \fi% + \fi% + \fi% + \fi% + \loopcount=\second@% + \if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% + \xdef\second@{\the\loopcount}% + \rule[\width@tmp]{\second@\box@width}{\temp@@length}% + \if\third@@ ,% + \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% + \else% + \if\third@@ |% + \kern-\temp@@length\rule{\temp@@length}{2\arrow@height}% + \else% + \if\third@@ O% + \rule[\width@tmp]{0.65ex}{\temp@@length}% + \kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}% + \else% + \if\third@@ >% + \kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}% + \else + \if\third@@ `\xdef\third@@{'}\fi% + \if\third@@ '% + \advance\width@tmp by 0.5\temp@@length% + \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}% + \fi% + \fi% + \fi% + \fi + \fi}% + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi + \fi +} +\def\next@featuretext#2;#3@{% + \xdef\first@{#3@}% + \xdef\last@{#2::&}\expandafter\test@fill\last@% + \ifx\f@color\comm@\xdef\f@color{Black}\fi% + \fontfamily{\featuretext@family}% + \fontseries{\featuretext@series}% + \fontshape{\featuretext@shape}% + \selectfont% + \xdef\last@{translate}% + \ifx\last@\second@@% + \xdef\fill@char{\fill@char &}% + \if\seq@type N + \loop% + \expandafter\get@firstfill\fill@char% + \if\second@@ -\def\second@@{\hss}\fi% + \hbox to \box@width{\hss\textcolor{\f@color}{% + \featuretext@size{\strut\second@@}}\hss}% + \ifx\fill@char\ampers@nd\else\repeat% + \else + \hbox to #1\box@width{\hss% + \temp@count=1% + \loop% + \expandafter\get@tripletfill\fill@char% + \if\second@@ -\ifnum\tr@nstextstyle>0\hbox to \box@width{\hss}\fi% + \else% + \ifcase\tr@nstextstyle% + \hbox{\transtext@size\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\,\hss}}% + \or% + \ifnum\temp@count=1% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% + \else% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}}% + \fi% + \or% + \ifnum\temp@count=1% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss}}}% + \else% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\hss}}% + \hbox to \box@width{\textcolor{\f@color}% + {\hss\second@@\second@@@\second@@@@\hss}}}% + \fi% + \or% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% + \or% + \vbox{\transtext@size% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% + \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@\hss}}}% + \fi% + \fi% + \ifx\fill@char\ampers@nd\else\repeat% + \hss} + \fi% + \else% + \textcolor{\f@color}{% + \hbox to #1\box@width{\hss\featuretext@size{\strut\fourth@}\hss}}% + \fi% +} +\def\put@featuretext{% + \if\first@ @% + \else + \expandafter\next@featuretext\first@% + \put@featuretext% + \fi} +\def\next@featurestyle#2;#3@{% + \xdef\first@{#2}% + \xdef\second@{#1}% + \ifx\first@\ampers@nd \hbox to \second@\box@width{\hss}% + \else% + \hbox to \second@\box@width% + {\hss\expandafter\putfeature@style{\first@}\hss}\fi% + \xdef\first@{#3@}% +} +\def\put@featurestyle{% + \if\first@ @% + \else + \expandafter\next@featurestyle\first@% + \put@featurestyle% + \fi +} +\def\put@feature{% + \vspace{-\baselineskip}% + \newline\hbox{}% + \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\temp@{ttop}% + \ifx\temp@\bottop@% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \put@featuretext% + \else% + \xdef\temp@{top}% + \ifx\temp@\bottop@% + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \put@featuretext% + \else + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \put@featurestyle% + \fi\fi% + \newline\hbox{}% + \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \ifx\temp@\bottop@% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \put@featurestyle% + \else% + \xdef\temp@{ttop}% + \ifx\temp@\bottop@% + \xdef\first@{\csname stylefeature\bottop@\endcsname @}% + \put@featurestyle% + \else + \xdef\first@{\csname textfeature\bottop@\endcsname @}% + \put@featuretext% + \fi\fi% + \newline\hbox{}% +} +\def\put@@@frame#1{% + \xdef\last@{#1[,]&}\expandafter\opt@color\last@% + \xdef\second@@{\fourth@}% + \ifx\f@color\comm@% + \xdef\third@@{0.2\box@width}% + \else% + \xdef\third@@{\f@color}% + \fi% + \setlength\arrow@width{\temp@@length}% + \advance\arrow@width by -\third@@% + \textcolor{\second@@}{% + \rule{\second@\box@width}{\third@@}% + \kern-\second@\box@width% + \rule{\third@@}{\arrow@width}% + \kern-\third@@% + \rule[\arrow@width]{\second@\box@width}{\third@@}% + \kern-\third@@% + \rule{\third@@}{\arrow@width}}% +} +\def\next@frame#2;#3@{% + \xdef\first@{#2}% + \xdef\second@{#1}% + \ifx\first@\ampers@nd \hbox to \second@\box@width{\hss}% + \else% + \expandafter\put@@@frame{\first@}% + \fi% + \xdef\first@{#3@}% +} +\def\put@@frame{% + \if\first@ @% + \else + \expandafter\next@frame\first@% + \put@@frame% + \fi% +} +\def\put@frame{% + \temp@count=\seq@count% + \setlength\temp@@length{\box@height}% + \advance\temp@@length by \box@depth% + \setlength\arrow@height{0.5\temp@@length}% + \setlength\temp@@length{\temp@count\temp@@length}% + \advance\temp@@length by \arrow@height% + \setlength\arrow@width{\sep@space}% + \setlength\arrow@width{\seq@gap@num\arrow@width}% + \advance\temp@@length by \arrow@width% + \vspace{\arrow@height}% + \vspace{-\temp@@length}% + \vspace{-\baselineskip}% + \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi% + \newline\hbox{}% + \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi% + \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% + \xdef\first@{\styleframe @}% + \put@@frame% + \vspace{-\arrow@height}% + \ifshow@cons\ifnum\cons@top=1 \vspace{\baselineskip}\fi\fi% + \newline\hbox{}% +} +\def\set@lines{% + \pos@count=1 + \xdef\frame@pos{1}% + \xdef\featurepostop{1}\xdef\featureposbottom{1}% + \xdef\featureposttop{1}\xdef\featureposbbottom{1}% + \findc@nsensus% + \noindent% + \ifnum\feature@ttop=1 + \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi + \xdef\bottop@{ttop}% + \put@feature% + \vspace{\tt@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\ifttopfeature \vspace{\tt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi + \ifnum\feature@top=1 + \ifnum\featureontop=0 \xdef\feature@top{0} \fi + \xdef\bottop@{top}% + \put@feature% + \vspace{\t@sp@ce}% + \vspace{-\baselineskip}% + \newline\hbox{}% + \else + \iffix@\iftopfeature \vspace{\t@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi + \fi + \ifnum\rule@num<0 \else \ifnum\rule@top=0 \loopcount=0 \put@ruler \fi\fi + \set@consensus + \ifshow@cons\ifnum\cons@top=0 + \xdef\cons@now{y}% + \xdef\first@{\consensus @}% + \xdef\first@@@{\c@nscol @}% + \loopcount=0\relax% + \put@line% + \xdef\c@nscol{}% + \xdef\cons@now{no}% + \fi\fi + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\second@{\csname hide@seq\the\loopcount\endcsname}% + \xdef\first@{noshade}\nosh@defalse% + \ifx\second@\first@ \nosh@detrue \xdef\second@{false}\fi + \xdef\first@{false}% + \ifx\second@\first@ + \ifnames@right + \ifnumbers@left + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + <\csname newseqname\the\loopcount\endcsname>}% + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + \the\csname res@count\the\loopcount\endcsname)% + <\csname newseqname\the\loopcount\endcsname>}% + \fi + \else + \ifnumbers@left + \else + \expandafter\xdef\csname seq\the\loopcount\endcsname{% + \csname seq\the\loopcount\endcsname% + \the\csname res@count\the\loopcount\endcsname)}% + \fi + \fi + \xdef\first@{\csname seq\the\loopcount\endcsname @}% + \expandafter\ifx\csname seq@gap\the\loopcount\endcsname\yes% + \ifnum\finger@linenum=0\seq@skip% + \else% + \ifnum\loopcount<\seq@count\seq@skip\fi% + \fi% + \fi% + \put@line% + \fi + \ifnum\loopcount<\seq@count\repeat + \ifshow@cons\ifnum\cons@top=1 + \xdef\cons@now{y}% + \xdef\first@{\consensus @}% + \xdef\first@@@{\c@nscol @}% + \loopcount=0\relax% + \put@line% + \xdef\c@nscol{}% + \xdef\cons@now{no}% + \fi\fi + \ifnum\frame@=1 + \ifnum\frame@on=0 \xdef\frame@{0}\fi + \put@frame + \fi + \ifnum\rule@num<0 + \else + \ifnum\rule@top=1 + \loopcount=0\relax% + \put@ruler% + \vspace{0.25\baselineskip}% + \fi + \fi + \ifnum\feature@bottom=1 + \ifnum\featureonbottom=0 \xdef\feature@bottom{0}\fi + \xdef\bottop@{bottom}% + \vspace{\b@sp@ce}% + \if\bottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature + \else + \iffix@ + \if\bottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbottomfeature + \vspace{\b@sp@ce}\newline\hbox{}\newline\hbox{} + \fi + \fi + \fi + \ifnum\feature@bbottom=1 + \ifnum\featureonbbottom=0 \xdef\feature@bbottom{0}\fi + \xdef\bottop@{bbottom}% + \vspace{\bb@sp@ce}% + \if\bbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \put@feature + \else + \iffix@ + \if\bbottom@stretch y% + \vspace{-\box@height}% + \vspace{\b@r@stretch\box@height}% + \fi% + \ifbbottomfeature + \vspace{\bb@sp@ce}\newline\hbox{}\newline\hbox{} + \fi + \fi + \fi + \xdef\consensus{} \xdef\ruler@{} + \xdef\styleframe{} + \xdef\textfeaturetop{} \xdef\textfeaturebottom{} + \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} + \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} + \xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{} + \loopcount=0 + \loop + \advance\loopcount by 1 + \xdef\seq@line{\csname sequence\the\loopcount\endcsname} + \expandafter\remove@fromseq\seq@line + \ifnum\loopcount<\seq@count \repeat} + +\def\block@output{% + \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax + \message{.} + \ifx\out@put\y@ + \vbox{\set@lines}\par +\block@skip + \else + \pos@count=1 + \findc@nsensus + \loopcount=0 + \loop + \advance\loopcount by 1\relax + \xdef\seq@line{\csname sequence\the\loopcount\endcsname} + \expandafter\remove@fromseq\seq@line + \ifnum\loopcount<\seq@count \repeat + \fi + \ifstop@ + \else + \advance\seq@pointer by -\res@perline + \ifnum\seq@pointer>\res@perline \block@output \fi + \fi + \fi} + +%%%%% Basic input routines + +\def\savedseqlength#1#2#3{% + \expandafter\xdef\csname savelength#1seq#2\endcsname{#3}} + +\def\set@savedseqlength{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\ifx% + \csname savelength\@lign@count seq\the\loopcount\endcsname\relax + \else + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{% + \csname savelength\@lign@count seq\the\loopcount\endcsname} + \fi + \ifnum\loopcount<\seq@count\repeat +} + +\def\save@lengths{% + \loopcount=0 + \loop + \advance\loopcount by 1\relax + \immediate\write\@auxout{% + \string\savedseqlength{\@lign@count}{\the\loopcount}% + {\expandafter\the\csname res@count\the\loopcount\endcsname}} + \ifnum\loopcount<\seq@count \repeat +} + +\def\do@cleanup{% + \expandafter\firstchar@get\third@ + \expandafter\check@char\first@ + \ifletter + \xdef\second@{\second@\first@} + \else + \ifnumber + \ifx\first@\gre@ter + \xdef\second@{\second@{$>$}} + \else + \ifx\first@\sm@ller + \xdef\second@{\second@{$<$}} + \else + \xdef\second@{\second@\first@} + \fi\fi + \else + \ifnum\code@num=6 + \xdef\second@{\second@\#} + \else + \ifnum\code@num=14 + \xdef\second@{\second@\%} + \else + \xdef\second@{\second@\noexpand\string\first@} + \fi\fi + \fi + \fi + \ifx\third@\@t \else \do@cleanup \fi +} + +\def\cleanup@name{% + \xdef\third@{\csname seqname\the\loopcount\endcsname @} + \xdef\second@{} + \do@cleanup + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{\second@} +} + +\def\clear@seq{% + \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\def\csname sequence\the\loopcount\endcsname{} + \ifnum\loopcount<\seq@count \repeat + \xdef\consensus{} + \xdef\constopo{} + \xdef\frame@on{0} + \xdef\textfeaturetop{} \xdef\featureontop{0} + \xdef\textfeaturettop{} \xdef\featureonttop{0} + \xdef\textfeaturebottom{} \xdef\featureonbottom{0} + \xdef\textfeaturebbottom{}\xdef\featureonbbottom{0} + \xdef\styleframe{} + \xdef\stylefeaturetop{} + \xdef\stylefeaturettop{} + \xdef\stylefeaturebottom{} + \xdef\stylefeaturebbottom{}} +\def\do@count{% + \expandafter\res@get\seq@line + \if\first@\ampers@nd + \else + \advance\innerloopcount by 1 + \expandafter\check@char\first@ + \ifletter + \global\advance\csname res@count\the\loopcount\endcsname by 1 + \expandafter\ifnum\csname res@count\the\loopcount\endcsname=0 + \global\advance\csname res@count\the\loopcount\endcsname by 1 + \fi + \fi + \do@count + \fi} +\def\residue@@count{% + \xdef\seq@line{\csname sequence\the\loopcount\endcsname &@} + \innerloopcount=0 \do@count + \advance\loopcount by 1 + \ifnum\loopcount>\seq@count \else\residue@@count\fi} +\def\residue@count{% + \expandafter\res@get\seq@line + \if\first@\ampers@nd + \else + \advance\innerloopcount by 1 + \ifstart@ \advance\res@count by 1 + \else + \ifnum\start@seq=0 + \advance\end@count by 1 + \else + \expandafter\check@char\first@ + \ifletter \advance\end@count by 1 \fi + \fi + \ifnum\end@count=\start@num\relax + \xdef\start@number{\the\innerloopcount} + \ifnum\start@seq=0 + \cons@count=\start@number + \advance\cons@count by -1 + \fi + \start@true \res@count=1 + \fi + \fi + \residue@count + \fi} +\def\read@loop{% + \read\alignfile to \inline + \xdef\last@{\expandafter\string\inline} + \ifx\last@\par@ + \else + \xdef\inline{\inline @} + \expandafter\seq@get\inline + \ifstop@ + \else + \innerloopcount=\csname @rd\the\loopcount\endcsname\relax + \expandafter\ifx\csname seq@name\the\loopcount\endcsname\first@ + \expandafter\xdef\csname sequence\the\innerloopcount\endcsname{% + \csname sequence\the\innerloopcount\endcsname\seq@line} + \ifnum\start@seq=0 + \ifnum\loopcount=1 + \res@count=0 \innerloopcount=0 + \xdef\seq@line{\seq@line &@} \residue@count + \fi + \else + \ifnum\innerloopcount=\start@seq + \res@count=0 \innerloopcount=0 + \xdef\seq@line{\seq@line &@} \residue@count + \fi + \fi + \advance\loopcount by 1 + \ifnum\loopcount>\seq@count + \ifstart@ + \else + \loopcount=1\residue@@count\clear@seq + \fi + \advance\seq@pointer by \res@count + \ifnum\seq@pointer>\res@perline \block@output \fi + \loopcount=1 + \fi + \fi + \fi + \fi + \ifeof\alignfile \else \read@loop \fi} +\def\read@fasta{% + \read\alignfile to \inline + \xdef\last@{\expandafter\string\inline} + \ifx\last@\par@ + \else + \xdef\seq@line{\inline} + \xdef\inline{\inline @} + \expandafter\firstchar@get\inline + \ifstop@ + \else + \ifx\first@\gre@ter + \advance\loopcount by 1\relax + \expandafter\seq@get\third@ + \xdef\seq@name{\first@} + \xdef\second@{\first@ &} + \ifx\second@\ampers@nd \xdef\seq@name{seq\the\loopcount}\fi + \innerloopcount=\csname @rd\the\loopcount\endcsname\relax + \else + \expandafter\ifx\csname seq@name\the\loopcount\endcsname\seq@name + \expandafter\xdef\csname sequence\the\innerloopcount\endcsname{% + \csname sequence\the\innerloopcount\endcsname\seq@line} + \fi + \fi + \fi + \fi + \ifeof\alignfile + \ifnum\start@seq=0 + \xdef\seq@line{\csname sequence1\endcsname &@} + \else + \xdef\seq@line{\csname sequence\start@seq\endcsname &@} + \fi + \res@count=0 + \innerloopcount=0 + \residue@count + \advance\seq@pointer by \res@count + \ifnum\seq@pointer>\res@perline \block@output \fi + \else + \read@fasta + \fi} +\def\read@lines{% + \openin\alignfile = \alignfilename + \clear@seq + \ifnum\start@seq>0 + \xdef\start@seq{\csname @rd\start@seq\endcsname} \fi + \loopcount=\start@num + \advance\loopcount by -\csname res@count\start@seq\endcsname\relax + \expandafter\ifnum\csname res@count\start@seq\endcsname<\start@num\relax + \xdef\start@num{\the\loopcount} + \else \start@true \fi + \loopcount=\end@num + \advance\loopcount by -\csname res@count\start@seq\endcsname\relax + \res@count=0 \seq@pointer=0 \end@count=0 + \xdef\start@number{0} + \ifx\f@st@\y@ + \loopcount=0 + \read@fasta + \else + \loopcount=1 + \read@loop + \fi + \ifnum\seq@pointer>0 + \ifstop@ + \else + \res@count=\res@perline + \res@perline=\seq@pointer + \block@output + \fi + \fi + \message{)} + \closein\alignfile} + +%%%%% Read alignment, decide whether MSF or ALN, interpret + +\def\readalignfile#1{% + \def\alignfilename{#1} + \xdef\first@{byhand} + \ifx\alignfilename\first@ + \else + \openin\alignfile = #1 + \ifeof\alignfile + \PackageError{TeXshade} + {File `#1' not found} + {\MessageBreak + The alignment file you specified is missing or you have \MessageBreak + misspelled it. \MessageBreak\MessageBreak + Stop here, otherwise you're likely getting in trouble. \MessageBreak + Type X to quit. \MessageBreak +} + \else + \message{(\alignfilename :} + \xdef\seq@type{} \xdef\he@der{no} \xdef\f@st@{no} + \xdef\first@line{y} + \seq@count=0 \loopcount=0 \innerloopcount=0 \temp@count=0 + \loop + \read\alignfile to \inline + \xdef\test@{\expandafter\string\inline} + \ifx\test@\par@ \innerloopcount=0 + \else + \xdef\msfline{\inline & & & & @} + \expandafter\inf@@get\msfline + \ifx\first@\@msf \expandafter\type@get\msfline \fi + \ifx\second@\@msf \expandafter\type@get\msfline \fi + \ifx\third@\@msf \expandafter\type@get\msfline \fi + \ifx\first@\n@me \advance\loopcount by 1\relax + \expandafter\xdef\csname seqname\the\loopcount\endcsname{\second@} + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{\fourth@} + \fi + \ifx\first@\he@derend + \ifnum\loopcount>0 \xdef\he@der{yes} \fi + \fi + \xdef\alnline{\inline @} + \expandafter\check@letter\alnline + \ifletter + \expandafter\seq@get\alnline + \advance\innerloopcount by 1\relax + \seq@count=\innerloopcount + \expandafter\xdef\csname newseqname\the\seq@count\endcsname{\first@} + \else + \expandafter\firstchar@get\alnline + \ifx\first@\gre@ter + \ifx\first@line\y@ \xdef\f@st@{y}\fi + \expandafter\seq@get\third@ + \advance\temp@count by 1\relax + \xdef\second@{\first@ &} + \ifx\second@\ampers@nd \xdef\first@{seq\the\temp@count}\fi + \expandafter\xdef\csname seq@name\the\temp@count\endcsname{\first@} + \fi + \fi + \fi + \xdef\first@line{n} + \ifeof\alignfile \else\repeat + \closein\alignfile + \xdef\first@{no} + \ifx\he@der\first@ + \loopcount=0 + \ifx\f@st@\y@ + \seq@count=\temp@count \loopcount=0 + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname seqname\the\loopcount\endcsname{% + \csname seq@name\the\loopcount\endcsname} + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% + \csname seq@name\the\loopcount\endcsname} + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999} + \ifnum\loopcount<\seq@count \repeat + \else + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname seqname\the\loopcount\endcsname{% + \csname newseqname\the\loopcount\endcsname} + \expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999} + \ifnum\loopcount<\seq@count \repeat + \fi + \else + \seq@count=\loopcount \loopcount=0 \box@width=0pt + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% + \csname seqname\the\loopcount\endcsname} + \ifnum\loopcount<\seq@count \repeat + \fi + \set@savedseqlength + \ifnum\seq@count>\max@seqnumber \set@maxseqnumber\seq@count \fi + \loopcount=0 \xdef\seq@order{} + \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} + \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@bottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} + \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} + \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes} + \loop + \advance\loopcount by 1 + \expandafter\xdef\csname @rd\the\loopcount\endcsname{\the\loopcount} + \csname res@count\the\loopcount\endcsname=0 + \cleanup@name + \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} + \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} + \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{false} + \expandafter\xdef\csname hide@name\the\loopcount\endcsname{no} + \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} + \expandafter\xdef\csname hide@number\the\loopcount\endcsname{no} + \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes} + \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} + \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} + \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{no} + \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} + \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{0} + \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{0} + \ifnum\loopcount=1 \xdef\seq@order{\the\loopcount} + \else \xdef\seq@order{\seq@order,\the\loopcount}\fi + \ifnum\loopcount<\seq@count \repeat + \xdef\seq@order{\seq@order,@} + \killseq@count=\seq@count + \seq@percent=100 + \ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi + \if\seq@type P \xdef\prefix@{pep} + \else \if\seq@type p \xdef\prefix@{pep} \xdef\seq@type{P} + \else \seqtype{N} \xdef\prefix@{DNA} \fi\fi + \fi + \fi +} + +%%%%% TeXshade + +\def\calc@widths{% + \fontfamily{\residues@family} + \fontseries{\residues@series} + \fontshape{\residues@shape} + \selectfont + \setbox1=\hbox{\residues@size{W}}\box@width=\wd1 + \global\setlength\box@width{\char@stretch\box@width} + \box@height=1.2\ht1 + \setbox1=\hbox{\residues@size{g}}\box@depth=1.1\dp1 + \global\setlength\box@height{\line@stretch\box@height} + \global\setlength\box@depth{\line@stretch\box@depth} + \baselineskip=\box@height \advance\baselineskip by \box@depth + \lineskip=0pt + \ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi + \loopcount=0 + \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\getregion@fromtintstack{\the\loopcount} + \expandafter\getregion@fromemphstack{\the\loopcount} + \expandafter\getregion@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} + \fontfamily{\namestext@family} + \fontseries{\namestext@series} + \fontshape{\namestext@shape} + \selectfont + \loopcount=1 + \loop + \setbox1=\hbox{\namestext@size\csname newseqname\the\loopcount\endcsname} + \ifnum\wd1>\name@width \name@width=\wd1 \fi + \ifnum\ht1>\box@height + \box@height=1.1\ht1 + \global\setlength\box@height{\line@stretch\box@height} + \baselineskip=\box@height \advance\baselineskip by \box@depth + \fi + \ifnum\dp1>\box@depth + \box@depth=1.1\dp1 + \global\setlength\box@depth{\line@stretch\box@depth} + \baselineskip=\box@height \advance\baselineskip by \box@depth + \fi + \expandafter\getregion@fromstack{\the\loopcount} + \expandafter\getregion@fromtintstack{\the\loopcount} + \expandafter\getregion@fromemphstack{\the\loopcount} + \expandafter\getregion@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} + \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 + \fontfamily{\numbertext@family} + \fontseries{\numbertext@series} + \fontshape{\numbertext@shape} + \selectfont + \setbox1=\hbox{\numbertext@size\num@width} + \number@width=\wd1 + \advance\number@width by 1em + \loopcount=\textwidth + \ifnames@ \advance\loopcount by -\name@width \fi + \ifnumbers@ \advance\loopcount by -\number@width \fi + \divide\loopcount by \box@width + \divide\loopcount by 5 \multiply\loopcount by 5 + \ifrpl@fix\else + \ifnum\res@perline>\loopcount \res@perline=\loopcount\fi\fi + \ifnum\finger@linenum>0 + \width@tmp=\textwidth + \ifnames@ \advance\width@tmp by -\name@width \fi + \ifnumbers@ \advance\width@tmp by -\number@width \fi + \divide\width@tmp by \finger@linenum + \global\setlength\box@width{\width@tmp} + \fi + \center@fill=\textwidth + \ifnames@ \advance\center@fill by -\name@width \fi + \ifnumbers@ \advance\center@fill by -\number@width \fi + \width@tmp=\box@width \multiply\width@tmp by \res@perline + \advance\center@fill by -\width@tmp + \ifx\out@put\y@\leftskip\c@factor\center@fill\fi +} + +\def\multiple@dssp{% + \advance\loopcount by 1 + \include@DSSP + \ifnum\loopcount<\dssp@num\multiple@dssp\fi} + +\def\multiple@stride{% + \advance\loopcount by 1 + \include@stride + \ifnum\loopcount<\stride@num\multiple@stride\fi} + +\def\multiple@PHD{% + \advance\loopcount by 1 + \include@PHD + \ifnum\loopcount<\PHD@num\multiple@PHD\fi} + +\def\multiple@HMMTOP{% + \advance\loopcount by 1 + \include@HMMTOP + \ifnum\loopcount<\HMMTOP@num\multiple@HMMTOP\fi} + +\newenvironment{texshade}[2][&]% + {\standarddefinitions + \c@d@ns + \xdef\first@{#1}\ifx\first@\ampers@nd\else\input{#1}\fi + \readalignfile{#2} + }% + {\ifnum\seq@count>0 + \loopcount=0 + \ifnum\loopcount<\dssp@num \multiple@dssp\fi + \loopcount=0 + \ifnum\loopcount<\stride@num \multiple@stride\fi + \loopcount=0 + \ifnum\loopcount<\PHD@num \multiple@PHD\fi + \loopcount=0 + \ifnum\loopcount<\HMMTOP@num \multiple@HMMTOP\fi + \loopcount=1 \kill@seqnow + \reorder@seqs\seq@order \seq@count=\killseq@count + \ifnum\csname res@count\start@seq\endcsname<0 + \ifnum\start@num>0 + \loopcount=\start@num + \advance\loopcount by -1 + \xdef\start@num{\the\loopcount} + \fi + \fi + \ifnum\rule@num>0 + \loopcount=\csname res@count\rule@num\endcsname + \divide\loopcount by \ruler@step + \multiply\loopcount by \ruler@step + \ifnum\loopcount<0 \else \advance\loopcount by \ruler@step \fi + \xdef\rule@tens{\the\loopcount} + \else + \xdef\rule@tens{\ruler@step} + \fi + \xdef\first@{top} + \ifx\cap@pos\first@ + \xdef\@captype{figure} + \ifx\c@pshort\n@ + \caption{\c@p} + \else + \caption[\c@pshort]{\c@p} + \fi + \fi + \bgroup + \ifx\out@put\y@\bigskip\fi + \iffuncmode \show@consfalse \fi + \ifall@fshade \iffuncmode \else \all@fshadefalse \fi\fi + \ifnum\finger@linenum>0 + \show@consfalse + \hidechartrue + \message{} + \fi + \calc@widths + \read@lines + \save@lengths + \iflegend@ + \vspace{\vspace@legend} + \setbox1=\vbox{\do@legend} + \vbox{\do@legend}\par + \ifnum\ht1<-\vspace@legend + \vspace{-\ht1}\vspace{-\vspace@legend} + \fi + \fi + \egroup + \xdef\first@{bottom} + \ifx\cap@pos\first@ + \vspace{-\baselineskip} + \xdef\@captype{figure} + \ifx\c@pshort\n@ + \caption{\c@p} + \else + \caption[\c@pshort]{\c@p} + \fi + \fi + \fi} + +\def\standarddefinitions{% +\xdef\prfx{pep}\clear@groups\clear@sims +\xdef\prfx{DNA}\clear@groups\clear@sims +\clearfuncgroups +\loopcount=\@lign@count +\advance\loopcount by 1\relax +\xdef\@lign@count{\the\loopcount} +\start@true \xdef\start@num{1} \xdef\start@seq{0} +\stop@false \xdef\end@num{99999999} \xdef\seq@regions{0} +\cons@count=0 \csname res@count0\endcsname=0 +\regionalshadefalse\regionalemphfalse\regionaltintfalse +\frame@false +\topfeaturefalse\bottomfeaturefalse +\ttopfeaturefalse\bbottomfeaturefalse +\all@fshadefalse\hidecharfalse +\xdef\finger@linenum{0} +\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\frame@{0} +\xdef\show@Hdssp{no} \xdef\show@Gdssp{no} \xdef\show@Idssp{no} +\xdef\show@Edssp{no} \xdef\show@Bdssp{no} \xdef\show@Tdssp{no} +\xdef\show@Sdssp{no} +\xdef\show@Hstride{no} \xdef\show@Gstride{no} \xdef\show@Istride{no} +\xdef\show@Estride{no} \xdef\show@Bstride{no} \xdef\show@Tstride{no} +\xdef\show@itop{no} \xdef\show@etop{no} \xdef\show@TMtop{no} +\xdef\show@i@HMMTOP{no} \xdef\show@e@HMMTOP{no} \xdef\show@TM@HMMTOP{no} +\xdef\show@Hsec{no} \xdef\show@Esec{no} +\xdef\collect@restop{no} \xdef\collect@resttop{no} +\xdef\collect@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\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\c@nscol{} \xdef\c@nssc@le{ColdHot} +\xdef\collect@cons@colors{no} \xdef\cons@now{no} + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% +%%%%% %%%%% +%%%%% Under any circumstances: %%%%% +%%%%% %%%%% +%%%%% DO NOT CHANGE ANY SETTINGS !!! %%%%% +%%%%% %%%%% +%%%%% Please define your personal parameter file! Store your new file %%%%% +%%%%% together with this style-file in the same directory and load the %%%%% +%%%%% file by naming it as an optional parameter in the `texshade' en- %%%%% +%%%%% vironment. The file `texshade.def' can be used as a template for %%%%% +%%%%% the new creation. See the manual for further help. %%%%% +%%%%% %%%%% +%%%%% THANK YOU !!! %%%%% +%%%%% %%%%% +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +\shadingmode{identical} % Shade identical residues only +\shadingcolors{blues} % Select the blue color scheme for shading +\constoallseqs % Calculate consensus considering all seqs +\threshold{50} % Consensus threshold percentage is 50 +\residuesperline{999} % As many residues as possible per line +\numberingwidth{9999} % Assign space for 4 digit numbering +\charstretch{1.15} % Stretch character width 1.15fold +\linestretch{1} % Do not stretch lines +\gapchar{.} % . is printed in sequence gaps +\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt +\gapcolors{Black}{White} % Gap symbols appear `Black on White' +\numberingcolor{Black} % Numbering color is `Black' +\shownumbering{left} % Show sequence numbering on the left +\namescolor{Black} % Names' color is `Black' +\shownames{right} % Show sequence names on the right +\consensuscolors{Black}{White} % All consensus symbols/letters + {Black}{White} % appear `Black on White' + {Black}{White} % +\showconsensus{bottom} % Show consensus line at bottom with +\defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match +\showleadinggaps % Show gap symbols before sequence start +\rulercolor{Black} % Ruler's color is `Black' +\hideruler % Do not show the ruler +\rulersteps{10} % Ruler ticks every 10 residues +\legendcolor{Black} % Legend text color is `Black' +\hidelegend % Do not show the legend +\alignment{center} % Center alignment on page +\medsepline % Medium height if separation line is on +\medblockskip % Medium skip between sequence blocks +\flexblockspace % Use optimized space between blocks +\featurerule{0.5ex} % Set feature rule thickness to 1/2 ex +\bargraphstretch{1} % Do not stretch bars in feature graphs +\colorscalestretch{1} % Do not stretch color scales in features +\backtranstext{horizontal} % Horizontal triplets in feature texts +\backtranslabel{alternating} % Alternating triplets in feature styles +\setfamily{residues}{tt} % Use typewriter family for residues +\setseries{residues}{md} % Use normal series for residues +\setshape {residues}{up} % Use upright shape for residues +\setsize {residues}{normalsize} % Use normal size for residues +\setfamily{numbering}{tt} % Use typewriter family for numbering +\setseries{numbering}{md} % Use normal series for numbering +\setshape {numbering}{up} % Use upright shape for numbering +\setsize {numbering}{normalsize} % Use normal size for numbering +\setfamily{names}{tt} % Use typewriter family for names +\setseries{names}{md} % Use normal series for names +\setshape {names}{up} % Use upright shape for names +\setsize {names}{normalsize} % Use normal size for names +\setfamily{features}{rm} % Use roman family for feature texts +\setseries{features}{md} % Use normal series for feature texts +\setshape {features}{it} % Use italics shape for feature texts +\setsize {features}{normalsize} % Use normal size for feature texts +\setfamily{featurestyles}{tt} % Use typewriter family for feature styles +\setseries{featurestyles}{md} % Use normal series for feature styles +\setshape {featurestyles}{up} % Use upright shape for feature styles +\setsize {featurestyles}{normalsize}% Use normal size for feature styles +\setfamily{legend}{tt} % Use typewriter family for legend texts +\setseries{legend}{md} % Use normal series for legend texts +\setshape {legend}{up} % Use upright shape for legend texts +\setsize {legend}{normalsize} % Use normal size for legend texts +\tintdefault{medium} % Use medium tint intensity +\emphdefault{it} % Use italics to emphasize regions +\showonPHDsec{alpha,beta} % Show helices and strands (PHD input) +\showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input) +\showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input) +\showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input) +\showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input) +\secondcolumnDSSP % Use numbering from 2. column in DSSP +\appearance{PHDtopo}{internal} % \ + {bottom}{'-'} % \ + {int.\ \Alphacount} % | +\appearance{PHDtopo}{external} % | + {top}{,-,} % | + {ext.\ \Alphacount} % | +\appearance{PHDtopo}{TM}{top} % | + {box[LightGray]:TM\numcount}{} % | +\appearance{HMMTOP}{internal} % | + {bottom}{'-'} % | + {int.\ \Alphacount} % | +\appearance{HMMTOP}{external} % | + {top}{,-,} % | + {ext.\ \Alphacount} % | +\appearance{HMMTOP}{TM}{top} % | + {helix}{TM\numcount} % | +\appearance{PHDsec}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{PHDsec}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | Definitions for the appearance of +\appearance{STRIDE}{3-10}{top} % \ + {fill:$\circ$}{3$_{10}$} % > secondary structures included from| +\appearance{STRIDE}{pi} % / + {top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files. +\appearance{STRIDE}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{STRIDE}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{STRIDE}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{alpha}{top} % | + {box:$\alpha$\numcount}{} % | +\appearance{DSSP}{3-10}{top} % | + {fill:$\circ$}{3$_{10}$} % | +\appearance{DSSP}{pi} % | + {top}{---}{$\pi$} % | +\appearance{DSSP}{beta}{top} % | + {-->}{$\beta$\numcount} % | +\appearance{DSSP}{bridge} % | + {top}{fill:$\uparrow$}{} % | +\appearance{DSSP}{turn} % | + {top}{,-,}{turn} % | +\appearance{DSSP}{bend}{top} % / + {fill:$\diamond$}{} % / + +\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity + +\pepsims{F}{YW} % Y and W are similar to F +\pepsims{Y}{WF} % W and F are similar to Y +\pepsims{W}{YF} % Y and F are similar to W + +\pepsims{I}{LVM} % L, V and M are similar to I +\pepsims{L}{VMI} % V, M and I are similar to L +\pepsims{V}{MIL} % M, I and L are similar to V + +\pepsims{R}{KH} % K and H are similar to R +\pepsims{K}{HR} % H and R are similar to K +\pepsims{H}{RK} % R and K are similar to H + +\pepsims{A}{GS} % G and S are similar to A +\pepsims{G}{A} % A (but not S) is similar to G + +\pepsims{S}{TA} % T and A are similar to S +\pepsims{T}{S} % S (but not A) is similar to T + +\pepsims{D}{EN} % E and N (but not Q) are similar to D +\pepsims{E}{DQ} % D and Q (but not N) are similar to E +\pepsims{N}{QD} % Q and D (but not E) are similar to N +\pepsims{Q}{NE} % N and E (but not D) are similar to Q + +\DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity + +\DNAsims{A}{GR} % G and R are similar to A +\DNAsims{G}{AR} % A and R are similar to G +\DNAsims{R}{AG} % A and G are similar to R + +\DNAsims{C}{TY} % T and Y are similar to C +\DNAsims{T}{CY} % C and Y are similar to T +\DNAsims{Y}{CT} % C and T are similar to Y + +} +\catcode`\@=12 +\endinput +%% +%% End of file `texshade.sty'. -- cgit v1.2.3