%% %% 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) 1999-2011 Eric Beitz %% See the file texshade.txt %% \NeedsTeXFormat{LaTeX2e} \ProvidesPackage{texshade}[2018/01/17 LaTeX TeXshade (v1.25)] \message{Package `texshade', Version 1.25 of 2018/01/17.} \PassOptionsToPackage{dvips}{color} \PassOptionsToPackage{dvips}{graphicx} \DeclareOption*{% \PassOptionsToPackage{\CurrentOption}{color}% \PassOptionsToPackage{\CurrentOption}{graphicx}% } \ProcessOptions \RequirePackage{color,graphics} \expandafter\ifx\csname TeXshade\endcsname\relax \else \endinput \fi \expandafter\ifx\csname TeXtopo\endcsname\relax \else \PackageError{TeXtopo} {TeXtopo loaded before TeXshade} {\MessageBreak For the proper function of the TeXtopo/TeXshade combo the \MessageBreak TeXshade package must be loaded before the TeXtopo package.\MessageBreak Please change the order of the \noexpand\usepackage commands in your \MessageBreak document header section or use the `biotex.sty'.\MessageBreak\MessageBreak Quit here by typing \space X . \MessageBreak } \fi \catcode`\@11 \def\rotopo#1{% \Grot@setangle{#1}% \setbox\z@\hbox\bgroup\ignorespaces} \def\endrotopo{% \unskip\egroup \Grot@x\z@ \Grot@y\z@ \wd0\z@\dp0\z@\ht0\z@ \Grot@box } \newread\structurefile \newwrite\featurefile \newread\alignfile \newread\sublogofile \newwrite\exp@rtfile \expandafter\ifx\csname blacktriangleright\endcsname\relax \openin\structurefile = amssymb.sty \ifeof\structurefile \message{} \def\blacktriangleright{% \rule[\width@tmp]{0.65ex}{\temp@@length}\kern-0.55ex\ensuremath{\bullet}% } \def\blacktriangleleft{% \ensuremath{\bullet}\kern-0.55ex\rule[\width@tmp]{0.65ex}{\temp@@length}% } \else \RequirePackage[]{amssymb} \fi \closein\structurefile \fi \DeclareSymbolFont{alphahelix}{OML}{cmm}{m}{it} \DeclareMathSymbol{\helixhook}{\mathrel}{alphahelix}{"5E} \newcount\loopcount \newcount\innerloopcount \newcount\outerloopcount \newcount\seq@count \newcount\killseq@count \newcount\seq@percent \newcount\res@count \newcount\seq@pointer \newcount\pos@count \newcount\res@perline \newcount\end@count \newcount\cons@count \newcount\total@count \newcount\temp@count \newcount\triple@count \newcount\temp@@count \newcount\pos@sum \newlength\box@width \newlength\name@width \newlength\box@depth \newlength\width@tmp \newlength\box@height \newlength\number@width \newlength\line@stretch \newlength\center@fill \newlength\arrow@width \newlength\arrow@height \newlength\rule@thick \newlength\arrow@thick \newlength\logo@height \newlength\equal@width \newlength\equal@tmp \newlength\equal@height \newlength\temp@@length \newlength\vspace@legend \newlength\hspace@legend \newlength\bar@length \newif\ifletter \newif\ifnumber \newif\ifnewres \newif\ifall@shade \newif\ifnames@right \newif\ifnumbers@left \newif\ifnumbers@right \newif\ifhide@cons \newif\ifshow@cons \newif\iffuncmode \newif\iflegend@ \newif\ifT@coffee \newif\ifnumbers@ \newif\ifnames@ \newif\ifgerm@n \newif\ifsp@nish \newif\ifrpl@fix \newif\ifnosh@de \newif\ifregionalshade \newif\ifstart@ \newif\ifstop@ \newif\iftopfeature \newif\ifbottomfeature \newif\ifttopfeature \newif\ifbbottomfeature \newif\iftttopfeature \newif\ifbbbottomfeature \newif\ifttttopfeature\newif\ifbbbbottomfeature \newif\ifall@fshade \newif\ifregionalemph \newif\ifregionallower \newif\ifframe@ \newif\ifregionaltint \newif\ifshading@ \newif\ifshow@logo \newif\ifshow@sublogo \newif\ifhidechar \newif\ifsh@wg@ps \newif\ifsimmode \newif\ifregionaltintnow \newif\ifregionalemphnow \newif\ifregionallowernow \newif\ifregionalshadenow \newif\iftopfeaturenow \newif\ifttopfeaturenow \newif\iftttopfeaturenow \newif\ifttttopfeaturenow \newif\ifbottomfeaturenow \newif\ifbbottomfeaturenow \newif\ifbbbottomfeaturenow \newif\ifbbbbottomfeaturenow \newif\ifframenow \newif\ifshadingnow \newif\iffix@ \expandafter\ifx\csname mdqon\endcsname\relax \germ@nfalse \sp@nishfalse \def\cons@name{consensus} \else \germ@ntrue \sp@nishfalse \def\cons@name{Konsensus} \fi \def\n@me{Name:} \def\@msf{MSF:} \def\he@derend{//} \def\ampers@nd{&} \def\comm@{,} \def\@loc{LOC} \def\@asg{ASG} \def\@t{@} \def\@HP{>HP:} \def\gre@ter{>} \def\sm@ller{<} \def\N@{N} \def\equ@l{=} \def\H@{H} \def\gap@char{.} \def\dom@char{{\dom@rule}} \def\yes{yes} \def\y@{y} \def\n@{n} \def\o@{o} \def\d@t{.} \def\questi@n{?} \def\st@p@char{*} \def\semic@n{;} \def\br@cket{[} \def\p@r@gr@ph{¤} \def\@TOM{ATOM} \def\C@lpha{CA} \def\@point@{point} \def\@line@{line} \def\@plane@{plane} \def\gap@rule{\rule[0.3\box@height]{\box@width}{\gap@rulethick}} \def\dom@rule{\vrule depth\box@depth height\box@height width\domgap@rulethick} \def\fgroup@num{0} \def\max@seqnumber{0} \def\@lign@count{0} \def\resn@m@tch{upper} \def\ressimm@tch{upper} \def\resm@tch{upper} \def\res@llm@tch{upper} \def\tr@ns{translate} \def\gr@ydef@ult{GrayDefault} \xdef\par@{\expandafter\string\par} \expandafter\def\csname fg@textcolor/\endcsname{White} \expandafter\def\csname fg@color/\endcsname{White} \expandafter\def\csname func@style/\endcsname{\csname textup\endcsname} \expandafter\def\csname func@style*\endcsname{\csname textup\endcsname} \expandafter\def\csname funcm@tch/\endcsname{upper} \expandafter\def\csname funcm@tch*\endcsname{upper} \setlength\hspace@legend{0pt} \setlength\vspace@legend{0pt} \expandafter\xdef\csname log2@1\endcsname{0} \expandafter\xdef\csname log2@2\endcsname{1000} \expandafter\xdef\csname log2@3\endcsname{1585} \expandafter\xdef\csname log2@4\endcsname{2000} \expandafter\xdef\csname log2@5\endcsname{2322} \expandafter\xdef\csname log2@6\endcsname{2585} \expandafter\xdef\csname log2@7\endcsname{2807} \expandafter\xdef\csname log2@8\endcsname{3000} \expandafter\xdef\csname log2@9\endcsname{3170} \expandafter\xdef\csname log2@10\endcsname{3322} \expandafter\xdef\csname log2@11\endcsname{3459} \expandafter\xdef\csname log2@12\endcsname{3585} \expandafter\xdef\csname log2@13\endcsname{3700} \expandafter\xdef\csname log2@14\endcsname{3807} \expandafter\xdef\csname log2@15\endcsname{3907} \expandafter\xdef\csname log2@16\endcsname{4000} \expandafter\xdef\csname log2@17\endcsname{4087} \expandafter\xdef\csname log2@18\endcsname{4170} \expandafter\xdef\csname log2@19\endcsname{4248} \expandafter\xdef\csname log2@20\endcsname{4322} \expandafter\xdef\csname log2@21\endcsname{4392} \expandafter\xdef\csname log2@22\endcsname{4459} \expandafter\xdef\csname log2@23\endcsname{4524} \expandafter\xdef\csname log2@24\endcsname{4585} \expandafter\xdef\csname log2@25\endcsname{4644} \expandafter\xdef\csname log2@26\endcsname{4700} \expandafter\xdef\csname log2@27\endcsname{4755} \expandafter\xdef\csname log2@28\endcsname{4807} \expandafter\xdef\csname log2@29\endcsname{4858} \expandafter\xdef\csname log2@30\endcsname{4907} \expandafter\xdef\csname log2@31\endcsname{4954} \expandafter\xdef\csname log2@32\endcsname{5000} \expandafter\xdef\csname log2@33\endcsname{5044} \expandafter\xdef\csname log2@34\endcsname{5087} \expandafter\xdef\csname log2@35\endcsname{5129} \expandafter\xdef\csname log2@36\endcsname{5170} \expandafter\xdef\csname log2@37\endcsname{5209} \expandafter\xdef\csname log2@38\endcsname{5248} \expandafter\xdef\csname log2@39\endcsname{5285} \expandafter\xdef\csname log2@40\endcsname{5322} \expandafter\xdef\csname log2@41\endcsname{5358} \expandafter\xdef\csname log2@42\endcsname{5392} \expandafter\xdef\csname log2@43\endcsname{5426} \expandafter\xdef\csname log2@44\endcsname{5459} \expandafter\xdef\csname log2@45\endcsname{5492} \expandafter\xdef\csname log2@46\endcsname{5524} \expandafter\xdef\csname log2@47\endcsname{5555} \expandafter\xdef\csname log2@48\endcsname{5585} \expandafter\xdef\csname log2@49\endcsname{5615} \expandafter\xdef\csname log2@50\endcsname{5644} \expandafter\xdef\csname log2@51\endcsname{5672} \expandafter\xdef\csname log2@52\endcsname{5700} \expandafter\xdef\csname log2@53\endcsname{5728} \expandafter\xdef\csname log2@54\endcsname{5755} \expandafter\xdef\csname log2@55\endcsname{5781} \expandafter\xdef\csname log2@56\endcsname{5807} \expandafter\xdef\csname log2@57\endcsname{5833} \expandafter\xdef\csname log2@58\endcsname{5858} \expandafter\xdef\csname log2@59\endcsname{5883} \expandafter\xdef\csname log2@60\endcsname{5907} \expandafter\xdef\csname log2@61\endcsname{5931} \expandafter\xdef\csname log2@62\endcsname{5954} \expandafter\xdef\csname log2@63\endcsname{5977} \expandafter\xdef\csname log2@64\endcsname{6000} \expandafter\xdef\csname log2@65\endcsname{6022} \expandafter\xdef\csname log2@66\endcsname{6044} \expandafter\xdef\csname log2@67\endcsname{6066} \expandafter\xdef\csname log2@68\endcsname{6087} \expandafter\xdef\csname log2@69\endcsname{6109} \expandafter\xdef\csname log2@70\endcsname{6129} \expandafter\xdef\csname log2@71\endcsname{6149} \expandafter\xdef\csname log2@72\endcsname{6170} \expandafter\xdef\csname log2@73\endcsname{6190} \expandafter\xdef\csname log2@74\endcsname{6209} \expandafter\xdef\csname log2@75\endcsname{6229} \expandafter\xdef\csname log2@76\endcsname{6248} \expandafter\xdef\csname log2@77\endcsname{6267} \expandafter\xdef\csname log2@78\endcsname{6285} \expandafter\xdef\csname log2@79\endcsname{6304} \expandafter\xdef\csname log2@80\endcsname{6322} \expandafter\xdef\csname log2@81\endcsname{6340} \expandafter\xdef\csname log2@82\endcsname{6358} \expandafter\xdef\csname log2@83\endcsname{6375} \expandafter\xdef\csname log2@84\endcsname{6392} \expandafter\xdef\csname log2@85\endcsname{6409} \expandafter\xdef\csname log2@86\endcsname{6426} \expandafter\xdef\csname log2@87\endcsname{6443} \expandafter\xdef\csname log2@88\endcsname{6459} \expandafter\xdef\csname log2@89\endcsname{6476} \expandafter\xdef\csname log2@90\endcsname{6492} \expandafter\xdef\csname log2@91\endcsname{6508} \expandafter\xdef\csname log2@92\endcsname{6524} \expandafter\xdef\csname log2@93\endcsname{6539} \expandafter\xdef\csname log2@94\endcsname{6555} \expandafter\xdef\csname log2@95\endcsname{6570} \expandafter\xdef\csname log2@96\endcsname{6585} \expandafter\xdef\csname log2@97\endcsname{6600} \expandafter\xdef\csname log2@98\endcsname{6615} \expandafter\xdef\csname log2@99\endcsname{6629} \expandafter\xdef\csname log2@100\endcsname{6644} \expandafter\xdef\csname log2@101\endcsname{6658} \expandafter\xdef\csname log2@102\endcsname{6672} \expandafter\xdef\csname log2@103\endcsname{6687} \expandafter\xdef\csname log2@104\endcsname{6700} \expandafter\xdef\csname log2@105\endcsname{6714} \expandafter\xdef\csname log2@106\endcsname{6728} \expandafter\xdef\csname log2@107\endcsname{6741} \expandafter\xdef\csname log2@108\endcsname{6755} \expandafter\xdef\csname log2@109\endcsname{6768} \expandafter\xdef\csname log2@110\endcsname{6781} \expandafter\xdef\csname 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log2@151\endcsname{7238} \expandafter\xdef\csname log2@152\endcsname{7248} \expandafter\xdef\csname log2@153\endcsname{7257} \expandafter\xdef\csname log2@154\endcsname{7267} \expandafter\xdef\csname log2@155\endcsname{7276} \expandafter\xdef\csname log2@156\endcsname{7285} \expandafter\xdef\csname log2@157\endcsname{7295} \expandafter\xdef\csname log2@158\endcsname{7304} \expandafter\xdef\csname log2@159\endcsname{7313} \expandafter\xdef\csname log2@160\endcsname{7323} \expandafter\xdef\csname log2@161\endcsname{7331} \expandafter\xdef\csname log2@162\endcsname{7340} \expandafter\xdef\csname log2@163\endcsname{7349} \expandafter\xdef\csname log2@164\endcsname{7358} \expandafter\xdef\csname log2@165\endcsname{7366} \expandafter\xdef\csname log2@166\endcsname{7375} \expandafter\xdef\csname log2@167\endcsname{7374} \expandafter\xdef\csname log2@168\endcsname{7392} \expandafter\xdef\csname log2@169\endcsname{7401} \expandafter\xdef\csname log2@170\endcsname{7409} \expandafter\xdef\csname log2@171\endcsname{7418} \expandafter\xdef\csname log2@172\endcsname{7463} \expandafter\xdef\csname log2@173\endcsname{7435} \expandafter\xdef\csname log2@174\endcsname{7443} \expandafter\xdef\csname log2@175\endcsname{7451} \expandafter\xdef\csname log2@176\endcsname{7460} \expandafter\xdef\csname log2@177\endcsname{7468} \expandafter\xdef\csname log2@178\endcsname{7476} \expandafter\xdef\csname log2@179\endcsname{7484} \expandafter\xdef\csname log2@180\endcsname{7492} \expandafter\xdef\csname log2@181\endcsname{7500} \expandafter\xdef\csname log2@182\endcsname{7508} \expandafter\xdef\csname log2@183\endcsname{7516} \expandafter\xdef\csname log2@184\endcsname{7524} \expandafter\xdef\csname log2@185\endcsname{7531} \expandafter\xdef\csname log2@186\endcsname{7539} \expandafter\xdef\csname log2@187\endcsname{7547} \expandafter\xdef\csname log2@188\endcsname{7555} \expandafter\xdef\csname log2@189\endcsname{7562} \expandafter\xdef\csname log2@190\endcsname{7570} \expandafter\xdef\csname log2@191\endcsname{7577} \expandafter\xdef\csname log2@192\endcsname{7585} \expandafter\xdef\csname log2@193\endcsname{7592} \expandafter\xdef\csname log2@194\endcsname{7600} \expandafter\xdef\csname log2@195\endcsname{7607} \expandafter\xdef\csname log2@196\endcsname{7615} \expandafter\xdef\csname log2@197\endcsname{7622} \expandafter\xdef\csname log2@198\endcsname{7629} \expandafter\xdef\csname log2@199\endcsname{7637} \expandafter\xdef\csname log2@200\endcsname{7644} \expandafter\xdef\csname log2@201\endcsname{7651} \expandafter\xdef\csname log2@202\endcsname{7658} \expandafter\xdef\csname log2@203\endcsname{7665} \expandafter\xdef\csname log2@204\endcsname{7672} \expandafter\xdef\csname log2@205\endcsname{7679} \expandafter\xdef\csname log2@206\endcsname{7687} \expandafter\xdef\csname log2@207\endcsname{7693} \expandafter\xdef\csname log2@208\endcsname{7700} \expandafter\xdef\csname log2@209\endcsname{7707} \expandafter\xdef\csname log2@210\endcsname{7714} \expandafter\xdef\csname log2@211\endcsname{7721} \expandafter\xdef\csname log2@212\endcsname{7728} \expandafter\xdef\csname log2@213\endcsname{7735} \expandafter\xdef\csname log2@214\endcsname{7741} \expandafter\xdef\csname log2@215\endcsname{7748} \expandafter\xdef\csname log2@216\endcsname{7755} \expandafter\xdef\csname log2@217\endcsname{7761} \expandafter\xdef\csname log2@218\endcsname{7768} \expandafter\xdef\csname log2@219\endcsname{7775} \expandafter\xdef\csname log2@220\endcsname{7781} \expandafter\xdef\csname ch@r@65\endcsname{A} \expandafter\xdef\csname ch@r@66\endcsname{B} \expandafter\xdef\csname ch@r@67\endcsname{C} \expandafter\xdef\csname ch@r@68\endcsname{D} \expandafter\xdef\csname ch@r@69\endcsname{E} \expandafter\xdef\csname ch@r@70\endcsname{F} \expandafter\xdef\csname ch@r@71\endcsname{G} \expandafter\xdef\csname ch@r@72\endcsname{H} \expandafter\xdef\csname ch@r@73\endcsname{I} \expandafter\xdef\csname ch@r@74\endcsname{J} \expandafter\xdef\csname ch@r@75\endcsname{K} \expandafter\xdef\csname ch@r@76\endcsname{L} \expandafter\xdef\csname ch@r@77\endcsname{M} \expandafter\xdef\csname ch@r@78\endcsname{N} \expandafter\xdef\csname ch@r@79\endcsname{O} \expandafter\xdef\csname ch@r@80\endcsname{P} \expandafter\xdef\csname ch@r@81\endcsname{Q} \expandafter\xdef\csname ch@r@82\endcsname{R} \expandafter\xdef\csname ch@r@83\endcsname{S} \expandafter\xdef\csname ch@r@84\endcsname{T} \expandafter\xdef\csname ch@r@85\endcsname{U} \expandafter\xdef\csname ch@r@86\endcsname{V} \expandafter\xdef\csname ch@r@87\endcsname{W} \expandafter\xdef\csname ch@r@88\endcsname{X} \expandafter\xdef\csname ch@r@89\endcsname{Y} \expandafter\xdef\csname ch@r@90\endcsname{Z} \def\clear@sims{% \expandafter\xdef\csname \prfx simA\endcsname{(1)A} \expandafter\xdef\csname \prfx simB\endcsname{(1)B} \expandafter\xdef\csname \prfx simC\endcsname{(1)C} \expandafter\xdef\csname \prfx simD\endcsname{(1)D} \expandafter\xdef\csname \prfx simE\endcsname{(1)E} \expandafter\xdef\csname \prfx simF\endcsname{(1)F} \expandafter\xdef\csname \prfx simG\endcsname{(1)G} \expandafter\xdef\csname \prfx simH\endcsname{(1)H} \expandafter\xdef\csname \prfx simI\endcsname{(1)I} \expandafter\xdef\csname \prfx simJ\endcsname{(1)J} \expandafter\xdef\csname \prfx simK\endcsname{(1)K} \expandafter\xdef\csname \prfx simL\endcsname{(1)L} \expandafter\xdef\csname \prfx simM\endcsname{(1)M} \expandafter\xdef\csname \prfx simN\endcsname{(1)N} \expandafter\xdef\csname \prfx simO\endcsname{(1)O} \expandafter\xdef\csname \prfx simP\endcsname{(1)P} \expandafter\xdef\csname \prfx simQ\endcsname{(1)Q} \expandafter\xdef\csname \prfx simR\endcsname{(1)R} \expandafter\xdef\csname \prfx simS\endcsname{(1)S} \expandafter\xdef\csname \prfx simT\endcsname{(1)T} \expandafter\xdef\csname \prfx simU\endcsname{(1)U} \expandafter\xdef\csname \prfx simV\endcsname{(1)V} \expandafter\xdef\csname \prfx simW\endcsname{(1)W} \expandafter\xdef\csname \prfx simX\endcsname{(1)X} \expandafter\xdef\csname \prfx simY\endcsname{(1)Y} \expandafter\xdef\csname \prfx simZ\endcsname{(1)Z} } \def\clear@simpairs{% \xdef\simpairCC{1} \xdef\simpairCS{0} \xdef\simpairCT{0} \xdef\simpairCP{0} \xdef\simpairCA{0} \xdef\simpairCG{0} \xdef\simpairCN{0} \xdef\simpairCD{0} \xdef\simpairCE{0} \xdef\simpairCQ{0} \xdef\simpairCH{0} \xdef\simpairCR{0} \xdef\simpairCK{0} \xdef\simpairCM{0} \xdef\simpairCI{0} \xdef\simpairCL{0} \xdef\simpairCV{0} \xdef\simpairCF{0} \xdef\simpairCY{0} \xdef\simpairCW{0} \xdef\simpairCB{0} \xdef\simpairCJ{0} \xdef\simpairCO{0} \xdef\simpairCU{0} \xdef\simpairCX{0} \xdef\simpairCZ{0} \xdef\simpairSC{0} \xdef\simpairSS{1} \xdef\simpairST{0} \xdef\simpairSP{0} \xdef\simpairSA{0} \xdef\simpairSG{0} \xdef\simpairSN{0} \xdef\simpairSD{0} \xdef\simpairSE{0} \xdef\simpairSQ{0} \xdef\simpairSH{0} \xdef\simpairSR{0} \xdef\simpairSK{0} \xdef\simpairSM{0} \xdef\simpairSI{0} \xdef\simpairSL{0} \xdef\simpairSV{0} \xdef\simpairSF{0} \xdef\simpairSY{0} \xdef\simpairSW{0} \xdef\simpairSB{0} \xdef\simpairSJ{0} \xdef\simpairSO{0} \xdef\simpairSU{0} \xdef\simpairSX{0} \xdef\simpairSZ{0} \xdef\simpairTC{0} \xdef\simpairTS{0} \xdef\simpairTT{1} \xdef\simpairTP{0} \xdef\simpairTA{0} \xdef\simpairTG{0} \xdef\simpairTN{0} \xdef\simpairTD{0} \xdef\simpairTE{0} \xdef\simpairTQ{0} \xdef\simpairTH{0} \xdef\simpairTR{0} \xdef\simpairTK{0} \xdef\simpairTM{0} \xdef\simpairTI{0} \xdef\simpairTL{0} \xdef\simpairTV{0} \xdef\simpairTF{0} \xdef\simpairTY{0} \xdef\simpairTW{0} \xdef\simpairTB{0} \xdef\simpairTJ{0} \xdef\simpairTO{0} \xdef\simpairTU{0} \xdef\simpairTX{0} \xdef\simpairTZ{0} \xdef\simpairPC{0} \xdef\simpairPS{0} \xdef\simpairPT{0} \xdef\simpairPP{1} \xdef\simpairPA{0} \xdef\simpairPG{0} \xdef\simpairPN{0} \xdef\simpairPD{0} \xdef\simpairPE{0} \xdef\simpairPQ{0} \xdef\simpairPH{0} \xdef\simpairPR{0} \xdef\simpairPK{0} \xdef\simpairPM{0} \xdef\simpairPI{0} \xdef\simpairPL{0} \xdef\simpairPV{0} \xdef\simpairPF{0} \xdef\simpairPY{0} \xdef\simpairPW{0} \xdef\simpairPB{0} \xdef\simpairPJ{0} \xdef\simpairPO{0} \xdef\simpairPU{0} \xdef\simpairPX{0} \xdef\simpairPZ{0} \xdef\simpairAC{0} \xdef\simpairAS{0} \xdef\simpairAT{0} \xdef\simpairAP{0} \xdef\simpairAA{1} \xdef\simpairAG{0} \xdef\simpairAN{0} \xdef\simpairAD{0} \xdef\simpairAE{0} \xdef\simpairAQ{0} \xdef\simpairAH{0} \xdef\simpairAR{0} \xdef\simpairAK{0} \xdef\simpairAM{0} \xdef\simpairAI{0} \xdef\simpairAL{0} \xdef\simpairAV{0} \xdef\simpairAF{0} \xdef\simpairAY{0} \xdef\simpairAW{0} \xdef\simpairAB{0} \xdef\simpairAJ{0} \xdef\simpairAO{0} \xdef\simpairAU{0} \xdef\simpairAX{0} \xdef\simpairAZ{0} \xdef\simpairGC{0} \xdef\simpairGS{0} \xdef\simpairGT{0} \xdef\simpairGP{0} \xdef\simpairGA{0} \xdef\simpairGG{1} \xdef\simpairGN{0} \xdef\simpairGD{0} \xdef\simpairGE{0} \xdef\simpairGQ{0} \xdef\simpairGH{0} \xdef\simpairGR{0} \xdef\simpairGK{0} \xdef\simpairGM{0} \xdef\simpairGI{0} \xdef\simpairGL{0} \xdef\simpairGV{0} \xdef\simpairGF{0} \xdef\simpairGY{0} \xdef\simpairGW{0} \xdef\simpairGB{0} \xdef\simpairGJ{0} \xdef\simpairGO{0} \xdef\simpairGU{0} \xdef\simpairGX{0} \xdef\simpairGZ{0} \xdef\simpairNC{0} \xdef\simpairNS{0} \xdef\simpairNT{0} \xdef\simpairNP{0} \xdef\simpairNA{0} \xdef\simpairNG{0} \xdef\simpairNN{1} \xdef\simpairND{0} \xdef\simpairNE{0} \xdef\simpairNQ{0} \xdef\simpairNH{0} \xdef\simpairNR{0} \xdef\simpairNK{0} \xdef\simpairNM{0} \xdef\simpairNI{0} \xdef\simpairNL{0} \xdef\simpairNV{0} \xdef\simpairNF{0} \xdef\simpairNY{0} \xdef\simpairNW{0} \xdef\simpairNB{0} \xdef\simpairNJ{0} \xdef\simpairNO{0} \xdef\simpairNU{0} \xdef\simpairNX{0} \xdef\simpairNZ{0} \xdef\simpairDC{0} \xdef\simpairDS{0} \xdef\simpairDT{0} \xdef\simpairDP{0} \xdef\simpairDA{0} \xdef\simpairDG{0} \xdef\simpairDN{0} \xdef\simpairDD{1} \xdef\simpairDE{0} \xdef\simpairDQ{0} \xdef\simpairDH{0} \xdef\simpairDR{0} \xdef\simpairDK{0} \xdef\simpairDM{0} \xdef\simpairDI{0} \xdef\simpairDL{0} \xdef\simpairDV{0} \xdef\simpairDF{0} \xdef\simpairDY{0} \xdef\simpairDW{0} \xdef\simpairDB{0} \xdef\simpairDJ{0} \xdef\simpairDO{0} \xdef\simpairDU{0} \xdef\simpairDX{0} \xdef\simpairDZ{0} \xdef\simpairEC{0} \xdef\simpairES{0} \xdef\simpairET{0} \xdef\simpairEP{0} \xdef\simpairEA{0} \xdef\simpairEG{0} \xdef\simpairEN{0} \xdef\simpairED{0} \xdef\simpairEE{1} \xdef\simpairEQ{0} \xdef\simpairEH{0} \xdef\simpairER{0} \xdef\simpairEK{0} \xdef\simpairEM{0} \xdef\simpairEI{0} \xdef\simpairEL{0} \xdef\simpairEV{0} \xdef\simpairEF{0} \xdef\simpairEY{0} \xdef\simpairEW{0} \xdef\simpairEB{0} \xdef\simpairEJ{0} \xdef\simpairEO{0} \xdef\simpairEU{0} \xdef\simpairEX{0} \xdef\simpairEZ{0} \xdef\simpairQC{0} \xdef\simpairQS{0} \xdef\simpairQT{0} \xdef\simpairQP{0} \xdef\simpairQA{0} \xdef\simpairQG{0} \xdef\simpairQN{0} \xdef\simpairQD{0} \xdef\simpairQE{0} \xdef\simpairQQ{1} \xdef\simpairQH{0} \xdef\simpairQR{0} \xdef\simpairQK{0} \xdef\simpairQM{0} \xdef\simpairQI{0} \xdef\simpairQL{0} \xdef\simpairQV{0} \xdef\simpairQF{0} \xdef\simpairQY{0} \xdef\simpairQW{0} \xdef\simpairQB{0} \xdef\simpairQJ{0} \xdef\simpairQO{0} \xdef\simpairQU{0} \xdef\simpairQX{0} \xdef\simpairQZ{0} \xdef\simpairHC{0} \xdef\simpairHS{0} \xdef\simpairHT{0} \xdef\simpairHP{0} \xdef\simpairHA{0} \xdef\simpairHG{0} \xdef\simpairHN{0} \xdef\simpairHD{0} \xdef\simpairHE{0} \xdef\simpairHQ{0} \xdef\simpairHH{1} \xdef\simpairHR{0} \xdef\simpairHK{0} \xdef\simpairHM{0} \xdef\simpairHI{0} \xdef\simpairHL{0} \xdef\simpairHV{0} \xdef\simpairHF{0} \xdef\simpairHY{0} \xdef\simpairHW{0} \xdef\simpairHB{0} \xdef\simpairHJ{0} \xdef\simpairHO{0} \xdef\simpairHU{0} \xdef\simpairHX{0} \xdef\simpairHZ{0} \xdef\simpairRC{0} \xdef\simpairRS{0} \xdef\simpairRT{0} \xdef\simpairRP{0} \xdef\simpairRA{0} \xdef\simpairRG{0} \xdef\simpairRN{0} \xdef\simpairRD{0} \xdef\simpairRE{0} \xdef\simpairRQ{0} \xdef\simpairRH{0} \xdef\simpairRR{1} \xdef\simpairRK{0} \xdef\simpairRM{0} \xdef\simpairRI{0} \xdef\simpairRL{0} \xdef\simpairRV{0} \xdef\simpairRF{0} \xdef\simpairRY{0} \xdef\simpairRW{0} \xdef\simpairRB{0} \xdef\simpairRJ{0} \xdef\simpairRO{0} \xdef\simpairRU{0} \xdef\simpairRX{0} \xdef\simpairRZ{0} \xdef\simpairKC{0} \xdef\simpairKS{0} \xdef\simpairKT{0} \xdef\simpairKP{0} \xdef\simpairKA{0} \xdef\simpairKG{0} \xdef\simpairKN{0} \xdef\simpairKD{0} \xdef\simpairKE{0} \xdef\simpairKQ{0} \xdef\simpairKH{0} \xdef\simpairKR{0} \xdef\simpairKK{1} \xdef\simpairKM{0} \xdef\simpairKI{0} \xdef\simpairKL{0} \xdef\simpairKV{0} \xdef\simpairKF{0} \xdef\simpairKY{0} \xdef\simpairKW{0} \xdef\simpairKB{0} \xdef\simpairKJ{0} \xdef\simpairKO{0} \xdef\simpairKU{0} \xdef\simpairKX{0} \xdef\simpairKZ{0} \xdef\simpairMC{0} \xdef\simpairMS{0} \xdef\simpairMT{0} \xdef\simpairMP{0} \xdef\simpairMA{0} \xdef\simpairMG{0} \xdef\simpairMN{0} \xdef\simpairMD{0} \xdef\simpairME{0} \xdef\simpairMQ{0} \xdef\simpairMH{0} \xdef\simpairMR{0} \xdef\simpairMK{0} \xdef\simpairMM{1} \xdef\simpairMI{0} \xdef\simpairML{0} \xdef\simpairMV{0} \xdef\simpairMF{0} \xdef\simpairMY{0} \xdef\simpairMW{0} \xdef\simpairMB{0} \xdef\simpairMJ{0} \xdef\simpairMO{0} \xdef\simpairMU{0} \xdef\simpairMX{0} \xdef\simpairMZ{0} \xdef\simpairIC{0} \xdef\simpairIS{0} \xdef\simpairIT{0} \xdef\simpairIP{0} \xdef\simpairIA{0} \xdef\simpairIG{0} \xdef\simpairIN{0} \xdef\simpairID{0} \xdef\simpairIE{0} \xdef\simpairIQ{0} \xdef\simpairIH{0} \xdef\simpairIR{0} \xdef\simpairIK{0} \xdef\simpairIM{0} \xdef\simpairII{1} \xdef\simpairIL{0} \xdef\simpairIV{0} \xdef\simpairIF{0} \xdef\simpairIY{0} \xdef\simpairIW{0} \xdef\simpairIB{0} \xdef\simpairIJ{0} \xdef\simpairIO{0} \xdef\simpairIU{0} \xdef\simpairIX{0} \xdef\simpairIZ{0} \xdef\simpairLC{0} \xdef\simpairLS{0} \xdef\simpairLT{0} \xdef\simpairLP{0} \xdef\simpairLA{0} \xdef\simpairLG{0} \xdef\simpairLN{0} \xdef\simpairLD{0} \xdef\simpairLE{0} \xdef\simpairLQ{0} \xdef\simpairLH{0} \xdef\simpairLR{0} \xdef\simpairLK{0} \xdef\simpairLM{0} \xdef\simpairLI{0} \xdef\simpairLL{1} \xdef\simpairLV{0} \xdef\simpairLF{0} \xdef\simpairLY{0} \xdef\simpairLW{0} \xdef\simpairLB{0} \xdef\simpairLJ{0} \xdef\simpairLO{0} \xdef\simpairLU{0} \xdef\simpairLX{0} \xdef\simpairLZ{0} \xdef\simpairVC{0} \xdef\simpairVS{0} \xdef\simpairVT{0} \xdef\simpairVP{0} \xdef\simpairVA{0} \xdef\simpairVG{0} \xdef\simpairVN{0} \xdef\simpairVD{0} \xdef\simpairVE{0} \xdef\simpairVQ{0} \xdef\simpairVH{0} \xdef\simpairVR{0} \xdef\simpairVK{0} \xdef\simpairVM{0} \xdef\simpairVI{0} \xdef\simpairVL{0} \xdef\simpairVV{1} \xdef\simpairVF{0} \xdef\simpairVY{0} \xdef\simpairVW{0} \xdef\simpairVB{0} \xdef\simpairVJ{0} \xdef\simpairVO{0} \xdef\simpairVU{0} \xdef\simpairVX{0} \xdef\simpairVZ{0} \xdef\simpairFC{0} \xdef\simpairFS{0} \xdef\simpairFT{0} \xdef\simpairFP{0} \xdef\simpairFA{0} \xdef\simpairFG{0} \xdef\simpairFN{0} \xdef\simpairFD{0} \xdef\simpairFE{0} \xdef\simpairFQ{0} \xdef\simpairFH{0} \xdef\simpairFR{0} \xdef\simpairFK{0} \xdef\simpairFM{0} \xdef\simpairFI{0} \xdef\simpairFL{0} \xdef\simpairFV{0} \xdef\simpairFF{1} \xdef\simpairFY{0} \xdef\simpairFW{0} \xdef\simpairFB{0} \xdef\simpairFJ{0} \xdef\simpairFO{0} \xdef\simpairFU{0} \xdef\simpairFX{0} \xdef\simpairFZ{0} \xdef\simpairYC{0} \xdef\simpairYS{0} \xdef\simpairYT{0} \xdef\simpairYP{0} \xdef\simpairYA{0} \xdef\simpairYG{0} \xdef\simpairYN{0} \xdef\simpairYD{0} \xdef\simpairYE{0} \xdef\simpairYQ{0} \xdef\simpairYH{0} \xdef\simpairYR{0} \xdef\simpairYK{0} \xdef\simpairYM{0} \xdef\simpairYI{0} \xdef\simpairYL{0} \xdef\simpairYV{0} \xdef\simpairYF{0} \xdef\simpairYY{1} \xdef\simpairYW{0} \xdef\simpairYB{0} \xdef\simpairYJ{0} \xdef\simpairYO{0} \xdef\simpairYU{0} \xdef\simpairYX{0} \xdef\simpairYZ{0} \xdef\simpairWC{0} \xdef\simpairWS{0} \xdef\simpairWT{0} \xdef\simpairWP{0} \xdef\simpairWA{0} \xdef\simpairWG{0} \xdef\simpairWN{0} \xdef\simpairWD{0} \xdef\simpairWE{0} \xdef\simpairWQ{0} \xdef\simpairWH{0} \xdef\simpairWR{0} \xdef\simpairWK{0} \xdef\simpairWM{0} \xdef\simpairWI{0} \xdef\simpairWL{0} \xdef\simpairWV{0} \xdef\simpairWF{0} \xdef\simpairWY{0} \xdef\simpairWW{1} \xdef\simpairWB{0} \xdef\simpairWJ{0} \xdef\simpairWO{0} \xdef\simpairWU{0} \xdef\simpairWX{0} \xdef\simpairWZ{0} \xdef\simpairBC{0} \xdef\simpairBS{0} \xdef\simpairBT{0} \xdef\simpairBP{0} \xdef\simpairBA{0} \xdef\simpairBG{0} \xdef\simpairBN{0} \xdef\simpairBD{0} \xdef\simpairBE{0} \xdef\simpairBQ{0} \xdef\simpairBH{0} \xdef\simpairBR{0} \xdef\simpairBK{0} \xdef\simpairBM{0} \xdef\simpairBI{0} \xdef\simpairBL{0} \xdef\simpairBV{0} \xdef\simpairBF{0} \xdef\simpairBY{0} \xdef\simpairBW{0} \xdef\simpairBB{1} \xdef\simpairBJ{0} \xdef\simpairBO{0} \xdef\simpairBU{0} \xdef\simpairBX{0} \xdef\simpairBZ{0} \xdef\simpairJC{0} \xdef\simpairJS{0} \xdef\simpairJT{0} \xdef\simpairJP{0} \xdef\simpairJA{0} \xdef\simpairJG{0} \xdef\simpairJN{0} \xdef\simpairJD{0} \xdef\simpairJE{0} \xdef\simpairJQ{0} \xdef\simpairJH{0} \xdef\simpairJR{0} \xdef\simpairJK{0} \xdef\simpairJM{0} \xdef\simpairJI{0} \xdef\simpairJL{0} \xdef\simpairJV{0} \xdef\simpairJF{0} \xdef\simpairJY{0} \xdef\simpairJW{0} \xdef\simpairJB{0} \xdef\simpairJJ{1} \xdef\simpairJO{0} \xdef\simpairJU{0} \xdef\simpairJX{0} \xdef\simpairJZ{0} \xdef\simpairOC{0} \xdef\simpairOS{0} \xdef\simpairOT{0} \xdef\simpairOP{0} \xdef\simpairOA{0} \xdef\simpairOG{0} \xdef\simpairON{0} \xdef\simpairOD{0} \xdef\simpairOE{0} \xdef\simpairOQ{0} \xdef\simpairOH{0} \xdef\simpairOR{0} \xdef\simpairOK{0} \xdef\simpairOM{0} \xdef\simpairOI{0} \xdef\simpairOL{0} \xdef\simpairOV{0} \xdef\simpairOF{0} \xdef\simpairOY{0} \xdef\simpairOW{0} \xdef\simpairOB{0} \xdef\simpairOJ{0} \xdef\simpairOO{1} \xdef\simpairOU{0} \xdef\simpairOX{0} \xdef\simpairOZ{0} \xdef\simpairUC{0} \xdef\simpairUS{0} \xdef\simpairUT{0} \xdef\simpairUP{0} \xdef\simpairUA{0} \xdef\simpairUG{0} \xdef\simpairUN{0} \xdef\simpairUD{0} \xdef\simpairUE{0} \xdef\simpairUQ{0} \xdef\simpairUH{0} \xdef\simpairUR{0} \xdef\simpairUK{0} \xdef\simpairUM{0} \xdef\simpairUI{0} \xdef\simpairUL{0} \xdef\simpairUV{0} \xdef\simpairUF{0} \xdef\simpairUY{0} \xdef\simpairUW{0} \xdef\simpairUB{0} \xdef\simpairUJ{0} \xdef\simpairUO{0} \xdef\simpairUU{1} \xdef\simpairUX{0} \xdef\simpairUZ{0} \xdef\simpairXC{0} \xdef\simpairXS{0} \xdef\simpairXT{0} \xdef\simpairXP{0} \xdef\simpairXA{0} \xdef\simpairXG{0} \xdef\simpairXN{0} \xdef\simpairXD{0} \xdef\simpairXE{0} \xdef\simpairXQ{0} \xdef\simpairXH{0} \xdef\simpairXR{0} \xdef\simpairXK{0} \xdef\simpairXM{0} \xdef\simpairXI{0} \xdef\simpairXL{0} \xdef\simpairXV{0} \xdef\simpairXF{0} \xdef\simpairXY{0} \xdef\simpairXW{0} \xdef\simpairXB{0} \xdef\simpairXJ{0} \xdef\simpairXO{0} \xdef\simpairXU{0} \xdef\simpairXX{1} \xdef\simpairXZ{0} \xdef\simpairZC{0} \xdef\simpairZS{0} \xdef\simpairZT{0} \xdef\simpairZP{0} \xdef\simpairZA{0} \xdef\simpairZG{0} \xdef\simpairZN{0} \xdef\simpairZD{0} \xdef\simpairZE{0} \xdef\simpairZQ{0} \xdef\simpairZH{0} \xdef\simpairZR{0} \xdef\simpairZK{0} \xdef\simpairZM{0} \xdef\simpairZI{0} \xdef\simpairZL{0} \xdef\simpairZV{0} \xdef\simpairZF{0} \xdef\simpairZY{0} \xdef\simpairZW{0} \xdef\simpairZB{0} \xdef\simpairZJ{0} \xdef\simpairZO{0} \xdef\simpairZU{0} \xdef\simpairZX{0} \xdef\simpairZZ{1} } \def\clear@sim@count{ \def\clear@sim@nums{% \advance\innerloopcount by 1 \ifnum\innerloopcount>\seq@count \else \expandafter\xdef\csname poscount\the\outerloopcount @\the\innerloopcount\endcsname{0} \expandafter\xdef\csname identcount\the\outerloopcount @\the\innerloopcount\endcsname{0} \expandafter\xdef\csname simcount\the\outerloopcount @\the\innerloopcount\endcsname{0} \clear@sim@nums \fi } \outerloopcount=1 \loop \innerloopcount=\outerloopcount \clear@sim@nums \advance\outerloopcount by 1 \ifnum\outerloopcount<\seq@count \repeat } \xdef\pepmwA{711} \xdef\pepmwB{1146} \xdef\pepmwC{1032} \xdef\pepmwD{1151} \xdef\pepmwE{1291} \xdef\pepmwF{1472} \xdef\pepmwG{571} \xdef\pepmwH{1372} \xdef\pepmwI{1132} \xdef\pepmwJ{0} \xdef\pepmwK{1282} \xdef\pepmwL{1132} \xdef\pepmwM{1312} \xdef\pepmwN{1141} \xdef\pepmwO{0} \xdef\pepmwP{971} \xdef\pepmwQ{1281} \xdef\pepmwR{1562} \xdef\pepmwS{871} \xdef\pepmwT{1011} \xdef\pepmwU{0} \xdef\pepmwV{991} \xdef\pepmwW{1862} \xdef\pepmwX{1282} \xdef\pepmwY{1632} \xdef\pepmwZ{1286} \xdef\DNAmwA{3462} \xdef\DNAmwB{0} \xdef\DNAmwC{3222} \xdef\DNAmwD{0} \xdef\DNAmwE{0} \xdef\DNAmwF{0} \xdef\DNAmwG{3622} \xdef\DNAmwH{0} \xdef\DNAmwI{0} \xdef\DNAmwJ{0} \xdef\DNAmwK{0} \xdef\DNAmwL{0} \xdef\DNAmwM{0} \xdef\DNAmwN{0} \xdef\DNAmwO{0} \xdef\DNAmwP{0} \xdef\DNAmwQ{0} \xdef\DNAmwR{0} \xdef\DNAmwS{0} \xdef\DNAmwT{3372} \xdef\DNAmwU{3232} \xdef\DNAmwV{0} \xdef\DNAmwW{0} \xdef\DNAmwX{0} \xdef\DNAmwY{0} \xdef\DNAmwZ{0} \xdef\pepchargeA{0} \xdef\pepchargeB{0} \xdef\pepchargeC{-30} \xdef\pepchargeD{-1000} \xdef\pepchargeE{-1000} \xdef\pepchargeF{0} \xdef\pepchargeG{0} \xdef\pepchargeH{165} \xdef\pepchargeI{0} \xdef\pepchargeJ{0} \xdef\pepchargeK{1000} \xdef\pepchargeL{0} \xdef\pepchargeM{0} \xdef\pepchargeN{0} \xdef\pepchargeO{0} \xdef\pepchargeP{0} \xdef\pepchargeQ{0} \xdef\pepchargeR{1000} \xdef\pepchargeS{0} \xdef\pepchargeT{0} \xdef\pepchargeU{0} \xdef\pepchargeV{0} \xdef\pepchargeW{0} \xdef\pepchargeX{0} \xdef\pepchargeY{0} \xdef\pepchargeZ{0} \xdef\chargeNterm{910} \xdef\chargeCterm{-1000} \xdef\chargeA{0} \xdef\chargeB{0} \xdef\chargeC{0} \xdef\chargeD{-50} \xdef\chargeE{-50} \xdef\chargeF{0} \xdef\chargeG{0} \xdef\chargeH{30} \xdef\chargeI{0} \xdef\chargeJ{0} \xdef\chargeK{50} \xdef\chargeL{0} \xdef\chargeM{0} \xdef\chargeN{0} \xdef\chargeO{0} \xdef\chargeP{0} \xdef\chargeQ{0} \xdef\chargeR{50} \xdef\chargeS{0} \xdef\chargeT{0} \xdef\chargeU{0} \xdef\chargeV{0} \xdef\chargeW{0} \xdef\chargeX{0} \xdef\chargeY{0} \xdef\chargeZ{0} \xdef\molwA{11} \xdef\molwB{45} \xdef\molwC{36} \xdef\molwD{45} \xdef\molwE{66} \xdef\molwF{70} \xdef\molwG{1} \xdef\molwH{62} \xdef\molwI{44} \xdef\molwJ{N} \xdef\molwK{55} \xdef\molwL{44} \xdef\molwM{58} \xdef\molwN{44} \xdef\molwO{N} \xdef\molwP{31} \xdef\molwQ{55} \xdef\molwR{77} \xdef\molwS{19} \xdef\molwT{34} \xdef\molwU{N} \xdef\molwV{33} \xdef\molwW{100} \xdef\molwX{55} \xdef\molwY{82} \xdef\molwZ{66} \xdef\HydroA{21} \xdef\HydroB{N} \xdef\HydroC{10} \xdef\HydroD{-31} \xdef\HydroE{-25} \xdef\HydroF{41} \xdef\HydroG{16} \xdef\HydroH{-14} \xdef\HydroI{47} \xdef\HydroJ{N} \xdef\HydroK{-52} \xdef\HydroL{36} \xdef\HydroM{22} \xdef\HydroN{-27} \xdef\HydroO{N} \xdef\HydroP{4} \xdef\HydroQ{-29} \xdef\HydroR{-53} \xdef\HydroS{-6} \xdef\HydroT{-2} \xdef\HydroU{N} \xdef\HydroV{37} \xdef\HydroW{28} \xdef\HydroX{N} \xdef\HydroY{9} \xdef\HydroZ{N} \xdef\consCB{0} \xdef\consCJ{0} \xdef\consCO{0} \xdef\consCU{0} \xdef\consCX{0} \xdef\consCZ{0} \expandafter\xdef\csname consC?\endcsname{0} \xdef\consSB{0} \xdef\consSJ{0} \xdef\consSO{0} \xdef\consSU{0} \xdef\consSX{0} \xdef\consSZ{0} \expandafter\xdef\csname consS?\endcsname{0} \xdef\consTB{0} \xdef\consTJ{0} \xdef\consTO{0} \xdef\consTU{0} \xdef\consTX{0} \xdef\consTZ{0} \expandafter\xdef\csname consT?\endcsname{0} \xdef\consPB{0} \xdef\consPJ{0} \xdef\consPO{0} \xdef\consPU{0} \xdef\consPX{0} \xdef\consPZ{0} \expandafter\xdef\csname consP?\endcsname{0} \xdef\consAB{0} \xdef\consAJ{0} \xdef\consAO{0} \xdef\consAU{0} \xdef\consAX{0} \xdef\consAZ{0} \expandafter\xdef\csname consA?\endcsname{0} \xdef\consGB{0} \xdef\consGJ{0} \xdef\consGO{0} \xdef\consGU{0} \xdef\consGX{0} \xdef\consGZ{0} \expandafter\xdef\csname consG?\endcsname{0} \xdef\consNB{0} \xdef\consNJ{0} \xdef\consNO{0} \xdef\consNU{0} \xdef\consNX{0} \xdef\consNZ{0} \expandafter\xdef\csname consN?\endcsname{0} \xdef\consDB{0} \xdef\consDJ{0} \xdef\consDO{0} \xdef\consDU{0} \xdef\consDX{0} \xdef\consDZ{0} \expandafter\xdef\csname consD?\endcsname{0} \xdef\consEB{0} \xdef\consEJ{0} \xdef\consEO{0} \xdef\consEU{0} \xdef\consEX{0} \xdef\consEZ{0} \expandafter\xdef\csname consE?\endcsname{0} \xdef\consQB{0} \xdef\consQJ{0} \xdef\consQO{0} \xdef\consQU{0} \xdef\consQX{0} \xdef\consQZ{0} \expandafter\xdef\csname consQ?\endcsname{0} \xdef\consHB{0} \xdef\consHJ{0} \xdef\consHO{0} \xdef\consHU{0} \xdef\consHX{0} \xdef\consHZ{0} \expandafter\xdef\csname consH?\endcsname{0} \xdef\consRB{0} \xdef\consRJ{0} \xdef\consRO{0} \xdef\consRU{0} \xdef\consRX{0} \xdef\consRZ{0} \expandafter\xdef\csname consR?\endcsname{0} \xdef\consKB{0} \xdef\consKJ{0} \xdef\consKO{0} \xdef\consKU{0} \xdef\consKX{0} \xdef\consKZ{0} \expandafter\xdef\csname consK?\endcsname{0} \xdef\consMB{0} \xdef\consMJ{0} \xdef\consMO{0} \xdef\consMU{0} \xdef\consMX{0} \xdef\consMZ{0} \expandafter\xdef\csname consM?\endcsname{0} \xdef\consIB{0} \xdef\consIJ{0} \xdef\consIO{0} \xdef\consIU{0} \xdef\consIX{0} \xdef\consIZ{0} \expandafter\xdef\csname consI?\endcsname{0} \xdef\consLB{0} \xdef\consLJ{0} \xdef\consLO{0} \xdef\consLU{0} \xdef\consLX{0} \xdef\consLZ{0} \expandafter\xdef\csname consL?\endcsname{0} \xdef\consVB{0} \xdef\consVJ{0} \xdef\consVO{0} \xdef\consVU{0} \xdef\consVX{0} \xdef\consVZ{0} \expandafter\xdef\csname consV?\endcsname{0} \xdef\consFB{0} \xdef\consFJ{0} \xdef\consFO{0} \xdef\consFU{0} \xdef\consFX{0} \xdef\consFZ{0} \expandafter\xdef\csname consF?\endcsname{0} \xdef\consYB{0} \xdef\consYJ{0} \xdef\consYO{0} \xdef\consYU{0} \xdef\consYX{0} \xdef\consYZ{0} \expandafter\xdef\csname consY?\endcsname{0} \xdef\consWB{0} \xdef\consWJ{0} \xdef\consWO{0} \xdef\consWU{0} \xdef\consWX{0} \xdef\consWZ{0} \expandafter\xdef\csname consW?\endcsname{0} \xdef\consBC{0} \xdef\consBS{0} \xdef\consBT{0} \xdef\consBP{0} \xdef\consBA{0} \xdef\consBG{0} \xdef\consBN{0} \xdef\consBD{0} \xdef\consBE{0} \xdef\consBQ{0} \xdef\consBH{0} \xdef\consBR{0} \xdef\consBK{0} \xdef\consBM{0} \xdef\consBI{0} \xdef\consBL{0} \xdef\consBV{0} \xdef\consBF{0} \xdef\consBY{0} \xdef\consBW{0} \xdef\consBB{10} \xdef\consBJ{0} \xdef\consBO{0} \xdef\consBU{0} \xdef\consBX{0} \xdef\consBZ{0} \expandafter\xdef\csname consB.\endcsname{0} \expandafter\xdef\csname consB?\endcsname{0} \xdef\consJC{0} \xdef\consJS{0} \xdef\consJT{0} \xdef\consJP{0} \xdef\consJA{0} \xdef\consJG{0} \xdef\consJN{0} \xdef\consJD{0} \xdef\consJE{0} \xdef\consJQ{0} \xdef\consJH{0} \xdef\consJR{0} \xdef\consJK{0} \xdef\consJM{0} \xdef\consJI{0} \xdef\consJL{0} \xdef\consJV{0} \xdef\consJF{0} \xdef\consJY{0} \xdef\consJW{0} \xdef\consJB{0} \xdef\consJJ{10} \xdef\consJO{0} \xdef\consJU{0} \xdef\consJX{0} \xdef\consJZ{0} \expandafter\xdef\csname consJ.\endcsname{0} \expandafter\xdef\csname consJ?\endcsname{0} \xdef\consOC{0} \xdef\consOS{0} \xdef\consOT{0} \xdef\consOP{0} \xdef\consOA{0} \xdef\consOG{0} \xdef\consON{0} \xdef\consOD{0} \xdef\consOE{0} \xdef\consOQ{0} \xdef\consOH{0} \xdef\consOR{0} \xdef\consOK{0} \xdef\consOM{0} \xdef\consOI{0} \xdef\consOL{0} \xdef\consOV{0} \xdef\consOF{0} \xdef\consOY{0} \xdef\consOW{0} \xdef\consOB{0} \xdef\consOJ{0} \xdef\consOO{10} \xdef\consOU{0} \xdef\consOX{0} \xdef\consOZ{0} \expandafter\xdef\csname consO.\endcsname{0} \expandafter\xdef\csname consO?\endcsname{0} \xdef\consUC{0} \xdef\consUS{0} \xdef\consUT{0} \xdef\consUP{0} \xdef\consUA{0} \xdef\consUG{0} \xdef\consUN{0} \xdef\consUD{0} \xdef\consUE{0} \xdef\consUQ{0} \xdef\consUH{0} \xdef\consUR{0} \xdef\consUK{0} \xdef\consUM{0} \xdef\consUI{0} \xdef\consUL{0} \xdef\consUV{0} \xdef\consUF{0} \xdef\consUY{0} \xdef\consUW{0} \xdef\consUB{0} \xdef\consUJ{0} \xdef\consUO{0} \xdef\consUU{10} \xdef\consUX{0} \xdef\consUZ{0} \expandafter\xdef\csname consU.\endcsname{0} \expandafter\xdef\csname consU?\endcsname{0} \xdef\consXC{0} \xdef\consXS{0} \xdef\consXT{0} \xdef\consXP{0} \xdef\consXA{0} \xdef\consXG{0} \xdef\consXN{0} \xdef\consXD{0} \xdef\consXE{0} \xdef\consXQ{0} \xdef\consXH{0} \xdef\consXR{0} \xdef\consXK{0} \xdef\consXM{0} \xdef\consXI{0} \xdef\consXL{0} \xdef\consXV{0} \xdef\consXF{0} \xdef\consXY{0} \xdef\consXW{0} \xdef\consXB{0} \xdef\consXJ{0} \xdef\consXO{0} \xdef\consXU{0} \xdef\consXX{10} \xdef\consXZ{0} \expandafter\xdef\csname consX.\endcsname{0} \expandafter\xdef\csname consX?\endcsname{0} \xdef\consZC{0} \xdef\consZS{0} \xdef\consZT{0} \xdef\consZP{0} \xdef\consZA{0} \xdef\consZG{0} \xdef\consZN{0} \xdef\consZD{0} \xdef\consZE{0} \xdef\consZQ{0} \xdef\consZH{0} \xdef\consZR{0} \xdef\consZK{0} \xdef\consZM{0} \xdef\consZI{0} \xdef\consZL{0} \xdef\consZV{0} \xdef\consZF{0} \xdef\consZY{0} \xdef\consZW{0} \xdef\consZB{0} \xdef\consZJ{0} \xdef\consZO{0} \xdef\consZU{0} \xdef\consZX{0} \xdef\consZZ{10} \expandafter\xdef\csname consZ.\endcsname{0} \expandafter\xdef\csname consZ?\endcsname{0} \expandafter\xdef\csname cons..\endcsname{0} \expandafter\xdef\csname cons.?\endcsname{0} \expandafter\xdef\csname cons?C\endcsname{0} \expandafter\xdef\csname cons?S\endcsname{0} \expandafter\xdef\csname cons?T\endcsname{0} \expandafter\xdef\csname cons?P\endcsname{0} \expandafter\xdef\csname cons?A\endcsname{0} \expandafter\xdef\csname cons?G\endcsname{0} \expandafter\xdef\csname cons?N\endcsname{0} \expandafter\xdef\csname cons?D\endcsname{0} \expandafter\xdef\csname cons?E\endcsname{0} \expandafter\xdef\csname cons?Q\endcsname{0} \expandafter\xdef\csname cons?H\endcsname{0} \expandafter\xdef\csname cons?R\endcsname{0} \expandafter\xdef\csname cons?K\endcsname{0} \expandafter\xdef\csname cons?M\endcsname{0} \expandafter\xdef\csname cons?I\endcsname{0} \expandafter\xdef\csname cons?L\endcsname{0} \expandafter\xdef\csname cons?V\endcsname{0} \expandafter\xdef\csname cons?F\endcsname{0} \expandafter\xdef\csname cons?Y\endcsname{0} \expandafter\xdef\csname cons?W\endcsname{0} \expandafter\xdef\csname cons?B\endcsname{0} \expandafter\xdef\csname cons?J\endcsname{0} \expandafter\xdef\csname cons?O\endcsname{0} \expandafter\xdef\csname cons?U\endcsname{0} \expandafter\xdef\csname cons?X\endcsname{0} \expandafter\xdef\csname cons?Z\endcsname{0} \expandafter\xdef\csname cons?.\endcsname{0} \expandafter\xdef\csname cons??\endcsname{0} \expandafter\xdef\csname cons==\endcsname{0} \def\gappenalty#1{% \expandafter\xdef\csname cons.C\endcsname{#1} \expandafter\xdef\csname consC.\endcsname{#1} \expandafter\xdef\csname cons.S\endcsname{#1} \expandafter\xdef\csname consS.\endcsname{#1} \expandafter\xdef\csname cons.T\endcsname{#1} \expandafter\xdef\csname consT.\endcsname{#1} \expandafter\xdef\csname cons.P\endcsname{#1} \expandafter\xdef\csname consP.\endcsname{#1} \expandafter\xdef\csname cons.A\endcsname{#1} \expandafter\xdef\csname consA.\endcsname{#1} \expandafter\xdef\csname cons.G\endcsname{#1} \expandafter\xdef\csname consG.\endcsname{#1} \expandafter\xdef\csname cons.N\endcsname{#1} \expandafter\xdef\csname consN.\endcsname{#1} \expandafter\xdef\csname cons.D\endcsname{#1} \expandafter\xdef\csname consD.\endcsname{#1} \expandafter\xdef\csname cons.E\endcsname{#1} \expandafter\xdef\csname consE.\endcsname{#1} \expandafter\xdef\csname cons.Q\endcsname{#1} \expandafter\xdef\csname consQ.\endcsname{#1} \expandafter\xdef\csname cons.H\endcsname{#1} \expandafter\xdef\csname consH.\endcsname{#1} \expandafter\xdef\csname cons.R\endcsname{#1} \expandafter\xdef\csname consR.\endcsname{#1} \expandafter\xdef\csname cons.K\endcsname{#1} \expandafter\xdef\csname consK.\endcsname{#1} \expandafter\xdef\csname cons.M\endcsname{#1} \expandafter\xdef\csname consM.\endcsname{#1} \expandafter\xdef\csname cons.I\endcsname{#1} \expandafter\xdef\csname consI.\endcsname{#1} \expandafter\xdef\csname cons.L\endcsname{#1} \expandafter\xdef\csname consL.\endcsname{#1} \expandafter\xdef\csname cons.V\endcsname{#1} \expandafter\xdef\csname consV.\endcsname{#1} \expandafter\xdef\csname cons.F\endcsname{#1} \expandafter\xdef\csname consF.\endcsname{#1} \expandafter\xdef\csname cons.Y\endcsname{#1} \expandafter\xdef\csname consY.\endcsname{#1} \expandafter\xdef\csname cons.W\endcsname{#1} \expandafter\xdef\csname consW.\endcsname{#1} \expandafter\xdef\csname cons.B\endcsname{#1} \expandafter\xdef\csname consB.\endcsname{#1} \expandafter\xdef\csname cons.J\endcsname{#1} \expandafter\xdef\csname consJ.\endcsname{#1} \expandafter\xdef\csname cons.O\endcsname{#1} \expandafter\xdef\csname consO.\endcsname{#1} \expandafter\xdef\csname cons.U\endcsname{#1} \expandafter\xdef\csname consU.\endcsname{#1} \expandafter\xdef\csname cons.X\endcsname{#1} \expandafter\xdef\csname consX.\endcsname{#1} \expandafter\xdef\csname cons.Z\endcsname{#1} \expandafter\xdef\csname consZ.\endcsname{#1} } \def\weighttable#1{% \xdef\first@{#1} \xdef\temp@{identity} \ifx\first@\temp@ %%%% identity matrix \xdef\consCC{10} \xdef\consCS{0} \xdef\consCT{0} \xdef\consCP{0} \xdef\consCA{0} \xdef\consCG{0} \xdef\consCN{0} \xdef\consCD{0} \xdef\consCE{0} \xdef\consCQ{0} \xdef\consCH{0} \xdef\consCR{0} \xdef\consCK{0} \xdef\consCM{0} \xdef\consCI{0} \xdef\consCL{0} \xdef\consCV{0} \xdef\consCF{0} \xdef\consCY{0} \xdef\consCW{0} \xdef\consSC{0} \xdef\consSS{10} \xdef\consST{0} \xdef\consSP{0} \xdef\consSA{0} \xdef\consSG{0} \xdef\consSN{0} \xdef\consSD{0} \xdef\consSE{0} \xdef\consSQ{0} \xdef\consSH{0} \xdef\consSR{0} \xdef\consSK{0} \xdef\consSM{0} \xdef\consSI{0} \xdef\consSL{0} \xdef\consSV{0} \xdef\consSF{0} \xdef\consSY{0} \xdef\consSW{0} \xdef\consTC{0} \xdef\consTS{0} \xdef\consTT{10} \xdef\consTP{0} \xdef\consTA{0} \xdef\consTG{0} \xdef\consTN{0} \xdef\consTD{0} \xdef\consTE{0} \xdef\consTQ{0} \xdef\consTH{0} \xdef\consTR{0} \xdef\consTK{0} \xdef\consTM{0} \xdef\consTI{0} \xdef\consTL{0} \xdef\consTV{0} \xdef\consTF{0} \xdef\consTY{0} \xdef\consTW{0} \xdef\consPC{0} \xdef\consPS{0} \xdef\consPT{0} \xdef\consPP{10} \xdef\consPA{0} \xdef\consPG{0} \xdef\consPN{0} \xdef\consPD{0} \xdef\consPE{0} \xdef\consPQ{0} \xdef\consPH{0} \xdef\consPR{0} \xdef\consPK{0} \xdef\consPM{0} \xdef\consPI{0} \xdef\consPL{0} \xdef\consPV{0} \xdef\consPF{0} \xdef\consPY{0} \xdef\consPW{0} \xdef\consAC{0} \xdef\consAS{0} \xdef\consAT{0} \xdef\consAP{0} \xdef\consAA{10} \xdef\consAG{0} \xdef\consAN{0} \xdef\consAD{0} \xdef\consAE{0} \xdef\consAQ{0} \xdef\consAH{0} \xdef\consAR{0} \xdef\consAK{0} \xdef\consAM{0} \xdef\consAI{0} \xdef\consAL{0} \xdef\consAV{0} \xdef\consAF{0} \xdef\consAY{0} \xdef\consAW{0} \xdef\consGC{0} \xdef\consGS{0} \xdef\consGT{0} \xdef\consGP{0} \xdef\consGA{0} \xdef\consGG{10} \xdef\consGN{0} \xdef\consGD{0} \xdef\consGE{0} \xdef\consGQ{0} \xdef\consGH{0} \xdef\consGR{0} \xdef\consGK{0} \xdef\consGM{0} \xdef\consGI{0} \xdef\consGL{0} \xdef\consGV{0} \xdef\consGF{0} \xdef\consGY{0} \xdef\consGW{0} \xdef\consNC{0} \xdef\consNS{0} \xdef\consNT{0} \xdef\consNP{0} \xdef\consNA{0} \xdef\consNG{0} \xdef\consNN{10} \xdef\consND{0} \xdef\consNE{0} \xdef\consNQ{0} \xdef\consNH{0} \xdef\consNR{0} \xdef\consNK{0} \xdef\consNM{0} \xdef\consNI{0} \xdef\consNL{0} \xdef\consNV{0} \xdef\consNF{0} \xdef\consNY{0} \xdef\consNW{0} \xdef\consDC{0} \xdef\consDS{0} \xdef\consDT{0} \xdef\consDP{0} \xdef\consDA{0} \xdef\consDG{0} \xdef\consDN{0} \xdef\consDD{10} \xdef\consDE{0} \xdef\consDQ{0} \xdef\consDH{0} \xdef\consDR{0} \xdef\consDK{0} \xdef\consDM{0} \xdef\consDI{0} \xdef\consDL{0} \xdef\consDV{0} \xdef\consDF{0} \xdef\consDY{0} \xdef\consDW{0} \xdef\consEC{0} \xdef\consES{0} \xdef\consET{0} \xdef\consEP{0} \xdef\consEA{0} \xdef\consEG{0} \xdef\consEN{0} \xdef\consED{0} \xdef\consEE{10} \xdef\consEQ{0} \xdef\consEH{0} \xdef\consER{0} \xdef\consEK{0} \xdef\consEM{0} \xdef\consEI{0} \xdef\consEL{0} \xdef\consEV{0} \xdef\consEF{0} \xdef\consEY{0} \xdef\consEW{0} \xdef\consQC{0} \xdef\consQS{0} \xdef\consQT{0} \xdef\consQP{0} \xdef\consQA{0} \xdef\consQG{0} \xdef\consQN{0} \xdef\consQD{0} \xdef\consQE{0} \xdef\consQQ{10} \xdef\consQH{0} \xdef\consQR{0} \xdef\consQK{0} \xdef\consQM{0} \xdef\consQI{0} \xdef\consQL{0} \xdef\consQV{0} \xdef\consQF{0} \xdef\consQY{0} \xdef\consQW{0} \xdef\consHC{0} \xdef\consHS{0} \xdef\consHT{0} \xdef\consHP{0} \xdef\consHA{0} \xdef\consHG{0} \xdef\consHN{0} \xdef\consHD{0} \xdef\consHE{0} \xdef\consHQ{0} \xdef\consHH{10} \xdef\consHR{0} \xdef\consHK{0} \xdef\consHM{0} \xdef\consHI{0} \xdef\consHL{0} \xdef\consHV{0} \xdef\consHF{0} \xdef\consHY{0} \xdef\consHW{0} \xdef\consRC{0} \xdef\consRS{0} \xdef\consRT{0} \xdef\consRP{0} \xdef\consRA{0} \xdef\consRG{0} \xdef\consRN{0} \xdef\consRD{0} \xdef\consRE{0} \xdef\consRQ{0} \xdef\consRH{0} \xdef\consRR{10} \xdef\consRK{0} \xdef\consRM{0} \xdef\consRI{0} \xdef\consRL{0} \xdef\consRV{0} \xdef\consRF{0} \xdef\consRY{0} \xdef\consRW{0} \xdef\consKC{0} \xdef\consKS{0} \xdef\consKT{0} \xdef\consKP{0} \xdef\consKA{0} \xdef\consKG{0} \xdef\consKN{0} \xdef\consKD{0} \xdef\consKE{0} \xdef\consKQ{0} \xdef\consKH{0} \xdef\consKR{0} \xdef\consKK{10} \xdef\consKM{0} \xdef\consKI{0} \xdef\consKL{0} \xdef\consKV{0} \xdef\consKF{0} \xdef\consKY{0} \xdef\consKW{0} \xdef\consMC{0} \xdef\consMS{0} \xdef\consMT{0} \xdef\consMP{0} \xdef\consMA{0} \xdef\consMG{0} \xdef\consMN{0} \xdef\consMD{0} \xdef\consME{0} \xdef\consMQ{0} \xdef\consMH{0} \xdef\consMR{0} \xdef\consMK{0} \xdef\consMM{10} \xdef\consMI{0} \xdef\consML{0} \xdef\consMV{0} \xdef\consMF{0} \xdef\consMY{0} \xdef\consMW{0} \xdef\consIC{0} \xdef\consIS{0} \xdef\consIT{0} \xdef\consIP{0} \xdef\consIA{0} \xdef\consIG{0} \xdef\consIN{0} \xdef\consID{0} \xdef\consIE{0} \xdef\consIQ{0} \xdef\consIH{0} \xdef\consIR{0} \xdef\consIK{0} \xdef\consIM{0} \xdef\consII{10} \xdef\consIL{0} \xdef\consIV{0} \xdef\consIF{0} \xdef\consIY{0} \xdef\consIW{0} \xdef\consLC{0} \xdef\consLS{0} \xdef\consLT{0} \xdef\consLP{0} \xdef\consLA{0} \xdef\consLG{0} \xdef\consLN{0} \xdef\consLD{0} \xdef\consLE{0} \xdef\consLQ{0} \xdef\consLH{0} \xdef\consLR{0} \xdef\consLK{0} \xdef\consLM{0} \xdef\consLI{0} \xdef\consLL{10} \xdef\consLV{0} \xdef\consLF{0} \xdef\consLY{0} \xdef\consLW{0} \xdef\consVC{0} \xdef\consVS{0} \xdef\consVT{0} \xdef\consVP{0} \xdef\consVA{0} \xdef\consVG{0} \xdef\consVN{0} \xdef\consVD{0} \xdef\consVE{0} \xdef\consVQ{0} \xdef\consVH{0} \xdef\consVR{0} \xdef\consVK{0} \xdef\consVM{0} \xdef\consVI{0} \xdef\consVL{0} \xdef\consVV{10} \xdef\consVF{0} \xdef\consVY{0} \xdef\consVW{0} \xdef\consFC{0} \xdef\consFS{0} \xdef\consFT{0} \xdef\consFP{0} \xdef\consFA{0} \xdef\consFG{0} \xdef\consFN{0} \xdef\consFD{0} \xdef\consFE{0} \xdef\consFQ{0} \xdef\consFH{0} \xdef\consFR{0} \xdef\consFK{0} \xdef\consFM{0} \xdef\consFI{0} \xdef\consFL{0} \xdef\consFV{0} \xdef\consFF{10} \xdef\consFY{0} \xdef\consFW{0} \xdef\consYC{0} \xdef\consYS{0} \xdef\consYT{0} \xdef\consYP{0} \xdef\consYA{0} \xdef\consYG{0} \xdef\consYN{0} \xdef\consYD{0} \xdef\consYE{0} \xdef\consYQ{0} \xdef\consYH{0} \xdef\consYR{0} \xdef\consYK{0} \xdef\consYM{0} \xdef\consYI{0} \xdef\consYL{0} \xdef\consYV{0} \xdef\consYF{0} \xdef\consYY{10} \xdef\consYW{0} \xdef\consWC{0} \xdef\consWS{0} \xdef\consWT{0} \xdef\consWP{0} \xdef\consWA{0} \xdef\consWG{0} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{0} \xdef\consWQ{0} \xdef\consWH{0} \xdef\consWR{0} \xdef\consWK{0} \xdef\consWM{0} \xdef\consWI{0} \xdef\consWL{0} \xdef\consWV{0} \xdef\consWF{0} \xdef\consWY{0} \xdef\consWW{10} \gappenalty{0} \xdef\m@trixf@ctor{10} \else \xdef\temp@{structural} \ifx\first@\temp@ %%%% structural \xdef\consCC{10} \xdef\consCS{6} \xdef\consCT{3} \xdef\consCP{3} \xdef\consCA{3} \xdef\consCG{5} \xdef\consCN{3} \xdef\consCD{1} \xdef\consCE{0} \xdef\consCQ{1} \xdef\consCH{3} \xdef\consCR{3} \xdef\consCK{0} \xdef\consCM{3} \xdef\consCI{3} \xdef\consCL{3} \xdef\consCV{3} \xdef\consCF{5} \xdef\consCY{5} \xdef\consCW{5} \xdef\consSC{6} \xdef\consSS{10} \xdef\consST{8} \xdef\consSP{6} \xdef\consSA{8} \xdef\consSG{8} \xdef\consSN{8} \xdef\consSD{6} \xdef\consSE{5} \xdef\consSQ{5} \xdef\consSH{5} \xdef\consSR{5} \xdef\consSK{5} \xdef\consSM{3} \xdef\consSI{3} \xdef\consSL{3} \xdef\consSV{6} \xdef\consSF{5} \xdef\consSY{5} \xdef\consSW{3} \xdef\consTC{3} \xdef\consTS{8} \xdef\consTT{10} \xdef\consTP{6} \xdef\consTA{8} \xdef\consTG{6} \xdef\consTN{6} \xdef\consTD{5} \xdef\consTE{5} \xdef\consTQ{5} \xdef\consTH{3} \xdef\consTR{5} \xdef\consTK{6} \xdef\consTM{5} \xdef\consTI{5} \xdef\consTL{3} \xdef\consTV{6} \xdef\consTF{3} \xdef\consTY{3} \xdef\consTW{1} \xdef\consPC{3} \xdef\consPS{6} \xdef\consPT{6} \xdef\consPP{10} \xdef\consPA{8} \xdef\consPG{6} \xdef\consPN{3} \xdef\consPD{5} \xdef\consPE{5} \xdef\consPQ{5} \xdef\consPH{5} \xdef\consPR{5} \xdef\consPK{3} \xdef\consPM{3} \xdef\consPI{3} \xdef\consPL{5} \xdef\consPV{6} \xdef\consPF{5} \xdef\consPY{3} \xdef\consPW{3} \xdef\consAC{3} \xdef\consAS{8} \xdef\consAT{8} \xdef\consAP{8} \xdef\consAA{10} \xdef\consAG{8} \xdef\consAN{5} \xdef\consAD{6} \xdef\consAE{6} \xdef\consAQ{5} \xdef\consAH{3} \xdef\consAR{3} \xdef\consAK{5} \xdef\consAM{5} \xdef\consAI{3} \xdef\consAL{3} \xdef\consAV{8} \xdef\consAF{5} \xdef\consAY{3} \xdef\consAW{3} \xdef\consGC{5} \xdef\consGS{8} \xdef\consGT{6} \xdef\consGP{6} \xdef\consGA{8} \xdef\consGG{10} \xdef\consGN{5} \xdef\consGD{6} \xdef\consGE{6} \xdef\consGQ{3} \xdef\consGH{1} \xdef\consGR{5} \xdef\consGK{3} \xdef\consGM{1} \xdef\consGI{3} \xdef\consGL{3} \xdef\consGV{6} \xdef\consGF{3} \xdef\consGY{3} \xdef\consGW{5} \xdef\consNC{3} \xdef\consNS{8} \xdef\consNT{6} \xdef\consNP{3} \xdef\consNA{5} \xdef\consNG{5} \xdef\consNN{10} \xdef\consND{8} \xdef\consNE{6} \xdef\consNQ{5} \xdef\consNH{6} \xdef\consNR{5} \xdef\consNK{6} \xdef\consNM{1} \xdef\consNI{3} \xdef\consNL{1} \xdef\consNV{3} \xdef\consNF{3} \xdef\consNY{5} \xdef\consNW{0} \xdef\consDC{1} \xdef\consDS{6} \xdef\consDT{5} \xdef\consDP{5} \xdef\consDA{6} \xdef\consDG{6} \xdef\consDN{8} \xdef\consDD{10} \xdef\consDE{8} \xdef\consDQ{6} \xdef\consDH{5} \xdef\consDR{3} \xdef\consDK{5} \xdef\consDM{3} \xdef\consDI{1} \xdef\consDL{1} \xdef\consDV{5} \xdef\consDF{1} \xdef\consDY{3} \xdef\consDW{0} \xdef\consEC{0} \xdef\consES{5} \xdef\consET{5} \xdef\consEP{5} \xdef\consEA{6} \xdef\consEG{6} \xdef\consEN{6} \xdef\consED{8} \xdef\consEE{10} \xdef\consEQ{6} \xdef\consEH{3} \xdef\consER{5} \xdef\consEK{6} \xdef\consEM{3} \xdef\consEI{1} \xdef\consEL{1} \xdef\consEV{6} \xdef\consEF{3} \xdef\consEY{1} \xdef\consEW{1} \xdef\consQC{1} \xdef\consQS{5} \xdef\consQT{5} \xdef\consQP{5} \xdef\consQA{5} \xdef\consQG{3} \xdef\consQN{5} \xdef\consQD{6} \xdef\consQE{6} \xdef\consQQ{10} \xdef\consQH{6} \xdef\consQR{5} \xdef\consQK{6} \xdef\consQM{3} \xdef\consQI{1} \xdef\consQL{3} \xdef\consQV{3} \xdef\consQF{1} \xdef\consQY{3} \xdef\consQW{1} \xdef\consHC{3} \xdef\consHS{5} \xdef\consHT{3} \xdef\consHP{5} \xdef\consHA{3} \xdef\consHG{1} \xdef\consHN{6} \xdef\consHD{5} \xdef\consHE{3} \xdef\consHQ{6} \xdef\consHH{10} \xdef\consHR{6} \xdef\consHK{5} \xdef\consHM{3} \xdef\consHI{3} \xdef\consHL{5} \xdef\consHV{1} \xdef\consHF{3} \xdef\consHY{5} \xdef\consHW{1} \xdef\consRC{3} \xdef\consRS{5} \xdef\consRT{5} \xdef\consRP{5} \xdef\consRA{3} \xdef\consRG{5} \xdef\consRN{5} \xdef\consRD{3} \xdef\consRE{5} \xdef\consRQ{5} \xdef\consRH{6} \xdef\consRR{10} \xdef\consRK{8} \xdef\consRM{3} \xdef\consRI{3} \xdef\consRL{3} \xdef\consRV{3} \xdef\consRF{1} \xdef\consRY{1} \xdef\consRW{3} \xdef\consKC{0} \xdef\consKS{5} \xdef\consKT{6} \xdef\consKP{3} \xdef\consKA{5} \xdef\consKG{3} \xdef\consKN{6} \xdef\consKD{5} \xdef\consKE{6} \xdef\consKQ{6} \xdef\consKH{5} \xdef\consKR{8} \xdef\consKK{10} \xdef\consKM{3} \xdef\consKI{3} \xdef\consKL{3} \xdef\consKV{5} \xdef\consKF{1} \xdef\consKY{1} \xdef\consKW{1} \xdef\consMC{3} \xdef\consMS{5} \xdef\consMT{5} \xdef\consMP{3} \xdef\consMA{5} \xdef\consMG{1} \xdef\consMN{1} \xdef\consMD{3} \xdef\consME{3} \xdef\consMQ{3} \xdef\consMH{3} \xdef\consMR{3} \xdef\consMK{3} \xdef\consMM{10} \xdef\consMI{6} \xdef\consML{8} \xdef\consMV{6} \xdef\consMF{5} \xdef\consMY{3} \xdef\consMW{5} \xdef\consIC{3} \xdef\consIS{3} \xdef\consIT{5} \xdef\consIP{3} \xdef\consIA{3} \xdef\consIG{3} \xdef\consIN{3} \xdef\consID{1} \xdef\consIE{1} \xdef\consIQ{1} \xdef\consIH{3} \xdef\consIR{3} \xdef\consIK{3} \xdef\consIM{6} \xdef\consII{10} \xdef\consIL{8} \xdef\consIV{3} \xdef\consIF{6} \xdef\consIY{5} \xdef\consIW{5} \xdef\consLC{3} \xdef\consLS{3} \xdef\consLT{3} \xdef\consLP{5} \xdef\consLA{3} \xdef\consLG{3} \xdef\consLN{1} \xdef\consLD{1} \xdef\consLE{1} \xdef\consLQ{3} \xdef\consLH{5} \xdef\consLR{3} \xdef\consLK{3} \xdef\consLM{8} \xdef\consLI{8} \xdef\consLL{10} \xdef\consLV{3} \xdef\consLF{6} \xdef\consLY{5} \xdef\consLW{6} \xdef\consVC{3} \xdef\consVS{6} \xdef\consVT{6} \xdef\consVP{6} \xdef\consVA{8} \xdef\consVG{6} \xdef\consVN{3} \xdef\consVD{5} \xdef\consVE{6} \xdef\consVQ{3} \xdef\consVH{1} \xdef\consVR{3} \xdef\consVK{5} \xdef\consVM{6} \xdef\consVI{3} \xdef\consVL{3} \xdef\consVV{10} \xdef\consVF{6} \xdef\consVY{5} \xdef\consVW{5} \xdef\consFC{5} \xdef\consFS{5} \xdef\consFT{3} \xdef\consFP{5} \xdef\consFA{5} \xdef\consFG{3} \xdef\consFN{3} \xdef\consFD{1} \xdef\consFE{3} \xdef\consFQ{1} \xdef\consFH{3} \xdef\consFR{1} \xdef\consFK{1} \xdef\consFM{5} \xdef\consFI{6} \xdef\consFL{6} \xdef\consFV{6} \xdef\consFF{10} \xdef\consFY{8} \xdef\consFW{5} \xdef\consYC{5} \xdef\consYS{5} \xdef\consYT{3} \xdef\consYP{3} \xdef\consYA{3} \xdef\consYG{3} \xdef\consYN{5} \xdef\consYD{3} \xdef\consYE{1} \xdef\consYQ{3} \xdef\consYH{5} \xdef\consYR{1} \xdef\consYK{1} \xdef\consYM{3} \xdef\consYI{5} \xdef\consYL{5} \xdef\consYV{5} \xdef\consYF{8} \xdef\consYY{10} \xdef\consYW{5} \xdef\consWC{5} \xdef\consWS{3} \xdef\consWT{1} \xdef\consWP{3} \xdef\consWA{3} \xdef\consWG{5} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{1} \xdef\consWQ{1} \xdef\consWH{1} \xdef\consWR{3} \xdef\consWK{1} \xdef\consWM{5} \xdef\consWI{5} \xdef\consWL{6} \xdef\consWV{5} \xdef\consWF{5} \xdef\consWY{5} \xdef\consWW{10} \gappenalty{0} \xdef\m@trixf@ctor{10} \else \xdef\temp@{PAM250} \ifx\first@\temp@ %%%% PAM250 \xdef\consCC{4} \xdef\consCS{0} \xdef\consCT{-2} \xdef\consCP{-3} \xdef\consCA{-2} \xdef\consCG{-3} \xdef\consCN{-4} \xdef\consCD{2} \xdef\consCE{-5} \xdef\consCQ{-5} \xdef\consCH{-3} \xdef\consCR{-4} \xdef\consCK{-5} \xdef\consCM{-5} \xdef\consCI{-2} \xdef\consCL{-6} \xdef\consCV{-2} \xdef\consCF{-4} \xdef\consCY{0} \xdef\consCW{-8} \xdef\consCB{-4} \xdef\consCZ{-5} \xdef\consCX{-3} \xdef\consSC{0} \xdef\consSS{3} \xdef\consST{1} \xdef\consSP{1} \xdef\consSA{1} \xdef\consSG{1} \xdef\consSN{1} \xdef\consSD{0} \xdef\consSE{0} \xdef\consSQ{-1} \xdef\consSH{-1} \xdef\consSR{0} \xdef\consSK{0} \xdef\consSM{-2} \xdef\consSI{-1} \xdef\consSL{-3} \xdef\consSV{-1} \xdef\consSF{-3} \xdef\consSY{-3} \xdef\consSW{-2} \xdef\consSB{0} \xdef\consSZ{0} \xdef\consSX{0} \xdef\consTC{-2} \xdef\consTS{1} \xdef\consTT{3} \xdef\consTP{0} \xdef\consTA{1} \xdef\consTG{0} \xdef\consTN{0} \xdef\consTD{0} \xdef\consTE{0} \xdef\consTQ{-1} \xdef\consTH{-1} \xdef\consTR{-1} \xdef\consTK{0} \xdef\consTM{-1} \xdef\consTI{0} \xdef\consTL{-2} \xdef\consTV{0} \xdef\consTF{-2} \xdef\consTY{-3} \xdef\consTW{-5} \xdef\consTB{0} \xdef\consTZ{-1} \xdef\consTX{0} \xdef\consPC{-3} \xdef\consPS{1} \xdef\consPT{0} \xdef\consPP{6} \xdef\consPA{1} \xdef\consPG{-1} \xdef\consPN{-1} \xdef\consPD{-1} \xdef\consPE{-1} \xdef\consPQ{0} \xdef\consPH{0} \xdef\consPR{0} \xdef\consPK{-1} \xdef\consPM{-2} \xdef\consPI{-2} \xdef\consPL{-3} \xdef\consPV{-1} \xdef\consPF{-5} \xdef\consPY{-5} \xdef\consPW{-6} \xdef\consPB{-1} \xdef\consPZ{0} \xdef\consPX{-1} \xdef\consAC{-2} \xdef\consAS{1} \xdef\consAT{1} \xdef\consAP{1} \xdef\consAA{2} \xdef\consAG{1} \xdef\consAN{0} \xdef\consAD{0} \xdef\consAE{0} \xdef\consAQ{0} \xdef\consAH{-1} \xdef\consAR{-2} \xdef\consAK{-1} \xdef\consAM{-1} \xdef\consAI{-1} \xdef\consAL{-2} \xdef\consAV{0} \xdef\consAF{-4} \xdef\consAY{-3} \xdef\consAW{-6} \xdef\consAB{0} \xdef\consAZ{0} \xdef\consAX{0} \xdef\consGC{-3} \xdef\consGS{1} \xdef\consGT{0} \xdef\consGP{-1} \xdef\consGA{1} \xdef\consGG{5} \xdef\consGN{0} \xdef\consGD{1} \xdef\consGE{0} \xdef\consGQ{-1} \xdef\consGH{-2} \xdef\consGR{-3} \xdef\consGK{-2} \xdef\consGM{-3} \xdef\consGI{-3} \xdef\consGL{-4} \xdef\consGV{-1} \xdef\consGF{-5} \xdef\consGY{-5} \xdef\consGW{-7} \xdef\consGB{0} \xdef\consGZ{0} \xdef\consGX{-1} \xdef\consNC{-4} \xdef\consNS{1} \xdef\consNT{0} \xdef\consNP{-1} \xdef\consNA{0} \xdef\consNG{0} \xdef\consNN{2} \xdef\consND{2} \xdef\consNE{1} \xdef\consNQ{1} \xdef\consNH{2} \xdef\consNR{0} \xdef\consNK{1} \xdef\consNM{-2} \xdef\consNI{-2} \xdef\consNL{-3} \xdef\consNV{-2} \xdef\consNF{-4} \xdef\consNY{-2} \xdef\consNW{-4} \xdef\consNB{2} \xdef\consNZ{1} \xdef\consNX{0} \xdef\consDC{-5} \xdef\consDS{0} \xdef\consDT{0} \xdef\consDP{-1} \xdef\consDA{0} \xdef\consDG{1} \xdef\consDN{2} \xdef\consDD{4} \xdef\consDE{3} \xdef\consDQ{2} \xdef\consDH{1} \xdef\consDR{-1} \xdef\consDK{0} \xdef\consDM{-3} \xdef\consDI{-2} \xdef\consDL{-4} \xdef\consDV{-2} \xdef\consDF{-6} \xdef\consDY{-4} \xdef\consDW{-7} \xdef\consDB{3} \xdef\consDZ{3} \xdef\consDX{-1} \xdef\consEC{-5} \xdef\consES{0} \xdef\consET{0} \xdef\consEP{-1} \xdef\consEA{0} \xdef\consEG{0} \xdef\consEN{1} \xdef\consED{3} \xdef\consEE{4} \xdef\consEQ{2} \xdef\consEH{1} \xdef\consER{-1} \xdef\consEK{0} \xdef\consEM{-2} \xdef\consEI{-2} \xdef\consEL{-3} \xdef\consEV{-2} \xdef\consEF{-5} \xdef\consEY{-4} \xdef\consEW{-7} \xdef\consEB{3} \xdef\consEZ{3} \xdef\consEX{-1} \xdef\consQC{-5} \xdef\consQS{-1} \xdef\consQT{-1} \xdef\consQP{0} \xdef\consQA{0} \xdef\consQG{-1} \xdef\consQN{1} \xdef\consQD{2} \xdef\consQE{2} \xdef\consQQ{4} \xdef\consQH{3} \xdef\consQR{1} \xdef\consQK{1} \xdef\consQM{-1} \xdef\consQI{-2} \xdef\consQL{-2} \xdef\consQV{-2} \xdef\consQF{-5} \xdef\consQY{-4} \xdef\consQW{-5} \xdef\consQB{1} \xdef\consQZ{3} \xdef\consQX{-1} \xdef\consHC{-3} \xdef\consHS{-1} \xdef\consHT{-1} \xdef\consHP{0} \xdef\consHA{-1} \xdef\consHG{-2} \xdef\consHN{2} \xdef\consHD{1} \xdef\consHE{1} \xdef\consHQ{3} \xdef\consHH{6} \xdef\consHR{2} \xdef\consHK{0} \xdef\consHM{-2} \xdef\consHI{-2} \xdef\consHL{-2} \xdef\consHV{-2} \xdef\consHF{-2} \xdef\consHY{-5} \xdef\consHW{-7} \xdef\consHB{1} \xdef\consHZ{2} \xdef\consHX{-1} \xdef\consRC{-4} \xdef\consRS{0} \xdef\consRT{-1} \xdef\consRP{0} \xdef\consRA{-2} \xdef\consRG{-3} \xdef\consRN{0} \xdef\consRD{-1} \xdef\consRE{-1} \xdef\consRQ{1} \xdef\consRH{2} \xdef\consRR{6} \xdef\consRK{3} \xdef\consRM{0} \xdef\consRI{-2} \xdef\consRL{-3} \xdef\consRV{-2} \xdef\consRF{-4} \xdef\consRY{-4} \xdef\consRW{2} \xdef\consRB{-1} \xdef\consRZ{0} \xdef\consRX{-1} \xdef\consKC{-5} \xdef\consKS{0} \xdef\consKT{0} \xdef\consKP{-1} \xdef\consKA{-1} \xdef\consKG{-2} \xdef\consKN{1} \xdef\consKD{0} \xdef\consKE{0} \xdef\consKQ{1} \xdef\consKH{0} \xdef\consKR{3} \xdef\consKK{5} \xdef\consKM{0} \xdef\consKI{-2} \xdef\consKL{-3} \xdef\consKV{-2} \xdef\consKF{-5} \xdef\consKY{-4} \xdef\consKW{-3} \xdef\consKB{1} \xdef\consKZ{-2} \xdef\consKX{-1} \xdef\consMC{-5} \xdef\consMS{-2} \xdef\consMT{-1} \xdef\consMP{-2} \xdef\consMA{-1} \xdef\consMG{-3} \xdef\consMN{-2} \xdef\consMD{-3} \xdef\consME{-2} \xdef\consMQ{-1} \xdef\consMH{-2} \xdef\consMR{0} \xdef\consMK{0} \xdef\consMM{6} \xdef\consMI{2} \xdef\consML{4} \xdef\consMV{2} \xdef\consMF{0} \xdef\consMY{-2} \xdef\consMW{-4} \xdef\consMB{-2} \xdef\consMZ{-2} \xdef\consMX{-1} \xdef\consIC{-2} \xdef\consIS{-1} \xdef\consIT{0} \xdef\consIP{-2} \xdef\consIA{-1} \xdef\consIG{-3} \xdef\consIN{-2} \xdef\consID{-2} \xdef\consIE{-2} \xdef\consIQ{-2} \xdef\consIH{-2} \xdef\consIR{-2} \xdef\consIK{-2} \xdef\consIM{2} \xdef\consII{5} \xdef\consIL{2} \xdef\consIV{4} \xdef\consIF{1} \xdef\consIY{-1} \xdef\consIW{-5} \xdef\consIB{-2} \xdef\consIZ{-2} \xdef\consIX{-1} \xdef\consLC{-6} \xdef\consLS{-3} \xdef\consLT{-2} \xdef\consLP{-3} \xdef\consLA{-2} \xdef\consLG{-4} \xdef\consLN{-3} \xdef\consLD{-4} \xdef\consLE{-3} \xdef\consLQ{-2} \xdef\consLH{-2} \xdef\consLR{-3} \xdef\consLK{-3} \xdef\consLM{4} \xdef\consLI{2} \xdef\consLL{6} \xdef\consLV{2} \xdef\consLF{2} \xdef\consLY{-1} \xdef\consLW{-2} \xdef\consLB{-3} \xdef\consLZ{-3} \xdef\consLX{-1} \xdef\consVC{-2} \xdef\consVS{-1} \xdef\consVT{0} \xdef\consVP{-1} \xdef\consVA{0} \xdef\consVG{-1} \xdef\consVN{-2} \xdef\consVD{-2} \xdef\consVE{-2} \xdef\consVQ{-2} \xdef\consVH{-2} \xdef\consVR{-2} \xdef\consVK{-2} \xdef\consVM{2} \xdef\consVI{4} \xdef\consVL{2} \xdef\consVV{4} \xdef\consVF{-1} \xdef\consVY{-2} \xdef\consVW{-6} \xdef\consVB{-2} \xdef\consVZ{-2} \xdef\consVX{-1} \xdef\consFC{-4} \xdef\consFS{-3} \xdef\consFT{-2} \xdef\consFP{-5} \xdef\consFA{-4} \xdef\consFG{-5} \xdef\consFN{-4} \xdef\consFD{-6} \xdef\consFE{-5} \xdef\consFQ{-5} \xdef\consFH{-2} \xdef\consFR{-4} \xdef\consFK{-5} \xdef\consFM{0} \xdef\consFI{1} \xdef\consFL{2} \xdef\consFV{-1} \xdef\consFF{9} \xdef\consFY{7} \xdef\consFW{0} \xdef\consFB{-4} \xdef\consFZ{-5} \xdef\consFX{-2} \xdef\consYC{0} \xdef\consYS{-3} \xdef\consYT{-3} \xdef\consYP{-5} \xdef\consYA{-3} \xdef\consYG{-5} \xdef\consYN{-2} \xdef\consYD{-4} \xdef\consYE{-4} \xdef\consYQ{-4} \xdef\consYH{0} \xdef\consYR{-4} \xdef\consYK{-4} \xdef\consYM{-2} \xdef\consYI{-1} \xdef\consYL{-1} \xdef\consYV{-2} \xdef\consYF{7} \xdef\consYY{10} \xdef\consYW{0} \xdef\consYB{-3} \xdef\consYZ{-4} \xdef\consYX{-2} \xdef\consWC{-8} \xdef\consWS{-2} \xdef\consWT{-5} \xdef\consWP{-6} \xdef\consWA{-6} \xdef\consWG{-7} \xdef\consWN{-4} \xdef\consWD{-7} \xdef\consWE{-7} \xdef\consWQ{-5} \xdef\consWH{-3} \xdef\consWR{2} \xdef\consWK{-3} \xdef\consWM{-4} \xdef\consWI{-5} \xdef\consWL{-2} \xdef\consWV{-6} \xdef\consWF{0} \xdef\consWY{0} \xdef\consWW{17} \xdef\consWB{-5} \xdef\consWZ{-6} \xdef\consWX{-4} \xdef\consBC{-4} \xdef\consBS{0} \xdef\consBT{0} \xdef\consBP{-1} \xdef\consBA{0} \xdef\consBG{0} \xdef\consBN{2} \xdef\consBD{3} \xdef\consBE{3} \xdef\consBQ{1} \xdef\consBH{1} \xdef\consBR{-1} \xdef\consBK{1} \xdef\consBM{-2} \xdef\consBI{-2} \xdef\consBL{-3} \xdef\consBV{-2} \xdef\consBF{-4} \xdef\consBY{-3} \xdef\consBW{-5} \xdef\consBB{3} \xdef\consBZ{2} \xdef\consBX{-1} \xdef\consZC{-5} \xdef\consZS{0} \xdef\consZT{-1} \xdef\consZP{0} \xdef\consZA{0} \xdef\consZG{0} \xdef\consZN{1} \xdef\consZD{3} \xdef\consZE{3} \xdef\consZQ{3} \xdef\consZH{2} \xdef\consZR{0} \xdef\consZK{0} \xdef\consZM{-2} \xdef\consZI{-2} \xdef\consZL{-3} \xdef\consZV{-2} \xdef\consZF{-5} \xdef\consZY{-4} \xdef\consZW{-6} \xdef\consZB{2} \xdef\consZZ{3} \xdef\consZX{-1} \xdef\consXC{-3} \xdef\consXS{0} \xdef\consXT{0} \xdef\consXP{-1} \xdef\consXA{0} \xdef\consXG{-1} \xdef\consXN{0} \xdef\consXD{-1} \xdef\consXE{-1} \xdef\consXQ{-1} \xdef\consXH{-1} \xdef\consXR{-1} \xdef\consXK{-1} \xdef\consXM{-1} \xdef\consXI{-1} \xdef\consXL{-1} \xdef\consXV{-1} \xdef\consXF{-2} \xdef\consXY{-2} \xdef\consXW{-4} \xdef\consXB{-1} \xdef\consXZ{-1} \xdef\consXX{-1} \expandafter\xdef\csname cons..\endcsname{1} \gappenalty{-8} \xdef\m@trixf@ctor{10} \else \xdef\temp@{PAM100} \xdef\m@trixf@ctor{10} \ifx\first@\temp@ %%%% PAM100 \xdef\consCC{14} \xdef\consCS{-1} \xdef\consCT{-5} \xdef\consCP{-6} \xdef\consCA{-5} \xdef\consCG{-8} \xdef\consCN{-8} \xdef\consCD{-11} \xdef\consCE{-11} \xdef\consCQ{-11} \xdef\consCH{-6} \xdef\consCR{-6} \xdef\consCK{-11} \xdef\consCM{-11} \xdef\consCI{-5} \xdef\consCL{-12} \xdef\consCV{-4} \xdef\consCF{-10} \xdef\consCY{-2} \xdef\consCW{-13} \xdef\consCB{-6} \xdef\consCZ{-8} \xdef\consCX{-5} \xdef\consSC{-1} \xdef\consSS{6} \xdef\consST{2} \xdef\consSP{1} \xdef\consSA{2} \xdef\consSG{1} \xdef\consSN{2} \xdef\consSD{-1} \xdef\consSE{-2} \xdef\consSQ{-3} \xdef\consSH{-4} \xdef\consSR{-1} \xdef\consSK{-2} \xdef\consSM{-4} \xdef\consSI{-4} \xdef\consSL{-7} \xdef\consSV{-4} \xdef\consSF{-5} \xdef\consSY{-6} \xdef\consSW{-4} \xdef\consSB{0} \xdef\consSZ{-2} \xdef\consSX{1} \xdef\consTC{-5} \xdef\consTS{2} \xdef\consTT{7} \xdef\consTP{-1} \xdef\consTA{2} \xdef\consTG{-3} \xdef\consTN{0} \xdef\consTD{-2} \xdef\consTE{-3} \xdef\consTQ{-3} \xdef\consTH{-5} \xdef\consTR{-4} \xdef\consTK{-1} \xdef\consTM{-2} \xdef\consTI{-1} \xdef\consTL{-5} \xdef\consTV{-1} \xdef\consTF{-6} \xdef\consTY{-6} \xdef\consTW{-10} \xdef\consTB{-1} \xdef\consTZ{-2} \xdef\consTX{-1} \xdef\consPC{-6} \xdef\consPS{1} \xdef\consPT{-1} \xdef\consPP{10} \xdef\consPA{1} \xdef\consPG{-3} \xdef\consPN{-3} \xdef\consPD{-4} \xdef\consPE{-3} \xdef\consPQ{-1} \xdef\consPH{-2} \xdef\consPR{-2} \xdef\consPK{-4} \xdef\consPM{-6} \xdef\consPI{-6} \xdef\consPL{-5} \xdef\consPV{-4} \xdef\consPF{-9} \xdef\consPY{-11} \xdef\consPW{-11} \xdef\consPB{-3} \xdef\consPZ{-1} \xdef\consPX{-2} \xdef\consAC{-5} \xdef\consAS{2} \xdef\consAT{2} \xdef\consAP{1} \xdef\consAA{6} \xdef\consAG{1} \xdef\consAN{-1} \xdef\consAD{-1} \xdef\consAE{0} \xdef\consAQ{-2} \xdef\consAH{-5} \xdef\consAR{-5} \xdef\consAK{-4} \xdef\consAM{-3} \xdef\consAI{-3} \xdef\consAL{-5} \xdef\consAV{0} \xdef\consAF{-7} \xdef\consAY{-6} \xdef\consAW{-11} \xdef\consAB{-1} \xdef\consAZ{-1} \xdef\consAX{-1} \xdef\consGC{-8} \xdef\consGS{1} \xdef\consGT{-3} \xdef\consGP{-3} \xdef\consGA{1} \xdef\consGG{8} \xdef\consGN{-1} \xdef\consGD{-1} \xdef\consGE{-2} \xdef\consGQ{-5} \xdef\consGH{-7} \xdef\consGR{-8} \xdef\consGK{-5} \xdef\consGM{-8} \xdef\consGI{-7} \xdef\consGL{-8} \xdef\consGV{-4} \xdef\consGF{-8} \xdef\consGY{-11} \xdef\consGW{-13} \xdef\consGB{-1} \xdef\consGZ{-2} \xdef\consGX{-2} \xdef\consNC{-8} \xdef\consNS{2} \xdef\consNT{0} \xdef\consNP{-3} \xdef\consNA{-1} \xdef\consNG{-1} \xdef\consNN{7} \xdef\consND{4} \xdef\consNE{1} \xdef\consNQ{-1} \xdef\consNH{2} \xdef\consNR{-3} \xdef\consNK{1} \xdef\consNM{-5} \xdef\consNI{-4} \xdef\consNL{-6} \xdef\consNV{-5} \xdef\consNF{-6} \xdef\consNY{-3} \xdef\consNW{-8} \xdef\consNB{4} \xdef\consNZ{0} \xdef\consNX{-1} \xdef\consDC{-11} \xdef\consDS{-1} \xdef\consDT{-2} \xdef\consDP{-4} \xdef\consDA{-1} \xdef\consDG{-1} \xdef\consDN{4} \xdef\consDD{8} \xdef\consDE{5} \xdef\consDQ{1} \xdef\consDH{-1} \xdef\consDR{-6} \xdef\consDK{-2} \xdef\consDM{-8} \xdef\consDI{-6} \xdef\consDL{-9} \xdef\consDV{-6} \xdef\consDF{-11} \xdef\consDY{-9} \xdef\consDW{-13} \xdef\consDB{4} \xdef\consDZ{3} \xdef\consDX{-2} \xdef\consEC{-11} \xdef\consES{-2} \xdef\consET{-3} \xdef\consEP{-3} \xdef\consEA{0} \xdef\consEG{-2} \xdef\consEN{1} \xdef\consED{5} \xdef\consEE{8} \xdef\consEQ{4} \xdef\consEH{-2} \xdef\consER{-5} \xdef\consEK{-2} \xdef\consEM{-6} \xdef\consEI{-5} \xdef\consEL{-7} \xdef\consEV{-5} \xdef\consEF{-11} \xdef\consEY{-7} \xdef\consEW{-14} \xdef\consEB{3} \xdef\consEZ{4} \xdef\consEX{-2} \xdef\consQC{-11} \xdef\consQS{-3} \xdef\consQT{-3} \xdef\consQP{-1} \xdef\consQA{-2} \xdef\consQG{-5} \xdef\consQN{-1} \xdef\consQD{1} \xdef\consQE{4} \xdef\consQQ{9} \xdef\consQH{4} \xdef\consQR{1} \xdef\consQK{-1} \xdef\consQM{-2} \xdef\consQI{-5} \xdef\consQL{-3} \xdef\consQV{-5} \xdef\consQF{-10} \xdef\consQY{-9} \xdef\consQW{-11} \xdef\consQB{0} \xdef\consQZ{5} \xdef\consQX{-2} \xdef\consHC{-6} \xdef\consHS{-4} \xdef\consHT{-5} \xdef\consHP{-2} \xdef\consHA{-5} \xdef\consHG{-7} \xdef\consHN{2} \xdef\consHD{-1} \xdef\consHE{-2} \xdef\consHQ{4} \xdef\consHH{11} \xdef\consHR{1} \xdef\consHK{-3} \xdef\consHM{-7} \xdef\consHI{-7} \xdef\consHL{-5} \xdef\consHV{-6} \xdef\consHF{-4} \xdef\consHY{-1} \xdef\consHW{-7} \xdef\consHB{1} \xdef\consHZ{1} \xdef\consHX{-2} \xdef\consRC{-6} \xdef\consRS{-1} \xdef\consRT{-4} \xdef\consRP{-2} \xdef\consRA{-5} \xdef\consRG{-8} \xdef\consRN{-3} \xdef\consRD{-6} \xdef\consRE{-5} \xdef\consRQ{1} \xdef\consRH{1} \xdef\consRR{10} \xdef\consRK{3} \xdef\consRM{-2} \xdef\consRI{-4} \xdef\consRL{-7} \xdef\consRV{-6} \xdef\consRF{-7} \xdef\consRY{-10} \xdef\consRW{1} \xdef\consRB{-3} \xdef\consRZ{-1} \xdef\consRX{-2} \xdef\consKC{-11} \xdef\consKS{-2} \xdef\consKT{-1} \xdef\consKP{-4} \xdef\consKA{-4} \xdef\consKG{-5} \xdef\consKN{1} \xdef\consKD{-2} \xdef\consKE{-2} \xdef\consKQ{-1} \xdef\consKH{-3} \xdef\consKR{3} \xdef\consKK{8} \xdef\consKM{1} \xdef\consKI{-4} \xdef\consKL{-6} \xdef\consKV{-6} \xdef\consKF{-11} \xdef\consKY{-10} \xdef\consKW{-9} \xdef\consKB{0} \xdef\consKZ{-1} \xdef\consKX{-2} \xdef\consMC{-11} \xdef\consMS{-4} \xdef\consMT{-2} \xdef\consMP{-6} \xdef\consMA{-3} \xdef\consMG{-8} \xdef\consMN{-5} \xdef\consMD{-8} \xdef\consME{-6} \xdef\consMQ{-2} \xdef\consMH{-7} \xdef\consMR{-2} \xdef\consMK{1} \xdef\consMM{13} \xdef\consMI{2} \xdef\consML{4} \xdef\consMV{1} \xdef\consMF{-2} \xdef\consMY{-8} \xdef\consMW{-11} \xdef\consMB{-4} \xdef\consMZ{-2} \xdef\consMX{-2} \xdef\consIC{-5} \xdef\consIS{-4} \xdef\consIT{-1} \xdef\consIP{-6} \xdef\consIA{-3} \xdef\consIG{-7} \xdef\consIN{-4} \xdef\consID{-6} \xdef\consIE{-5} \xdef\consIQ{-5} \xdef\consIH{-7} \xdef\consIR{-4} \xdef\consIK{-4} \xdef\consIM{2} \xdef\consII{9} \xdef\consIL{2} \xdef\consIV{5} \xdef\consIF{0} \xdef\consIY{-4} \xdef\consIW{-12} \xdef\consIB{-3} \xdef\consIZ{-3} \xdef\consIX{-2} \xdef\consLC{-12} \xdef\consLS{-7} \xdef\consLT{-5} \xdef\consLP{-5} \xdef\consLA{-5} \xdef\consLG{-8} \xdef\consLN{-6} \xdef\consLD{-9} \xdef\consLE{-7} \xdef\consLQ{-3} \xdef\consLH{-5} \xdef\consLR{-7} \xdef\consLK{-6} \xdef\consLM{4} \xdef\consLI{2} \xdef\consLL{9} \xdef\consLV{1} \xdef\consLF{0} \xdef\consLY{-5} \xdef\consLW{-7} \xdef\consLB{-5} \xdef\consLZ{-4} \xdef\consLX{-3} \xdef\consVC{-4} \xdef\consVS{-4} \xdef\consVT{-1} \xdef\consVP{-4} \xdef\consVA{0} \xdef\consVG{-4} \xdef\consVN{-5} \xdef\consVD{-6} \xdef\consVE{-5} \xdef\consVQ{-5} \xdef\consVH{-6} \xdef\consVR{-6} \xdef\consVK{-6} \xdef\consVM{1} \xdef\consVI{5} \xdef\consVL{1} \xdef\consVV{8} \xdef\consVF{-5} \xdef\consVY{-6} \xdef\consVW{-14} \xdef\consVB{-4} \xdef\consVZ{-3} \xdef\consVX{-2} \xdef\consFC{-10} \xdef\consFS{-5} \xdef\consFT{-6} \xdef\consFP{-9} \xdef\consFA{-7} \xdef\consFG{-8} \xdef\consFN{-6} \xdef\consFD{-11} \xdef\consFE{-11} \xdef\consFQ{-10} \xdef\consFH{-4} \xdef\consFR{-7} \xdef\consFK{-11} \xdef\consFM{-2} \xdef\consFI{0} \xdef\consFL{0} \xdef\consFV{-5} \xdef\consFF{12} \xdef\consFY{6} \xdef\consFW{-2} \xdef\consFB{-6} \xdef\consFZ{-7} \xdef\consFX{-4} \xdef\consYC{-2} \xdef\consYS{-6} \xdef\consYT{-6} \xdef\consYP{-11} \xdef\consYA{-6} \xdef\consYG{-11} \xdef\consYN{-3} \xdef\consYD{-9} \xdef\consYE{-7} \xdef\consYQ{-9} \xdef\consYH{-1} \xdef\consYR{-10} \xdef\consYK{-10} \xdef\consYM{-8} \xdef\consYI{-4} \xdef\consYL{-5} \xdef\consYV{-6} \xdef\consYF{6} \xdef\consYY{13} \xdef\consYW{-2} \xdef\consYB{-4} \xdef\consYZ{-6} \xdef\consYX{-4} \xdef\consWC{-13} \xdef\consWS{-4} \xdef\consWT{-10} \xdef\consWP{-11} \xdef\consWA{-11} \xdef\consWG{-13} \xdef\consWN{-8} \xdef\consWD{-13} \xdef\consWE{-14} \xdef\consWQ{-11} \xdef\consWH{-7} \xdef\consWR{1} \xdef\consWK{-9} \xdef\consWM{-11} \xdef\consWI{-12} \xdef\consWL{-7} \xdef\consWV{-14} \xdef\consWF{-2} \xdef\consWY{-2} \xdef\consWW{19} \xdef\consWB{-6} \xdef\consWZ{-8} \xdef\consWX{-6} \xdef\consBC{-6} \xdef\consBS{0} \xdef\consBT{-1} \xdef\consBP{-3} \xdef\consBA{-1} \xdef\consBG{-1} \xdef\consBN{4} \xdef\consBD{4} \xdef\consBE{3} \xdef\consBQ{0} \xdef\consBH{1} \xdef\consBR{-3} \xdef\consBK{0} \xdef\consBM{-4} \xdef\consBI{-3} \xdef\consBL{-5} \xdef\consBV{-4} \xdef\consBF{-6} \xdef\consBY{-4} \xdef\consBW{-6} \xdef\consBB{4} \xdef\consBZ{2} \xdef\consBX{-2} \xdef\consZC{-8} \xdef\consZS{-2} \xdef\consZT{-2} \xdef\consZP{-1} \xdef\consZA{-1} \xdef\consZG{-2} \xdef\consZN{0} \xdef\consZD{3} \xdef\consZE{4} \xdef\consZQ{5} \xdef\consZH{1} \xdef\consZR{-1} \xdef\consZK{-1} \xdef\consZM{-2} \xdef\consZI{-3} \xdef\consZL{-4} \xdef\consZV{-3} \xdef\consZF{-7} \xdef\consZY{-6} \xdef\consZW{-8} \xdef\consZB{2} \xdef\consZZ{5} \xdef\consZX{-2} \xdef\consXC{-5} \xdef\consXS{-1} \xdef\consXT{-1} \xdef\consXP{-2} \xdef\consXA{-1} \xdef\consXG{-2} \xdef\consXN{-1} \xdef\consXD{-2} \xdef\consXE{-2} \xdef\consXQ{-2} \xdef\consXH{-2} \xdef\consXR{-2} \xdef\consXK{-2} \xdef\consXM{-2} \xdef\consXI{-2} \xdef\consXL{-3} \xdef\consXV{-2} \xdef\consXF{-4} \xdef\consXY{-4} \xdef\consXW{-6} \xdef\consXB{-2} \xdef\consXZ{-2} \xdef\consXX{-2} \expandafter\xdef\csname cons..\endcsname{1} \gappenalty{-9} \xdef\m@trixf@ctor{10} \else \xdef\temp@{BLOSUM62} \ifx\first@\temp@ %%%% BLOSUM62 \xdef\consCC{9} \xdef\consCS{-1} \xdef\consCT{-1} \xdef\consCP{-3} \xdef\consCA{0} \xdef\consCG{-3} \xdef\consCN{-3} \xdef\consCD{-3} \xdef\consCE{-4} \xdef\consCQ{-3} \xdef\consCH{-3} \xdef\consCR{-3} \xdef\consCK{-3} \xdef\consCM{-1} \xdef\consCI{-1} \xdef\consCL{-1} \xdef\consCV{-1} \xdef\consCF{-2} \xdef\consCY{-2} \xdef\consCW{-2} \xdef\consSC{-1} \xdef\consSS{4} \xdef\consST{1} \xdef\consSP{-1} \xdef\consSA{1} \xdef\consSG{0} \xdef\consSN{1} \xdef\consSD{0} \xdef\consSE{0} \xdef\consSQ{0} \xdef\consSH{-1} \xdef\consSR{-1} \xdef\consSK{0} \xdef\consSM{-1} \xdef\consSI{-2} \xdef\consSL{-2} \xdef\consSV{-2} \xdef\consSF{-2} \xdef\consSY{-2} \xdef\consSW{-3} \xdef\consTC{-1} \xdef\consTS{1} \xdef\consTT{4} \xdef\consTP{1} \xdef\consTA{-1} \xdef\consTG{1} \xdef\consTN{0} \xdef\consTD{1} \xdef\consTE{0} \xdef\consTQ{0} \xdef\consTH{0} \xdef\consTR{-1} \xdef\consTK{0} \xdef\consTM{-1} \xdef\consTI{-2} \xdef\consTL{-2} \xdef\consTV{-2} \xdef\consTF{-2} \xdef\consTY{-2} \xdef\consTW{-3} \xdef\consPC{-3} \xdef\consPS{-1} \xdef\consPT{1} \xdef\consPP{7} \xdef\consPA{-1} \xdef\consPG{-2} \xdef\consPN{-1} \xdef\consPD{-1} \xdef\consPE{-1} \xdef\consPQ{-1} \xdef\consPH{-2} \xdef\consPR{-2} \xdef\consPK{-1} \xdef\consPM{-2} \xdef\consPI{-3} \xdef\consPL{-3} \xdef\consPV{-2} \xdef\consPF{-4} \xdef\consPY{-3} \xdef\consPW{-4} \xdef\consAC{0} \xdef\consAS{1} \xdef\consAT{-1} \xdef\consAP{-1} \xdef\consAA{4} \xdef\consAG{0} \xdef\consAN{-1} \xdef\consAD{-2} \xdef\consAE{-1} \xdef\consAQ{-1} \xdef\consAH{-2} \xdef\consAR{-1} \xdef\consAK{-1} \xdef\consAM{-1} \xdef\consAI{-1} \xdef\consAL{-1} \xdef\consAV{-2} \xdef\consAF{-2} \xdef\consAY{-2} \xdef\consAW{-3} \xdef\consGC{-3} \xdef\consGS{0} \xdef\consGT{1} \xdef\consGP{-2} \xdef\consGA{0} \xdef\consGG{6} \xdef\consGN{-2} \xdef\consGD{-1} \xdef\consGE{-2} \xdef\consGQ{-2} \xdef\consGH{-2} \xdef\consGR{-2} \xdef\consGK{-2} \xdef\consGM{-3} \xdef\consGI{-4} \xdef\consGL{-4} \xdef\consGV{0} \xdef\consGF{-3} \xdef\consGY{-3} \xdef\consGW{-2} \xdef\consNC{-3} \xdef\consNS{1} \xdef\consNT{0} \xdef\consNP{-2} \xdef\consNA{-2} \xdef\consNG{0} \xdef\consNN{6} \xdef\consND{1} \xdef\consNE{0} \xdef\consNQ{0} \xdef\consNH{-1} \xdef\consNR{0} \xdef\consNK{0} \xdef\consNM{-2} \xdef\consNI{-3} \xdef\consNL{-3} \xdef\consNV{-3} \xdef\consNF{-3} \xdef\consNY{-2} \xdef\consNW{-4} \xdef\consDC{-3} \xdef\consDS{0} \xdef\consDT{1} \xdef\consDP{-1} \xdef\consDA{-2} \xdef\consDG{-1} \xdef\consDN{1} \xdef\consDD{6} \xdef\consDE{2} \xdef\consDQ{0} \xdef\consDH{-1} \xdef\consDR{-2} \xdef\consDK{-1} \xdef\consDM{-3} \xdef\consDI{-3} \xdef\consDL{-4} \xdef\consDV{-3} \xdef\consDF{-3} \xdef\consDY{-3} \xdef\consDW{-4} \xdef\consEC{-4} \xdef\consES{0} \xdef\consET{0} \xdef\consEP{-1} \xdef\consEA{-1} \xdef\consEG{-2} \xdef\consEN{0} \xdef\consED{2} \xdef\consEE{5} \xdef\consEQ{2} \xdef\consEH{0} \xdef\consER{0} \xdef\consEK{1} \xdef\consEM{-2} \xdef\consEI{-3} \xdef\consEL{-3} \xdef\consEV{-3} \xdef\consEF{-3} \xdef\consEY{-2} \xdef\consEW{-3} \xdef\consQC{-3} \xdef\consQS{0} \xdef\consQT{0} \xdef\consQP{-1} \xdef\consQA{-1} \xdef\consQG{-2} \xdef\consQN{0} \xdef\consQD{0} \xdef\consQE{2} \xdef\consQQ{5} \xdef\consQH{0} \xdef\consQR{1} \xdef\consQK{1} \xdef\consQM{0} \xdef\consQI{-3} \xdef\consQL{-2} \xdef\consQV{-2} \xdef\consQF{-3} \xdef\consQY{-1} \xdef\consQW{-2} \xdef\consHC{-3} \xdef\consHS{-1} \xdef\consHT{0} \xdef\consHP{-2} \xdef\consHA{-2} \xdef\consHG{-2} \xdef\consHN{1} \xdef\consHD{1} \xdef\consHE{0} \xdef\consHQ{0} \xdef\consHH{8} \xdef\consHR{0} \xdef\consHK{-1} \xdef\consHM{-2} \xdef\consHI{-3} \xdef\consHL{-3} \xdef\consHV{-2} \xdef\consHF{-1} \xdef\consHY{2} \xdef\consHW{-2} \xdef\consRC{-3} \xdef\consRS{-1} \xdef\consRT{-1} \xdef\consRP{-2} \xdef\consRA{-1} \xdef\consRG{-2} \xdef\consRN{0} \xdef\consRD{-2} \xdef\consRE{0} \xdef\consRQ{1} \xdef\consRH{0} \xdef\consRR{5} \xdef\consRK{2} \xdef\consRM{-1} \xdef\consRI{-3} \xdef\consRL{-2} \xdef\consRV{-3} \xdef\consRF{-3} \xdef\consRY{-2} \xdef\consRW{-3} \xdef\consKC{-3} \xdef\consKS{0} \xdef\consKT{0} \xdef\consKP{-1} \xdef\consKA{-1} \xdef\consKG{-2} \xdef\consKN{0} \xdef\consKD{-1} \xdef\consKE{1} \xdef\consKQ{1} \xdef\consKH{-1} \xdef\consKR{2} \xdef\consKK{5} \xdef\consKM{-1} \xdef\consKI{-3} \xdef\consKL{-2} \xdef\consKV{-3} \xdef\consKF{-3} \xdef\consKY{-2} \xdef\consKW{-3} \xdef\consMC{-1} \xdef\consMS{-1} \xdef\consMT{-1} \xdef\consMP{-2} \xdef\consMA{-1} \xdef\consMG{-3} \xdef\consMN{-2} \xdef\consMD{-3} \xdef\consME{-2} \xdef\consMQ{0} \xdef\consMH{-2} \xdef\consMR{-1} \xdef\consMK{-1} \xdef\consMM{5} \xdef\consMI{1} \xdef\consML{2} \xdef\consMV{-2} \xdef\consMF{0} \xdef\consMY{-1} \xdef\consMW{-1} \xdef\consIC{-1} \xdef\consIS{-2} \xdef\consIT{-2} \xdef\consIP{-3} \xdef\consIA{-1} \xdef\consIG{-4} \xdef\consIN{-3} \xdef\consID{-3} \xdef\consIE{-3} \xdef\consIQ{-3} \xdef\consIH{-3} \xdef\consIR{-3} \xdef\consIK{-3} \xdef\consIM{1} \xdef\consII{4} \xdef\consIL{2} \xdef\consIV{1} \xdef\consIF{0} \xdef\consIY{-1} \xdef\consIW{-3} \xdef\consLC{-1} \xdef\consLS{-2} \xdef\consLT{-2} \xdef\consLP{-3} \xdef\consLA{-1} \xdef\consLG{-4} \xdef\consLN{-3} \xdef\consLD{-4} \xdef\consLE{-3} \xdef\consLQ{-2} \xdef\consLH{-3} \xdef\consLR{-2} \xdef\consLK{-2} \xdef\consLM{2} \xdef\consLI{2} \xdef\consLL{4} \xdef\consLV{3} \xdef\consLF{0} \xdef\consLY{-1} \xdef\consLW{-2} \xdef\consVC{-1} \xdef\consVS{-2} \xdef\consVT{-2} \xdef\consVP{-2} \xdef\consVA{0} \xdef\consVG{-3} \xdef\consVN{-3} \xdef\consVD{-3} \xdef\consVE{-2} \xdef\consVQ{-2} \xdef\consVH{-3} \xdef\consVR{-3} \xdef\consVK{-2} \xdef\consVM{1} \xdef\consVI{3} \xdef\consVL{1} \xdef\consVV{4} \xdef\consVF{-1} \xdef\consVY{-1} \xdef\consVW{-3} \xdef\consFC{-2} \xdef\consFS{-2} \xdef\consFT{-2} \xdef\consFP{-4} \xdef\consFA{-2} \xdef\consFG{-3} \xdef\consFN{-3} \xdef\consFD{-3} \xdef\consFE{-3} \xdef\consFQ{-3} \xdef\consFH{-1} \xdef\consFR{-3} \xdef\consFK{-3} \xdef\consFM{0} \xdef\consFI{0} \xdef\consFL{0} \xdef\consFV{-1} \xdef\consFF{6} \xdef\consFY{3} \xdef\consFW{1} \xdef\consYC{-2} \xdef\consYS{-2} \xdef\consYT{-2} \xdef\consYP{-3} \xdef\consYA{-2} \xdef\consYG{-3} \xdef\consYN{-2} \xdef\consYD{-3} \xdef\consYE{-2} \xdef\consYQ{-1} \xdef\consYH{2} \xdef\consYR{-2} \xdef\consYK{-2} \xdef\consYM{-1} \xdef\consYI{-1} \xdef\consYL{-1} \xdef\consYV{-1} \xdef\consYF{3} \xdef\consYY{7} \xdef\consYW{2} \xdef\consWC{-2} \xdef\consWS{-3} \xdef\consWT{-3} \xdef\consWP{-4} \xdef\consWA{-3} \xdef\consWG{-2} \xdef\consWN{-4} \xdef\consWD{-4} \xdef\consWE{-3} \xdef\consWQ{-2} \xdef\consWH{-2} \xdef\consWR{-3} \xdef\consWK{-3} \xdef\consWM{-1} \xdef\consWI{-3} \xdef\consWL{-2} \xdef\consWV{-3} \xdef\consWF{1} \xdef\consWY{2} \xdef\consWW{11} \gappenalty{0} \xdef\m@trixf@ctor{10} \else \message{} \weighttable{identity} \fi \fi \fi \fi \fi } \def\setweight#1#2#3{% \expandafter\xdef\csname cons#1#2\endcsname{#3} \expandafter\xdef\csname cons#2#1\endcsname{#3} } \weighttable{identity} \gappenalty{0} \def\c@d@ns{% \codon{A}{GCA,GCG,GCC,GCT,GCU,GCN} \codon{B}{---} \codon{C}{TGC,TGT,UGC,UGU,TGY} \codon{D}{GAC,GAT,GAU,GAY} \codon{E}{GAA,GAG,GAR} \codon{F}{TTC,TTT,UUC,UUU,TTY} \codon{G}{GGA,GGG,GGC,GGT,GGU,GGN} \codon{H}{CAC,CAT,CAY} \codon{I}{ATA,ATC,ATT,AUA,AUC,AUU,ATH} \codon{J}{---} \codon{K}{AAA,AAG,AAG,AAR} \codon{L}{CTA,CTG,CTC,CTT,TTA,TTG,CUG,CUG,CUC,CUU,UUA,UUG,YTN} \codon{M}{ATG,AUG,ATG} \codon{N}{AAC,AAT,AAU,AAY} \codon{O}{---} \codon{P}{CCA,CCG,CCC,CCT,CCU,CCN} \codon{Q}{CAA,CAG,CAR} \codon{R}{AGA,AGG,CGA,CGG,CGC,CGT,CGU,MGN} \codon{S}{TCT,TCC,TCG,TCA,AGT,AGC,UCU,UCC,UCG,UCA,AGU,WSN} \codon{T}{ACT,ACC,ACG,ACA,ACU,ACN} \codon{U}{---} \codon{V}{GTA,GTG,GTC,GTT,GUA,GUG,GUC,GUU,GTN} \codon{W}{TGG,UGG,TGG} \codon{X}{---} \codon{Y}{TAC,TAT,UAC,UAU,TAY} \codon{Z}{---} \codon{.}{TAA,TAG,TGA,UAA,UAG,UGA,TRR} } \definecolor{GreenYellow} {cmyk}{0.15,0,0.69,0} \definecolor{Yellow} {cmyk}{0,0,1,0} \definecolor{Goldenrod} {cmyk}{0,0.10,0.84,0} \definecolor{Dandelion} {cmyk}{0,0.29,0.84,0} \definecolor{Apricot} {cmyk}{0,0.32,0.52,0} \definecolor{Peach} {cmyk}{0,0.50,0.70,0} \definecolor{Melon} {cmyk}{0,0.46,0.50,0} \definecolor{YellowOrange} {cmyk}{0,0.42,1,0} \definecolor{Orange} {cmyk}{0,0.61,0.87,0} \definecolor{BurntOrange} {cmyk}{0,0.51,1,0} \definecolor{Bittersweet} {cmyk}{0,0.75,1,0.24} \definecolor{RedOrange} {cmyk}{0,0.77,0.87,0} \definecolor{Mahagony} {cmyk}{0,0.85,0.87,0.35} \definecolor{Maroon} {cmyk}{0,0.87,0.68,0.32} \definecolor{BrickRed} {cmyk}{0,0.89,0.94,0.28} \definecolor{Red} {cmyk}{0,1,1,0} \definecolor{OrangeRed} {cmyk}{0,1,0.50,0} \definecolor{RubineRed} {cmyk}{0,1,0.13,0} \definecolor{WildStrawberry}{cmyk}{0,0.96,0.39,0} \definecolor{Salmon} {cmyk}{0,0.53,0.38,0} \definecolor{CarnationPink} {cmyk}{0,0.63,0,0} \definecolor{Magenta} {cmyk}{0,1,0,0} \definecolor{VioletRed} {cmyk}{0,0.81,0,0} \definecolor{Rhodamine} {cmyk}{0,0.82,0,0} \definecolor{Mulberry} {cmyk}{0.34,0.90,0,0.02} \definecolor{RedViolet} {cmyk}{0.07,0.90,0,0.34} \definecolor{Fuchsia} {cmyk}{0.47,0.91,0,0.08} \definecolor{Lavender} {cmyk}{0,0.48,0,0} \definecolor{Thistle} {cmyk}{0.12,0.59,0,0} \definecolor{Orchid} {cmyk}{0.32,0.64,0,0} \definecolor{DarkOrchid} {cmyk}{0.40,0.80,0.20,0} \definecolor{Purple} {cmyk}{0.45,0.86,0,0} \definecolor{Plum} {cmyk}{0.50,1,0,0} \definecolor{Violet} {cmyk}{0.79,0.88,0,0} \definecolor{RoyalPurple} {cmyk}{0.75,0.90,0,0} \definecolor{BlueViolet} {cmyk}{0.86,0.91,0,0.04} \definecolor{Periwinkle} {cmyk}{0.57,0.55,0,0} \definecolor{CadetBlue} {cmyk}{0.62,0.57,0.23,0} \definecolor{CornflowerBlue}{cmyk}{0.65,0.13,0,0} \definecolor{MidnightBlue} {cmyk}{0.98,0.13,0,0.43} \definecolor{NavyBlue} {cmyk}{0.94,0.54,0,0} \definecolor{RoyalBlue} {cmyk}{1,0.50,0,0} \definecolor{Blue} {cmyk}{1,1,0,0} \definecolor{Cerulean} {cmyk}{0.94,0.11,0,0} \definecolor{Cyan} {cmyk}{1,0,0,0} \definecolor{ProcessBlue} {cmyk}{0.96,0,0,0} \definecolor{SkyBlue} {cmyk}{0.62,0,0.12,0} \definecolor{Turquoise} {cmyk}{0.85,0,0.20,0} \definecolor{TealBlue} {cmyk}{0.86,0,0.34,0.02} \definecolor{Aquamarine} {cmyk}{0.82,0,0.30,0} \definecolor{BlueGreen} {cmyk}{0.85,0,0.33,0} \definecolor{Emerald} {cmyk}{1,0,0.50,0} \definecolor{JungleGreen} {cmyk}{0.99,0,0.52,0} \definecolor{SeaGreen} {cmyk}{0.69,0,0.50,0} \definecolor{Green} {cmyk}{1,0,1,0} \definecolor{ForestGreen} {cmyk}{0.91,0,0.88,0.12} \definecolor{PineGreen} {cmyk}{0.92,0,0.59,0.25} \definecolor{LimeGreen} {cmyk}{0.50,0,1,0} \definecolor{YellowGreen} {cmyk}{0.44,0,0.74,0} \definecolor{SpringGreen} {cmyk}{0.26,0,0.76,0} \definecolor{OliveGreen} {cmyk}{0.64,0,0.95,0.40} \definecolor{RawSienna} {cmyk}{0,0.72,1,0.45} \definecolor{Sepia} {cmyk}{0,0.83,1,0.70} \definecolor{Brown} {cmyk}{0,0.81,1,0.60} \definecolor{Tan} {cmyk}{0.14,0.42,0.56,0} \definecolor{White} {cmyk}{0,0,0,0} \definecolor{Gray0} {cmyk}{0,0,0,0} \definecolor{Gray5} {cmyk}{0,0,0,0.05} \definecolor{Gray10} {cmyk}{0,0,0,0.10} \definecolor{Gray15} {cmyk}{0,0,0,0.15} \definecolor{Gray20} {cmyk}{0,0,0,0.20} \definecolor{Gray25} {cmyk}{0,0,0,0.25} \definecolor{Gray30} {cmyk}{0,0,0,0.30} \definecolor{LightGray} {cmyk}{0,0,0,0.33} \definecolor{Gray35} {cmyk}{0,0,0,0.35} \definecolor{Gray40} {cmyk}{0,0,0,0.40} \definecolor{Gray45} {cmyk}{0,0,0,0.45} \definecolor{Gray50} {cmyk}{0,0,0,0.50} \definecolor{Gray} {cmyk}{0,0,0,0.50} \definecolor{GrayDefault} {cmyk}{0,0,0,0.50} \definecolor{Gray55} {cmyk}{0,0,0,0.55} \definecolor{Gray60} {cmyk}{0,0,0,0.60} \definecolor{Gray65} {cmyk}{0,0,0,0.65} \definecolor{DarkGray} {cmyk}{0,0,0,0.66} \definecolor{Gray70} {cmyk}{0,0,0,0.70} \definecolor{Gray75} {cmyk}{0,0,0,0.75} \definecolor{Gray80} {cmyk}{0,0,0,0.80} \definecolor{Gray85} {cmyk}{0,0,0,0.85} \definecolor{Gray90} {cmyk}{0,0,0,0.90} \definecolor{Gray95} {cmyk}{0,0,0,0.95} \definecolor{Black} {cmyk}{0,0,0,1} \definecolor{Gray100} {cmyk}{0,0,0,1} \definecolor{TC0} {cmyk}{0.4,0.4,0,0} \definecolor{TC1} {cmyk}{0.6,0,0.7,0} \definecolor{TC2} {cmyk}{0.4,0,0.7,0} \definecolor{TC3} {cmyk}{0.2,0,1,0} \definecolor{TC4} {cmyk}{0,0,1,0} \definecolor{TC5} {cmyk}{0,0.2,1,0} \definecolor{TC6} {cmyk}{0,0.4,1,0} \definecolor{TC7} {cmyk}{0,0.6,1,0} \definecolor{TC8} {cmyk}{0,0.8,1,0} \definecolor{TC9} {cmyk}{0,0.875,1,0} \definecolor{TC99} {cmyk}{0,0,0,0} \definecolor{LightGreenYellow} {cmyk}{0.08,0,0.35,0} \definecolor{LightYellow} {cmyk}{0,0,0.50,0} \definecolor{LightGoldenrod} {cmyk}{0,0.05,0.42,0} \definecolor{LightDandelion} {cmyk}{0,0.15,0.42,0} \definecolor{LightApricot} {cmyk}{0,0.16,0.26,0} \definecolor{LightPeach} {cmyk}{0,0.25,0.35,0} \definecolor{LightMelon} {cmyk}{0,0.23,0.25,0} \definecolor{LightYellowOrange} {cmyk}{0,0.21,0.50,0} \definecolor{LightOrange} {cmyk}{0,0.31,0.44,0} \definecolor{LightBurntOrange} {cmyk}{0,0.26,0.50,0} \definecolor{LightBittersweet} {cmyk}{0,0.38,0.50,0.12} \definecolor{LightRedOrange} {cmyk}{0,0.39,0.44,0} \definecolor{LightMahagony} {cmyk}{0,0.43,0.44,0.18} \definecolor{LightMaroon} {cmyk}{0,0.44,0.34,0.16} \definecolor{LightBrickRed} {cmyk}{0,0.45,0.47,0.14} \definecolor{LightRed} {cmyk}{0,0.50,0.50,0} \definecolor{LightOrangeRed} {cmyk}{0,0.50,0.25,0} \definecolor{LightRubineRed} {cmyk}{0,0.50,0.07,0} \definecolor{LightWildStrawberry}{cmyk}{0,0.48,0.20,0} \definecolor{LightSalmon} {cmyk}{0,0.27,0.19,0} \definecolor{LightCarnationPink} {cmyk}{0,0.32,0,0} \definecolor{LightMagenta} {cmyk}{0,0.50,0,0} \definecolor{LightVioletRed} {cmyk}{0,0.40,0,0} \definecolor{LightRhodamine} {cmyk}{0,0.41,0,0} \definecolor{LightMulberry} {cmyk}{0.17,0.45,0,0.01} \definecolor{LightRedViolet} {cmyk}{0.04,0.45,0,0.17} \definecolor{LightFuchsia} {cmyk}{0.24,0.46,0,0.04} \definecolor{LightLavender} {cmyk}{0,0.24,0,0} \definecolor{LightThistle} {cmyk}{0.06,0.30,0,0} \definecolor{LightOrchid} {cmyk}{0.16,0.32,0,0} \definecolor{LightDarkOrchid} {cmyk}{0.20,0.40,0.10,0} \definecolor{LightPurple} {cmyk}{0.23,0.43,0,0} \definecolor{LightPlum} {cmyk}{0.25,0.50,0,0} \definecolor{LightViolet} {cmyk}{0.40,0.44,0,0} \definecolor{LightRoyalPurple} {cmyk}{0.38,0.45,0,0} \definecolor{LightBlueViolet} {cmyk}{0.43,0.46,0,0.02} \definecolor{LightPeriwinkle} {cmyk}{0.29,0.28,0,0} \definecolor{LightCadetBlue} {cmyk}{0.31,0.29,0.12,0} \definecolor{LightCornflowerBlue}{cmyk}{0.33,0.07,0,0} \definecolor{LightMidnightBlue} {cmyk}{0.49,0.07,0,0.22} \definecolor{LightNavyBlue} {cmyk}{0.47,0.27,0,0} \definecolor{LightRoyalBlue} {cmyk}{0.50,0.25,0,0} \definecolor{LightBlue} {cmyk}{0.50,0.50,0,0} \definecolor{LightCerulean} {cmyk}{0.47,0.06,0,0} \definecolor{LightCyan} {cmyk}{0.50,0,0,0} \definecolor{LightProcessBlue} {cmyk}{0.48,0,0,0} \definecolor{LightSkyBlue} {cmyk}{0.31,0,0.06,0} \definecolor{LightTurquoise} {cmyk}{0.43,0,0.10,0} \definecolor{LightTealBlue} {cmyk}{0.43,0,0.17,0.01} \definecolor{LightAquamarine} {cmyk}{0.41,0,0.15,0} \definecolor{LightBlueGreen} {cmyk}{0.43,0,0.17,0} \definecolor{LightEmerald} {cmyk}{0.50,0,0.25,0} \definecolor{LightJungleGreen} {cmyk}{0.50,0,0.26,0} \definecolor{LightSeaGreen} {cmyk}{0.35,0,0.25,0} \definecolor{LightGreen} {cmyk}{0.50,0,0.50,0} \definecolor{LightForestGreen} {cmyk}{0.46,0,0.44,0.06} \definecolor{LightPineGreen} {cmyk}{0.46,0,0.30,0.13} \definecolor{LightLimeGreen} {cmyk}{0.25,0,0.50,0} \definecolor{LightYellowGreen} {cmyk}{0.22,0,0.37,0} \definecolor{LightSpringGreen} {cmyk}{0.13,0,0.38,0} \definecolor{LightOliveGreen} {cmyk}{0.32,0,0.48,0.20} \definecolor{LightRawSienna} {cmyk}{0,0.36,0.50,0.23} \definecolor{LightSepia} {cmyk}{0,0.44,0.50,0.35} \definecolor{LightBrown} {cmyk}{0,0.41,0.50,0.30} \definecolor{LightTan} {cmyk}{0.07,0.21,0.28,0} \definecolor{LightWhite} {cmyk}{0,0,0,0} \definecolor{LightGray0} {cmyk}{0,0,0,0} \definecolor{LightGray5} {cmyk}{0,0,0,0.02} \definecolor{LightGray10} {cmyk}{0,0,0,0.05} \definecolor{LightGray15} {cmyk}{0,0,0,0.07} \definecolor{LightGray20} {cmyk}{0,0,0,0.10} \definecolor{LightGray25} {cmyk}{0,0,0,0.12} \definecolor{LightGray30} {cmyk}{0,0,0,0.15} \definecolor{LightLightGray} {cmyk}{0,0,0,0.16} \definecolor{LightGray35} {cmyk}{0,0,0,0.17} \definecolor{LightGray40} {cmyk}{0,0,0,0.20} \definecolor{LightGray45} {cmyk}{0,0,0,0.22} \definecolor{LightGray50} {cmyk}{0,0,0,0.25} \definecolor{LightGray} {cmyk}{0,0,0,0.25} \definecolor{LightGray55} {cmyk}{0,0,0,0.27} \definecolor{LightGray60} {cmyk}{0,0,0,0.30} \definecolor{LightGray65} {cmyk}{0,0,0,0.32} \definecolor{LightDarkGray} {cmyk}{0,0,0,0.33} \definecolor{LightGray70} {cmyk}{0,0,0,0.35} \definecolor{LightGray75} {cmyk}{0,0,0,0.37} \definecolor{LightGray80} {cmyk}{0,0,0,0.40} \definecolor{LightGray85} {cmyk}{0,0,0,0.42} \definecolor{LightGray90} {cmyk}{0,0,0,0.45} \definecolor{LightGray95} {cmyk}{0,0,0,0.47} \definecolor{LightBlack} {cmyk}{0,0,0,0.50} \definecolor{LightGray100} {cmyk}{0,0,0,0.50} \definecolor{LightTC0} {cmyk}{0.2,0.2,0,0} \definecolor{LightTC1} {cmyk}{0.3,0,0.35,0} \definecolor{LightTC2} {cmyk}{0.2,0,0.35,0} \definecolor{LightTC3} {cmyk}{0.1,0,0.5,0} \definecolor{LightTC4} {cmyk}{0,0,0.5,0} \definecolor{LightTC5} {cmyk}{0,0.1,0.5,0} \definecolor{LightTC6} {cmyk}{0,0.2,0.5,0} \definecolor{LightTC7} {cmyk}{0,0.3,0.5,0} \definecolor{LightTC8} {cmyk}{0,0.4,0.5,0} \definecolor{LightTC99} {cmyk}{0,0,0,0} \definecolor{LightLightGreenYellow} {cmyk}{0.04,0,0.17,0} \definecolor{LightLightYellow} {cmyk}{0,0,0.25,0} \definecolor{LightLightGoldenrod} {cmyk}{0,0.02,0.21,0} \definecolor{LightLightDandelion} {cmyk}{0,0.07,0.21,0} \definecolor{LightLightApricot} {cmyk}{0,0.08,0.13,0} \definecolor{LightLightPeach} {cmyk}{0,0.12,0.17,0} \definecolor{LightLightMelon} {cmyk}{0,0.11,0.12,0} \definecolor{LightLightYellowOrange} {cmyk}{0,0.10,0.25,0} \definecolor{LightLightOrange} {cmyk}{0,0.15,0.22,0} \definecolor{LightLightBurntOrange} {cmyk}{0,0.13,0.25,0} \definecolor{LightLightBittersweet} {cmyk}{0,0.19,0.25,0.06} \definecolor{LightLightRedOrange} {cmyk}{0,0.14,0.22,0} \definecolor{LightLightMahagony} {cmyk}{0,0.21,0.22,0.09} \definecolor{LightLightMaroon} {cmyk}{0,0.22,0.17,0.08} \definecolor{LightLightBrickRed} {cmyk}{0,0.22,0.23,0.07} \definecolor{LightLightRed} {cmyk}{0,0.25,0.25,0} \definecolor{LightLightOrangeRed} {cmyk}{0,0.25,0.12,0} \definecolor{LightLightRubineRed} {cmyk}{0,0.25,0.03,0} \definecolor{LightLightWildStrawberry}{cmyk}{0,0.24,0.10,0} \definecolor{LightLightSalmon} {cmyk}{0,0.13,0.09,0} \definecolor{LightLightCarnationPink} {cmyk}{0,0.16,0,0} \definecolor{LightLightMagenta} {cmyk}{0,0.25,0,0} \definecolor{LightLightVioletRed} {cmyk}{0,0.20,0,0} \definecolor{LightLightRhodamine} {cmyk}{0,0.20,0,0} \definecolor{LightLightMulberry} {cmyk}{0.08,0.22,0,0.005} \definecolor{LightLightRedViolet} {cmyk}{0.02,0.22,0,0.08} \definecolor{LightLightFuchsia} {cmyk}{0.12,0.23,0,0.02} \definecolor{LightLightLavender} {cmyk}{0,0.12,0,0} \definecolor{LightLightThistle} {cmyk}{0.03,0.15,0,0} \definecolor{LightLightOrchid} {cmyk}{0.08,0.16,0,0} \definecolor{LightLightDarkOrchid} {cmyk}{0.10,0.20,0.05,0} \definecolor{LightLightPurple} {cmyk}{0.11,0.21,0,0} \definecolor{LightLightPlum} {cmyk}{0.12,0.25,0,0} \definecolor{LightLightViolet} {cmyk}{0.20,0.22,0,0} \definecolor{LightLightRoyalPurple} {cmyk}{0.19,0.22,0,0} \definecolor{LightLightBlueViolet} {cmyk}{0.21,0.23,0,0.01} \definecolor{LightLightPeriwinkle} {cmyk}{0.14,0.14,0,0} \definecolor{LightLightCadetBlue} {cmyk}{0.15,0.14,0.06,0} \definecolor{LightLightCornflowerBlue}{cmyk}{0.16,0.03,0,0} \definecolor{LightLightMidnightBlue} {cmyk}{0.24,0.03,0,0.11} \definecolor{LightLightNavyBlue} {cmyk}{0.23,0.13,0,0} \definecolor{LightLightRoyalBlue} {cmyk}{0.25,0.12,0,0} \definecolor{LightLightBlue} {cmyk}{0.25,0.25,0,0} \definecolor{LightLightCerulean} {cmyk}{0.23,0.03,0,0} \definecolor{LightLightCyan} {cmyk}{0.25,0,0,0} \definecolor{LightLightProcessBlue} {cmyk}{0.24,0,0,0} \definecolor{LightLightSkyBlue} {cmyk}{0.15,0,0.03,0} \definecolor{LightLightTurquoise} {cmyk}{0.21,0,0.05,0} \definecolor{LightLightTealBlue} {cmyk}{0.21,0,0.08,0.005} \definecolor{LightLightAquamarine} {cmyk}{0.20,0,0.07,0} \definecolor{LightLightBlueGreen} {cmyk}{0.21,0,0.08,0} \definecolor{LightLightEmerald} {cmyk}{0.25,0,0.12,0} \definecolor{LightLightJungleGreen} {cmyk}{0.25,0,0.13,0} \definecolor{LightLightSeaGreen} {cmyk}{0.17,0,0.12,0} \definecolor{LightLightGreen} {cmyk}{0.25,0,0.25,0} \definecolor{LightLightForestGreen} {cmyk}{0.23,0,0.22,0.03} \definecolor{LightLightPineGreen} {cmyk}{0.23,0,0.15,0.06} \definecolor{LightLightLimeGreen} {cmyk}{0.12,0,0.25,0} \definecolor{LightLightYellowGreen} {cmyk}{0.11,0,0.18,0} \definecolor{LightLightSpringGreen} {cmyk}{0.06,0,0.19,0} \definecolor{LightLightOliveGreen} {cmyk}{0.16,0,0.24,0.10} \definecolor{LightLightRawSienna} {cmyk}{0,0.18,0.25,0.11} \definecolor{LightLightSepia} {cmyk}{0,0.22,0.25,0.17} \definecolor{LightLightBrown} {cmyk}{0,0.20,0.25,0.15} \definecolor{LightLightTan} {cmyk}{0.03,0.10,0.14,0} \definecolor{LightLightWhite} {cmyk}{0,0,0,0} \definecolor{LightLightGray0} {cmyk}{0,0,0,0} \definecolor{LightLightGray5} {cmyk}{0,0,0,0.01} \definecolor{LightLightGray10} {cmyk}{0,0,0,0.02} \definecolor{LightLightGray15} {cmyk}{0,0,0,0.03} \definecolor{LightLightGray20} {cmyk}{0,0,0,0.05} \definecolor{LightLightGray25} {cmyk}{0,0,0,0.06} \definecolor{LightLightGray30} {cmyk}{0,0,0,0.07} \definecolor{LightLightLightGray} {cmyk}{0,0,0,0.08} \definecolor{LightLightGray35} {cmyk}{0,0,0,0.09} \definecolor{LightLightGray40} {cmyk}{0,0,0,0.10} \definecolor{LightLightGray45} {cmyk}{0,0,0,0.11} \definecolor{LightLightGray50} {cmyk}{0,0,0,0.12} \definecolor{LightLightGray} {cmyk}{0,0,0,0.13} \definecolor{LightLightGray55} {cmyk}{0,0,0,0.14} \definecolor{LightLightGray60} {cmyk}{0,0,0,0.15} \definecolor{LightLightGray65} {cmyk}{0,0,0,0.16} \definecolor{LightLightDarkGray} {cmyk}{0,0,0,0.17} \definecolor{LightLightGray70} {cmyk}{0,0,0,0.18} \definecolor{LightLightGray75} {cmyk}{0,0,0,0.19} \definecolor{LightLightGray80} {cmyk}{0,0,0,0.20} \definecolor{LightLightGray85} {cmyk}{0,0,0,0.21} \definecolor{LightLightGray90} {cmyk}{0,0,0,0.22} \definecolor{LightLightGray95} {cmyk}{0,0,0,0.23} \definecolor{LightLightBlack} {cmyk}{0,0,0,0.25} \definecolor{LightLightGray100} {cmyk}{0,0,0,0.25} \definecolor{LightLightTC0} {cmyk}{0.1,0.1,0,0} \definecolor{LightLightTC1} {cmyk}{0.15,0,0.175,0} \definecolor{LightLightTC2} {cmyk}{0.1,0,0.175,0} \definecolor{LightLightTC3} {cmyk}{0.05,0,0.25,0} \definecolor{LightLightTC4} {cmyk}{0,0,0.25,0} \definecolor{LightLightTC5} {cmyk}{0,0.05,0.25,0} \definecolor{LightLightTC6} {cmyk}{0,0.1,0.25,0} \definecolor{LightLightTC7} {cmyk}{0,0.15,0.25,0} \definecolor{LightLightTC8} {cmyk}{0,0.2,0.25,0} \definecolor{LightLightTC99} {cmyk}{0,0,0,0} \definecolor{LightLightLightGreenYellow} {cmyk}{0.02,0,0.08,0} \definecolor{LightLightLightYellow} {cmyk}{0,0,0.12,0} \definecolor{LightLightLightGoldenrod} {cmyk}{0,0.01,0.10,0} \definecolor{LightLightLightDandelion} {cmyk}{0,0.03,0.10,0} \definecolor{LightLightLightApricot} {cmyk}{0,0.04,0.06,0} \definecolor{LightLightLightPeach} {cmyk}{0,0.06,0.08,0} \definecolor{LightLightLightMelon} {cmyk}{0,0.05,0.06,0} \definecolor{LightLightLightYellowOrange} {cmyk}{0,0.05,0.12,0} \definecolor{LightLightLightOrange} {cmyk}{0,0.07,0.11,0} \definecolor{LightLightLightBurntOrange} {cmyk}{0,0.06,0.12,0} \definecolor{LightLightLightBittersweet} {cmyk}{0,0.09,0.12,0.03} \definecolor{LightLightLightRedOrange} {cmyk}{0,0.07,0.11,0} \definecolor{LightLightLightMahagony} {cmyk}{0,0.10,0.11,0.04} \definecolor{LightLightLightMaroon} {cmyk}{0,0.11,0.08,0.04} \definecolor{LightLightLightBrickRed} {cmyk}{0,0.11,0.11,0.03} \definecolor{LightLightLightRed} {cmyk}{0,0.12,0.12,0} \definecolor{LightLightLightOrangeRed} {cmyk}{0,0.12,0.06,0} \definecolor{LightLightLightRubineRed} {cmyk}{0,0.12,0.01,0} \definecolor{LightLightLightWildStrawberry}{cmyk}{0,0.12,0.05,0} \definecolor{LightLightLightSalmon} {cmyk}{0,0.06,0.04,0} \definecolor{LightLightLightCarnationPink} {cmyk}{0,0.08,0,0} \definecolor{LightLightLightMagenta} {cmyk}{0,0.12,0,0} \definecolor{LightLightLightLightMagenta} {cmyk}{0,0.06,0,0} \definecolor{LightLightLightVioletRed} {cmyk}{0,0.10,0,0} \definecolor{LightLightLightRhodamine} {cmyk}{0,0.10,0,0} \definecolor{LightLightLightMulberry} {cmyk}{0.04,0.11,0,0.002} \definecolor{LightLightLightRedViolet} {cmyk}{0.01,0.11,0,0.04} \definecolor{LightLightLightFuchsia} {cmyk}{0.06,0.11,0,0.01} \definecolor{LightLightLightLavender} {cmyk}{0,0.06,0,0} \definecolor{LightLightLightThistle} {cmyk}{0.01,0.07,0,0} \definecolor{LightLightLightOrchid} {cmyk}{0.04,0.08,0,0} \definecolor{LightLightLightDarkOrchid} {cmyk}{0.05,0.10,0.02,0} \definecolor{LightLightLightPurple} {cmyk}{0.05,0.10,0,0} \definecolor{LightLightLightPlum} {cmyk}{0.06,0.12,0,0} \definecolor{LightLightLightViolet} {cmyk}{0.10,0.11,0,0} \definecolor{LightLightLightRoyalPurple} {cmyk}{0.09,0.11,0,0} \definecolor{LightLightLightBlueViolet} {cmyk}{0.10,0.11,0,0.005} \definecolor{LightLightLightPeriwinkle} {cmyk}{0.07,0.07,0,0} \definecolor{LightLightLightCadetBlue} {cmyk}{0.07,0.07,0.03,0} \definecolor{LightLightLightCornflowerBlue}{cmyk}{0.08,0.01,0,0} \definecolor{LightLightLightMidnightBlue} {cmyk}{0.12,0.01,0,0.05} \definecolor{LightLightLightNavyBlue} {cmyk}{0.11,0.06,0,0} \definecolor{LightLightLightRoyalBlue} {cmyk}{0.12,0.06,0,0} \definecolor{LightLightLightBlue} {cmyk}{0.12,0.12,0,0} \definecolor{LightLightLightCerulean} {cmyk}{0.11,0.01,0,0} \definecolor{LightLightLightCyan} {cmyk}{0.12,0,0,0} \definecolor{LightLightLightProcessBlue} {cmyk}{0.12,0,0,0} \definecolor{LightLightLightSkyBlue} {cmyk}{0.07,0,0.01,0} \definecolor{LightLightLightTurquoise} {cmyk}{0.10,0,0.02,0} \definecolor{LightLightLightTealBlue} {cmyk}{0.10,0,0.04,0.002} \definecolor{LightLightLightAquamarine} {cmyk}{0.10,0,0.03,0} \definecolor{LightLightLightBlueGreen} {cmyk}{0.10,0,0.04,0} \definecolor{LightLightLightEmerald} {cmyk}{0.12,0,0.06,0} \definecolor{LightLightLightJungleGreen} {cmyk}{0.12,0,0.06,0} \definecolor{LightLightLightSeaGreen} {cmyk}{0.08,0,0.06,0} \definecolor{LightLightLightGreen} {cmyk}{0.12,0,0.12,0} \definecolor{LightLightLightForestGreen} {cmyk}{0.11,0,0.11,0.01} \definecolor{LightLightLightPineGreen} {cmyk}{0.11,0,0.07,0.03} \definecolor{LightLightLightLimeGreen} {cmyk}{0.06,0,0.12,0} \definecolor{LightLightLightYellowGreen} {cmyk}{0.05,0,0.09,0} \definecolor{LightLightLightSpringGreen} {cmyk}{0.03,0,0.09,0} \definecolor{LightLightLightOliveGreen} {cmyk}{0.08,0,0.12,0.05} \definecolor{LightLightLightRawSienna} {cmyk}{0,0.09,0.12,0.05} \definecolor{LightLightLightSepia} {cmyk}{0,0.11,0.12,0.06} \definecolor{LightLightLightBrown} {cmyk}{0,0.10,0.12,0.07} \definecolor{LightLightLightTan} {cmyk}{0.01,0.05,0.07,0} \definecolor{LightLightLightWhite} {cmyk}{0,0,0,0} \definecolor{LightLightLightGray0} {cmyk}{0,0,0,0} \definecolor{LightLightLightGray5} {cmyk}{0,0,0,0.005} \definecolor{LightLightLightGray10} {cmyk}{0,0,0,0.01} \definecolor{LightLightLightGray15} {cmyk}{0,0,0,0.015} \definecolor{LightLightLightGray20} {cmyk}{0,0,0,0.025} \definecolor{LightLightLightGray25} {cmyk}{0,0,0,0.03} \definecolor{LightLightLightGray30} {cmyk}{0,0,0,0.035} \definecolor{LightLightLightLightGray} {cmyk}{0,0,0,0.04} \definecolor{LightLightLightGray35} {cmyk}{0,0,0,0.045} \definecolor{LightLightLightGray40} {cmyk}{0,0,0,0.05} \definecolor{LightLightLightGray45} {cmyk}{0,0,0,0.055} \definecolor{LightLightLightGray50} {cmyk}{0,0,0,0.06} \definecolor{LightLightLightGray} {cmyk}{0,0,0,0.065} \definecolor{LightLightLightGray55} {cmyk}{0,0,0,0.07} \definecolor{LightLightLightGray60} {cmyk}{0,0,0,0.075} \definecolor{LightLightLightGray65} {cmyk}{0,0,0,0.08} \definecolor{LightLightLightDarkGray} {cmyk}{0,0,0,0.085} \definecolor{LightLightLightGray70} {cmyk}{0,0,0,0.09} \definecolor{LightLightLightGray75} {cmyk}{0,0,0,0.095} \definecolor{LightLightLightGray80} {cmyk}{0,0,0,0.10} \definecolor{LightLightLightGray85} {cmyk}{0,0,0,0.105} \definecolor{LightLightLightGray90} {cmyk}{0,0,0,0.11} \definecolor{LightLightLightGray95} {cmyk}{0,0,0,0.115} \definecolor{LightLightLightBlack} {cmyk}{0,0,0,0.12} \definecolor{LightLightLightGray100} {cmyk}{0,0,0,0.125} \definecolor{LightLightLightTC0} {cmyk}{0.05,0.05,0,0} \definecolor{LightLightLightTC1} {cmyk}{0.075,0,0.086,0} \definecolor{LightLightLightTC2} {cmyk}{0.05,0,0.086,0} \definecolor{LightLightLightTC3} {cmyk}{0.025,0,0.125,0} \definecolor{LightLightLightTC4} {cmyk}{0,0,0.125,0} \definecolor{LightLightLightTC5} {cmyk}{0,0.025,0.125,0} \definecolor{LightLightLightTC6} {cmyk}{0,0.05,0.125,0} \definecolor{LightLightLightTC7} {cmyk}{0,0.0175,0.125,0} \definecolor{LightLightLightTC8} {cmyk}{0,0.1,0.125,0} \definecolor{LightLightLightTC99} {cmyk}{0,0,0,0} \definecolor{BlueRed5} {rgb} {0.15,0.17,0.55} \definecolor{BlueRed10} {rgb} {0.20,0.23,0.57} \definecolor{BlueRed15} {rgb} {0.24,0.29,0.60} \definecolor{BlueRed20} {rgb} {0.33,0.35,0.64} \definecolor{BlueRed25} {rgb} {0.43,0.43,0.68} \definecolor{BlueRed30} {rgb} {0.52,0.52,0.73} \definecolor{BlueRed35} {rgb} {0.60,0.60,0.78} \definecolor{BlueRed40} {rgb} {0.70,0.70,0.84} \definecolor{BlueRed45} {rgb} {0.80,0.80,0.85} \definecolor{BlueRed50} {rgb} {0.86,0.82,0.82} \definecolor{BlueRed55} {rgb} {0.87,0.73,0.73} \definecolor{BlueRed60} {rgb} {0.89,0.64,0.64} \definecolor{BlueRed65} {rgb} {0.90,0.55,0.55} \definecolor{BlueRed70} {rgb} {0.91,0.47,0.46} \definecolor{BlueRed75} {rgb} {0.91,0.39,0.37} \definecolor{BlueRed80} {rgb} {0.90,0.33,0.28} \definecolor{BlueRed85} {rgb} {0.89,0.25,0.20} \definecolor{BlueRed90} {rgb} {0.88,0.23,0.14} \definecolor{BlueRed95} {rgb} {0.87,0.21,0.09} \definecolor{BlueRed100} {rgb} {0.87,0.16,0.04} \definecolor{RedBlue100} {rgb} {0.15,0.17,0.55} \definecolor{RedBlue95} {rgb} {0.15,0.17,0.55} \definecolor{RedBlue90} {rgb} {0.20,0.23,0.57} \definecolor{RedBlue85} {rgb} {0.24,0.29,0.60} \definecolor{RedBlue80} {rgb} {0.33,0.35,0.64} \definecolor{RedBlue75} {rgb} {0.43,0.43,0.68} \definecolor{RedBlue70} {rgb} {0.52,0.52,0.73} \definecolor{RedBlue65} {rgb} {0.60,0.60,0.78} \definecolor{RedBlue60} {rgb} {0.70,0.70,0.84} \definecolor{RedBlue55} {rgb} {0.80,0.80,0.85} \definecolor{RedBlue50} {rgb} {0.86,0.82,0.82} \definecolor{RedBlue45} {rgb} {0.87,0.73,0.73} \definecolor{RedBlue40} {rgb} {0.89,0.64,0.64} \definecolor{RedBlue35} {rgb} {0.90,0.55,0.55} \definecolor{RedBlue30} {rgb} {0.91,0.47,0.46} \definecolor{RedBlue25} {rgb} {0.91,0.39,0.37} \definecolor{RedBlue20} {rgb} {0.90,0.33,0.28} \definecolor{RedBlue15} {rgb} {0.89,0.25,0.20} \definecolor{RedBlue10} {rgb} {0.88,0.23,0.14} \definecolor{RedBlue5} {rgb} {0.87,0.21,0.09} \definecolor{GreenRed5} {rgb} {0,1,0} \definecolor{GreenRed10} {rgb} {0.05,0.95,0} \definecolor{GreenRed15} {rgb} {0.10,0.90,0} \definecolor{GreenRed20} {rgb} {0.15,0.85,0} \definecolor{GreenRed25} {rgb} {0.20,0.80,0} \definecolor{GreenRed30} {rgb} {0.25,0.75,0} \definecolor{GreenRed35} {rgb} {0.30,0.70,0} \definecolor{GreenRed40} {rgb} {0.35,0.65,0} \definecolor{GreenRed45} {rgb} {0.40,0.60,0} \definecolor{GreenRed50} {rgb} {0.45,0.55,0} \definecolor{GreenRed55} {rgb} {0.50,0.50,0} \definecolor{GreenRed60} {rgb} {0.55,0.45,0} \definecolor{GreenRed65} {rgb} {0.60,0.40,0} \definecolor{GreenRed70} {rgb} {0.65,0.35,0} \definecolor{GreenRed75} {rgb} {0.70,0.30,0} \definecolor{GreenRed80} {rgb} {0.75,0.25,0} \definecolor{GreenRed85} {rgb} {0.80,0.20,0} \definecolor{GreenRed90} {rgb} {0.85,0.15,0} \definecolor{GreenRed95} {rgb} {0.90,0.10,0} \definecolor{GreenRed100} {rgb} {0.95,0.05,0} \definecolor{RedGreen100} {rgb} {0.05,0.95,0} \definecolor{RedGreen95} {rgb} {0.10,0.90,0} \definecolor{RedGreen90} {rgb} {0.15,0.85,0} \definecolor{RedGreen85} {rgb} {0.20,0.80,0} \definecolor{RedGreen80} {rgb} {0.25,0.75,0} \definecolor{RedGreen75} {rgb} {0.30,0.70,0} \definecolor{RedGreen70} {rgb} {0.35,0.65,0} \definecolor{RedGreen65} {rgb} {0.40,0.60,0} \definecolor{RedGreen60} {rgb} {0.45,0.55,0} \definecolor{RedGreen55} {rgb} {0.50,0.50,0} \definecolor{RedGreen50} {rgb} {0.55,0.45,0} \definecolor{RedGreen45} {rgb} {0.60,0.40,0} \definecolor{RedGreen40} {rgb} {0.65,0.35,0} \definecolor{RedGreen35} {rgb} {0.70,0.30,0} \definecolor{RedGreen30} {rgb} {0.75,0.25,0} \definecolor{RedGreen25} {rgb} {0.80,0.20,0} \definecolor{RedGreen20} {rgb} {0.85,0.15,0} \definecolor{RedGreen15} {rgb} {0.90,0.10,0} \definecolor{RedGreen10} {rgb} {0.95,0.05,0} \definecolor{RedGreen5} {rgb} {1,0,0} \definecolor{ColdHot5} {rgb} {0,0.08,1} \definecolor{ColdHot10} {rgb} {0,0.29,1} \definecolor{ColdHot15} {rgb} {0,0.49,1} \definecolor{ColdHot20} {rgb} {0,0.70,1} \definecolor{ColdHot25} {rgb} {0,0.90,1} \definecolor{ColdHot30} {rgb} {0,1,0.87} \definecolor{ColdHot35} {rgb} {0,1,0.68} \definecolor{ColdHot40} {rgb} {0,1,0.46} \definecolor{ColdHot45} {rgb} {0,1,0.25} \definecolor{ColdHot50} {rgb} {0,1,0.04} \definecolor{ColdHot55} {rgb} {0.16,1,0} \definecolor{ColdHot60} {rgb} {0.35,1,0} \definecolor{ColdHot65} {rgb} {0.56,1,0} \definecolor{ColdHot70} {rgb} {0.79,1,0} \definecolor{ColdHot75} {rgb} {0.98,1,0} \definecolor{ColdHot80} {rgb} {1,0.82,0} \definecolor{ColdHot85} {rgb} {1,0.60,0} \definecolor{ColdHot90} {rgb} {1,0.40,0} \definecolor{ColdHot95} {rgb} {1,0.20,0} \definecolor{ColdHot100} {rgb} {0.91,0,0} \definecolor{HotCold100} {rgb} {0,0.08,1} \definecolor{HotCold95} {rgb} {0,0.29,1} \definecolor{HotCold90} {rgb} {0,0.49,1} \definecolor{HotCold85} {rgb} {0,0.70,1} \definecolor{HotCold80} {rgb} {0,0.90,1} \definecolor{HotCold75} {rgb} {0,1,0.87} \definecolor{HotCold70} {rgb} {0,1,0.68} \definecolor{HotCold65} {rgb} {0,1,0.46} \definecolor{HotCold60} {rgb} {0,1,0.25} \definecolor{HotCold55} {rgb} {0,1,0.04} \definecolor{HotCold50} {rgb} {0.16,1,0} \definecolor{HotCold45} {rgb} {0.35,1,0} \definecolor{HotCold40} {rgb} {0.56,1,0} \definecolor{HotCold35} {rgb} {0.79,1,0} \definecolor{HotCold30} {rgb} {0.98,1,0} \definecolor{HotCold25} {rgb} {1,0.82,0} \definecolor{HotCold20} {rgb} {1,0.60,0} \definecolor{HotCold15} {rgb} {1,0.40,0} \definecolor{HotCold10} {rgb} {1,0.20,0} \definecolor{HotCold5} {rgb} {0.91,0,0} \expandafter\def\csname BlueRed5\endcsname{[0.15,0.17,0.55]} \expandafter\def\csname BlueRed10\endcsname{[0.20,0.23,0.57]} \expandafter\def\csname BlueRed15\endcsname{[0.24,0.29,0.60]} \expandafter\def\csname BlueRed20\endcsname{[0.33,0.35,0.64]} \expandafter\def\csname BlueRed25\endcsname{[0.43,0.43,0.68]} \expandafter\def\csname BlueRed30\endcsname{[0.52,0.52,0.73]} \expandafter\def\csname BlueRed35\endcsname{[0.60,0.60,0.78]} \expandafter\def\csname BlueRed40\endcsname{[0.70,0.70,0.84]} \expandafter\def\csname BlueRed45\endcsname{[0.80,0.80,0.85]} \expandafter\def\csname BlueRed50\endcsname{[0.86,0.82,0.82]} \expandafter\def\csname BlueRed55\endcsname{[0.87,0.73,0.73]} \expandafter\def\csname BlueRed60\endcsname{[0.89,0.64,0.64]} \expandafter\def\csname BlueRed65\endcsname{[0.90,0.55,0.55]} \expandafter\def\csname BlueRed70\endcsname{[0.91,0.47,0.46]} \expandafter\def\csname BlueRed75\endcsname{[0.91,0.39,0.37]} \expandafter\def\csname BlueRed80\endcsname{[0.90,0.33,0.28]} \expandafter\def\csname BlueRed85\endcsname{[0.89,0.25,0.20]} \expandafter\def\csname BlueRed90\endcsname{[0.88,0.23,0.14]} \expandafter\def\csname BlueRed95\endcsname{[0.87,0.21,0.09]} \expandafter\def\csname BlueRed100\endcsname{[0.87,0.16,0.04]} \expandafter\def\csname RedBlue100\endcsname{[0.15,0.17,0.55]} \expandafter\def\csname RedBlue95\endcsname{[0.15,0.17,0.55]} \expandafter\def\csname RedBlue90\endcsname{[0.20,0.23,0.57]} \expandafter\def\csname RedBlue85\endcsname{[0.24,0.29,0.60]} \expandafter\def\csname RedBlue80\endcsname{[0.33,0.35,0.64]} \expandafter\def\csname RedBlue75\endcsname{[0.43,0.43,0.68]} \expandafter\def\csname RedBlue70\endcsname{[0.52,0.52,0.73]} \expandafter\def\csname RedBlue65\endcsname{[0.60,0.60,0.78]} \expandafter\def\csname RedBlue60\endcsname{[0.70,0.70,0.84]} \expandafter\def\csname RedBlue55\endcsname{[0.80,0.80,0.85]} \expandafter\def\csname RedBlue50\endcsname{[0.86,0.82,0.82]} \expandafter\def\csname RedBlue45\endcsname{[0.87,0.73,0.73]} \expandafter\def\csname RedBlue40\endcsname{[0.89,0.64,0.64]} \expandafter\def\csname RedBlue35\endcsname{[0.90,0.55,0.55]} \expandafter\def\csname RedBlue30\endcsname{[0.91,0.47,0.46]} \expandafter\def\csname RedBlue25\endcsname{[0.91,0.39,0.37]} \expandafter\def\csname RedBlue20\endcsname{[0.90,0.33,0.28]} \expandafter\def\csname RedBlue15\endcsname{[0.89,0.25,0.20]} \expandafter\def\csname RedBlue10\endcsname{[0.88,0.23,0.14]} \expandafter\def\csname RedBlue5\endcsname{[0.87,0.21,0.09]} \expandafter\def\csname GreenRed5\endcsname{[0,1,0]} \expandafter\def\csname GreenRed10\endcsname{[0.05,0.95,0]} \expandafter\def\csname GreenRed15\endcsname{[0.10,0.90,0]} \expandafter\def\csname GreenRed20\endcsname{[0.15,0.85,0]} \expandafter\def\csname GreenRed25\endcsname{[0.20,0.80,0]} \expandafter\def\csname GreenRed30\endcsname{[0.25,0.75,0]} \expandafter\def\csname GreenRed35\endcsname{[0.30,0.70,0]} \expandafter\def\csname GreenRed40\endcsname{[0.35,0.65,0]} \expandafter\def\csname GreenRed45\endcsname{[0.40,0.60,0]} \expandafter\def\csname GreenRed50\endcsname{[0.45,0.55,0]} \expandafter\def\csname GreenRed55\endcsname{[0.50,0.50,0]} \expandafter\def\csname GreenRed60\endcsname{[0.55,0.45,0]} \expandafter\def\csname GreenRed65\endcsname{[0.60,0.40,0]} \expandafter\def\csname GreenRed70\endcsname{[0.65,0.35,0]} \expandafter\def\csname GreenRed75\endcsname{[0.70,0.30,0]} \expandafter\def\csname GreenRed80\endcsname{[0.75,0.25,0]} \expandafter\def\csname GreenRed85\endcsname{[0.80,0.20,0]} \expandafter\def\csname GreenRed90\endcsname{[0.85,0.15,0]} \expandafter\def\csname GreenRed95\endcsname{[0.90,0.10,0]} \expandafter\def\csname GreenRed100\endcsname{[0.95,0.05,0]} \expandafter\def\csname RedGreen100\endcsname{[0.05,0.95,0]} \expandafter\def\csname RedGreen95\endcsname{[0.10,0.90,0]} \expandafter\def\csname RedGreen90\endcsname{[0.15,0.85,0]} \expandafter\def\csname RedGreen85\endcsname{[0.20,0.80,0]} \expandafter\def\csname RedGreen80\endcsname{[0.25,0.75,0]} \expandafter\def\csname RedGreen75\endcsname{[0.30,0.70,0]} \expandafter\def\csname RedGreen70\endcsname{[0.35,0.65,0]} \expandafter\def\csname RedGreen65\endcsname{[0.40,0.60,0]} \expandafter\def\csname RedGreen60\endcsname{[0.45,0.55,0]} \expandafter\def\csname RedGreen55\endcsname{[0.50,0.50,0]} \expandafter\def\csname RedGreen50\endcsname{[0.55,0.45,0]} \expandafter\def\csname RedGreen45\endcsname{[0.60,0.40,0]} \expandafter\def\csname RedGreen40\endcsname{[0.65,0.35,0]} \expandafter\def\csname RedGreen35\endcsname{[0.70,0.30,0]} \expandafter\def\csname RedGreen30\endcsname{[0.75,0.25,0]} \expandafter\def\csname RedGreen25\endcsname{[0.80,0.20,0]} \expandafter\def\csname RedGreen20\endcsname{[0.85,0.15,0]} \expandafter\def\csname RedGreen15\endcsname{[0.90,0.10,0]} \expandafter\def\csname RedGreen10\endcsname{[0.95,0.05,0]} \expandafter\def\csname RedGreen5\endcsname{[1,0,0]} \expandafter\def\csname ColdHot5\endcsname{[0,0.08,1]} \expandafter\def\csname ColdHot10\endcsname{[0,0.29,1]} \expandafter\def\csname ColdHot15\endcsname{[0,0.49,1]} \expandafter\def\csname ColdHot20\endcsname{[0,0.70,1]} \expandafter\def\csname ColdHot25\endcsname{[0,0.90,1]} \expandafter\def\csname ColdHot30\endcsname{[0,1,0.87]} \expandafter\def\csname ColdHot35\endcsname{[0,1,0.68]} \expandafter\def\csname ColdHot40\endcsname{[0,1,0.46]} \expandafter\def\csname ColdHot45\endcsname{[0,1,0.25]} \expandafter\def\csname ColdHot50\endcsname{[0,1,0.04]} \expandafter\def\csname ColdHot55\endcsname{[0.16,1,0]} \expandafter\def\csname ColdHot60\endcsname{[0.35,1,0]} \expandafter\def\csname ColdHot65\endcsname{[0.56,1,0]} \expandafter\def\csname ColdHot70\endcsname{[0.79,1,0]} \expandafter\def\csname ColdHot75\endcsname{[0.98,1,0]} \expandafter\def\csname ColdHot80\endcsname{[1,0.82,0]} \expandafter\def\csname ColdHot85\endcsname{[1,0.60,0]} \expandafter\def\csname ColdHot90\endcsname{[1,0.40,0]} \expandafter\def\csname ColdHot95\endcsname{[1,0.20,0]} \expandafter\def\csname ColdHot100\endcsname{[0.91,0,0]} \expandafter\def\csname HotCold100\endcsname{[0,0.08,1]} \expandafter\def\csname HotCold95\endcsname{[0,0.29,1]} \expandafter\def\csname HotCold90\endcsname{[0,0.49,1]} \expandafter\def\csname HotCold85\endcsname{[0,0.70,1]} \expandafter\def\csname HotCold80\endcsname{[0,0.90,1]} \expandafter\def\csname HotCold75\endcsname{[0,1,0.87]} \expandafter\def\csname HotCold70\endcsname{[0,1,0.68]} \expandafter\def\csname HotCold65\endcsname{[0,1,0.46]} \expandafter\def\csname HotCold60\endcsname{[0,1,0.25]} \expandafter\def\csname HotCold55\endcsname{[0,1,0.04]} \expandafter\def\csname HotCold50\endcsname{[0.16,1,0]} \expandafter\def\csname HotCold45\endcsname{[0.35,1,0]} \expandafter\def\csname HotCold40\endcsname{[0.56,1,0]} \expandafter\def\csname HotCold35\endcsname{[0.79,1,0]} \expandafter\def\csname HotCold30\endcsname{[0.98,1,0]} \expandafter\def\csname HotCold25\endcsname{[1,0.82,0]} \expandafter\def\csname HotCold20\endcsname{[1,0.60,0]} \expandafter\def\csname HotCold15\endcsname{[1,0.40,0]} \expandafter\def\csname HotCold10\endcsname{[1,0.20,0]} \expandafter\def\csname HotCold5\endcsname{[0.91,0,0]} \def\make@lower{% \if\first@ A\xdef\first@{a}\else \if\first@ B\xdef\first@{b}\else \if\first@ C\xdef\first@{c}\else \if\first@ D\xdef\first@{d}\else \if\first@ E\xdef\first@{e}\else \if\first@ F\xdef\first@{f}\else \if\first@ G\xdef\first@{g}\else \if\first@ H\xdef\first@{h}\else \if\first@ I\xdef\first@{i}\else \if\first@ J\xdef\first@{j}\else \if\first@ K\xdef\first@{k}\else \if\first@ L\xdef\first@{l}\else \if\first@ M\xdef\first@{m}\else \if\first@ N\xdef\first@{n}\else \if\first@ O\xdef\first@{o}\else \if\first@ P\xdef\first@{p}\else \if\first@ Q\xdef\first@{q}\else \if\first@ R\xdef\first@{r}\else \if\first@ S\xdef\first@{s}\else \if\first@ T\xdef\first@{t}\else \if\first@ U\xdef\first@{u}\else \if\first@ V\xdef\first@{v}\else \if\first@ W\xdef\first@{w}\else \if\first@ X\xdef\first@{x}\else \if\first@ Y\xdef\first@{y}\else \if\first@ Z\xdef\first@{z}\else \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi} \def\make@upper{% \if\first@ a\xdef\first@{A}\else \if\first@ b\xdef\first@{B}\else \if\first@ c\xdef\first@{C}\else \if\first@ d\xdef\first@{D}\else \if\first@ e\xdef\first@{E}\else \if\first@ f\xdef\first@{F}\else \if\first@ g\xdef\first@{G}\else \if\first@ h\xdef\first@{H}\else \if\first@ i\xdef\first@{I}\else \if\first@ j\xdef\first@{J}\else \if\first@ k\xdef\first@{K}\else \if\first@ l\xdef\first@{L}\else \if\first@ m\xdef\first@{M}\else \if\first@ n\xdef\first@{N}\else \if\first@ o\xdef\first@{O}\else \if\first@ p\xdef\first@{P}\else \if\first@ q\xdef\first@{Q}\else \if\first@ r\xdef\first@{R}\else \if\first@ s\xdef\first@{S}\else \if\first@ t\xdef\first@{T}\else \if\first@ u\xdef\first@{U}\else \if\first@ v\xdef\first@{V}\else \if\first@ w\xdef\first@{W}\else \if\first@ x\xdef\first@{X}\else \if\first@ y\xdef\first@{Y}\else \if\first@ z\xdef\first@{Z}\else \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi} \def\type@get#1 MSF: #2 Type: #3 #4@{\seqtype{#3}} \def\inf@@get#1 #2 #3 #4 #5 #6@{% \def\first@{#1} \def\second@{#2} \def\third@{#3} \xdef\fourth@{#4 @} \expandafter\check@letter\fourth@ \ifnumber \def\fourth@{#4} \else \xdef\fourth@{#5 @} \expandafter\check@letter\fourth@ \ifnumber \def\fourth@{#5} \else \def\fourth@{99999999} \fi \fi \def\fifth@{#5} \def\last@{#6}} \def\check@char#1{\letterfalse \ifnum\catcode`#1=11 \lettertrue \fi \numberfalse \ifnum\catcode`#1=12 \numbertrue \fi \xdef\code@num{\the\catcode`#1} \xdef\char@num{`#1}} \def\check@letter#1#2@{\letterfalse\ifnum\catcode`#1=11 \lettertrue\fi% \numberfalse\ifnum\catcode`#1=12 \numbertrue\fi} \def\seq@get#1 #2@{\def\first@{#1} \def\seq@line{#2}} \def\res@get#1#2@{\def\first@{#1} \def\seq@line{#2&@}} \def\tot@get#1#2@{% \xdef\first@{#1} \expandafter\xdef\csname seq\the\triple@count\endcsname{#2&@}} \def\dis@get#1#2@{% \xdef\first@{#1} \expandafter\xdef\csname res\the\triple@count\endcsname{#1} \expandafter\xdef\csname seq\the\triple@count\endcsname{#2&@}} \def\firstchar@get#1#2@{\def\first@{#1}\def\third@{#2@}} \def\residue@get#1#2@{\xdef\first@{#1} \xdef\char@num{`#1} \expandafter\xdef\csname res\the\loopcount\endcsname{\first@} \expandafter\xdef\csname sequence\the\loopcount\endcsname{#2@}} \def\remove@fromseq#1@{\expandafter\xdef\csname sequence\the\loopcount\endcsname{#1}} \def\get@temp#1@{\xdef\temp@{#1}} \def\TC@get#1#2@{\xdef\char@num{`#1} \ifnum\char@num=45 \xdef\TC@first@{*} \else \ifnum\char@num>57 \xdef\TC@first@{*} \else \xdef\TC@first@{#1} \fi \fi \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\TC@first@} \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{#2@}} \def\sublogo@get#1 @{\xdef\first@{#1}} \def\re@write#1,#2@{% \xdef\third@{#2,@} \xdef\first@{\csname hide@@@seq#1\endcsname} \ifx\first@\last@ \else \xdef\first@{#1&} \ifx\first@\ampers@nd \else \advance\innerloopcount by 1 \fi \if\second@ e \xdef\second@{\csname @rd#1\endcsname} \else \xdef\second@{\second@,\csname @rd#1\endcsname}\fi \fi } \def\order@set#1,#2@{% \xdef\second@{#2,@} \expandafter\xdef\csname @rd#1\endcsname{\the\loopcount} \expandafter\xdef\csname res@count\the\loopcount\endcsname{% \csname pos#1\endcsname} \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{% \csname hide@@seq#1\endcsname} \expandafter\xdef\csname hide@name\the\loopcount\endcsname{% \csname hide@@name#1\endcsname} \expandafter\xdef\csname hide@number\the\loopcount\endcsname{% \csname hide@@number#1\endcsname} \expandafter\xdef\csname seq@start\the\loopcount\endcsname{% \csname seq@@start#1\endcsname} \expandafter\xdef\csname seq@len\the\loopcount\endcsname{% \csname seq@@len#1\endcsname} \expandafter\xdef\csname seqname\the\loopcount\endcsname{% \csname seq@name#1\endcsname} \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% \csname newseq@name#1\endcsname} \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{% \csname seq@@gap#1\endcsname} \expandafter\xdef\csname name@col\the\loopcount\endcsname{% \csname name@@col#1\endcsname} \expandafter\xdef\csname number@col\the\loopcount\endcsname{% \csname number@@col#1\endcsname} \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{% \csname stack@@reg#1\endcsname} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% \csname stack@@tintreg#1\endcsname} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% \csname stack@@emphreg#1\endcsname} \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{% \csname stack@@lowerreg#1\endcsname} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% \csname stack@@framereg#1\endcsname} \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{% \csname stack@@shadingreg#1\endcsname} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{% \csname stack@@top#1\endcsname} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% \csname stack@@ttop#1\endcsname} \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% \csname stack@@tttop#1\endcsname} \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% \csname stack@@ttttop#1\endcsname} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% \csname stack@@bottom#1\endcsname} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% \csname stack@@bbottom#1\endcsname} \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% \csname stack@@bbbottom#1\endcsname} \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% \csname stack@@bbbbottom#1\endcsname} } \def\reorder@seqs#1{% \loopcount=0 \loop \advance\loopcount by 1 \expandafter\xdef\csname pos\the\loopcount\endcsname{% \csname res@count\the\loopcount\endcsname} \expandafter\xdef\csname hide@@seq\the\loopcount\endcsname{% \csname hide@seq\the\loopcount\endcsname} \expandafter\xdef\csname hide@@name\the\loopcount\endcsname{% \csname hide@name\the\loopcount\endcsname} \expandafter\xdef\csname hide@@number\the\loopcount\endcsname{% \csname hide@number\the\loopcount\endcsname} \expandafter\xdef\csname seq@@start\the\loopcount\endcsname{% \csname seq@start\the\loopcount\endcsname} \expandafter\xdef\csname seq@@len\the\loopcount\endcsname{% \csname seq@len\the\loopcount\endcsname} \expandafter\xdef\csname seq@name\the\loopcount\endcsname{% \csname seqname\the\loopcount\endcsname} \expandafter\xdef\csname newseq@name\the\loopcount\endcsname{% \csname newseqname\the\loopcount\endcsname} \expandafter\xdef\csname seq@@gap\the\loopcount\endcsname{% \csname seq@gap\the\loopcount\endcsname} \expandafter\xdef\csname name@@col\the\loopcount\endcsname{% \csname name@col\the\loopcount\endcsname} \expandafter\xdef\csname number@@col\the\loopcount\endcsname{% \csname number@col\the\loopcount\endcsname} \expandafter\xdef\csname stack@@reg\the\loopcount\endcsname{% \csname stack@reg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{% \csname stack@tintreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{% \csname stack@emphreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@lowerreg\the\loopcount\endcsname{% \csname stack@lowerreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{% \csname stack@framereg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@shadingreg\the\loopcount\endcsname{% \csname stack@shadingreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@@top\the\loopcount\endcsname{% \csname stack@top\the\loopcount\endcsname} \expandafter\xdef\csname stack@@ttop\the\loopcount\endcsname{% \csname stack@ttop\the\loopcount\endcsname} \expandafter\xdef\csname stack@@tttop\the\loopcount\endcsname{% \csname stack@tttop\the\loopcount\endcsname} \expandafter\xdef\csname stack@@ttttop\the\loopcount\endcsname{% \csname stack@ttttop\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bottom\the\loopcount\endcsname{% \csname stack@bottom\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bbottom\the\loopcount\endcsname{% \csname stack@bbottom\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bbbottom\the\loopcount\endcsname{% \csname stack@bbbottom\the\loopcount\endcsname} \expandafter\xdef\csname stack@@bbbbottom\the\loopcount\endcsname{% \csname stack@bbbbottom\the\loopcount\endcsname} \ifnum\loopcount<\killseq@count \repeat \xdef\third@{#1} \loopcount=0 \innerloopcount=0 \xdef\last@{kill} \xdef\second@{e} \loop \advance\loopcount by 1 \expandafter\re@write\third@ \ifnum\loopcount<\seq@count \repeat \ifnum\innerloopcount<\killseq@count \@latex@error{Not enough sequences specified in `orderseqs' (\the\innerloopcount/\the\killseq@count)}\@ehc \fi \loopcount=0 \xdef\second@{\second@,@} \loop \advance\loopcount by 1 \expandafter\order@set\second@ \ifnum\loopcount<\killseq@count \repeat \ifnum\cons@num>0 \xdef\cons@num{\csname @rd\cons@num\endcsname} \fi \ifnum\rule@num>0 \xdef\rule@num{\csname @rd\rule@num\endcsname} \fi \ifnum\divref@>0 \xdef\divref@{\csname @rd\divref@\endcsname} \fi \loopcount=0 \loop \advance\loopcount by 1 \expandafter\xdef\csname pos\the\loopcount\endcsname{0} \ifnum\loopcount<\killseq@count \repeat } \def\group@get#1,#2@{% \def\group@set{\expandafter\residue@get\second@ \ifnum\char@num>96 \make@upper \fi \ifx\first@\ampers@nd \else \expandafter\xdef\csname \prfx grp\first@\endcsname{\the\loopcount} \xdef\second@{\csname sequence\the\loopcount\endcsname} \group@set \fi} \xdef\second@{#1 &@} \xdef\third@{#2&,@} \group@set} \def\get@item#1,#2@{\xdef\first@{#2@}\xdef\first@@{#2}\xdef\fourth@{#1}} \def\get@first@@#1-#2@{\xdef\first@@{#1}} \def\get@digit#1,#2@{% \def\check@series##1-##2##3@{% \xdef\first@@{##2}\xdef\fourth@{##1}\xdef\fourth@@{##3}} \xdef\first@{#2@} \xdef\fourth@{#1-&@} \expandafter\check@series\fourth@ \ifx\first@@\ampers@nd \else \xdef\first@@{\first@@\fourth@@-&@} \expandafter\get@first@@\first@@ \loopcount=\fourth@ \ifnum\first@@>\fourth@ \advance\loopcount by 1 \xdef\first@{\the\loopcount-\first@@,#2@} \else \ifnum\first@@<\fourth@ \advance\loopcount by -1 \xdef\first@{\the\loopcount-\first@@,#2@} \fi \fi \fi } \def\donot@shade{% \expandafter\check@letter\first@ \ifletter \expandafter\get@item\first@ \xdef\first@{\fourth@} \get@name@number \xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill} \ifx\third@\second@ \else \expandafter\xdef\csname hide@seq\first@\endcsname{noshade} \fi \xdef\first@{\first@@ @} \donot@shade \else \expandafter\get@digit\first@ \ifx\fourth@\ampers@nd \else \xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill} \ifx\third@\second@ \else \expandafter\xdef\csname hide@seq\fourth@\endcsname{noshade} \fi \donot@shade \fi \fi} \def\clear@res@nums#1{% \temp@count=65 \loop \xdef\first@@{\csname ch@r@\the\temp@count\endcsname} \expandafter\xdef\csname res@num\first@@ #1\endcsname{0} \advance\temp@count by 1 \ifnum\temp@count>90\else\repeat \expandafter\xdef\csname res@num\d@t #1\endcsname{0} \expandafter\xdef\csname res@num\questi@n #1\endcsname{0} } \def\setsubfamily@{% \expandafter\check@letter\first@ \ifletter \expandafter\get@item\first@ \xdef\first@{\fourth@} \get@name@number \advance\res@count by 1 \expandafter\xdef\csname subfamily@num\first@\endcsname{\subfamily@count} \xdef\first@{\first@@ @} \setsubfamily@ \else \expandafter\get@digit\first@ \ifx\fourth@\ampers@nd \else \advance\res@count by 1 \expandafter\xdef\csname subfamily@num\fourth@\endcsname{\subfamily@count} \setsubfamily@ \fi \fi } \def\hideseq@{% \expandafter\check@letter\first@ \ifletter \expandafter\get@item\first@ \xdef\first@{\fourth@} \get@name@number \xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill} \ifx\third@\second@ \else \expandafter\xdef\csname hide@seq\first@\endcsname{true} \fi \xdef\first@{\first@@ @} \hideseq@ \else \expandafter\get@digit\first@ \ifx\fourth@\ampers@nd \else \xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill} \ifx\third@\second@ \else \expandafter\xdef\csname hide@seq\fourth@\endcsname{true} \fi \hideseq@ \fi \fi} \def\hidename@{% \expandafter\check@letter\first@ \ifletter \expandafter\get@item\first@ \xdef\first@{\fourth@} \get@name@number \expandafter\xdef\csname hide@name\first@\endcsname{yes} \xdef\first@{\first@@ @} \hidename@ \else \expandafter\get@digit\first@ \ifx\fourth@\ampers@nd \else \expandafter\xdef\csname hide@name\fourth@\endcsname{yes} \hidename@ \fi \fi} \def\hidenumber@{% \expandafter\check@letter\first@ \ifletter \expandafter\get@item\first@ \xdef\first@{\fourth@} \get@name@number \expandafter\xdef\csname hide@number\first@\endcsname{yes} \xdef\first@{\first@@ @} \hidenumber@ \else \expandafter\get@digit\first@ \ifx\fourth@\ampers@nd \else \expandafter\xdef\csname hide@number\fourth@\endcsname{yes} \hidenumber@ \fi \fi} \def\namecolor@{% \expandafter\check@letter\first@ \ifletter \expandafter\get@item\first@ \xdef\first@{\fourth@} \get@name@number \expandafter\xdef\csname name@col\first@\endcsname{\third@} \xdef\first@{\first@@ @} \namecolor@ \else \expandafter\get@digit\first@ \ifx\fourth@\ampers@nd \else \expandafter\xdef\csname name@col\fourth@\endcsname{\third@} \namecolor@ \fi \fi} \def\numbercolor@{% \expandafter\check@letter\first@ \ifletter \expandafter\get@item\first@ \xdef\first@{\fourth@} \get@name@number \expandafter\xdef\csname number@col\first@\endcsname{\third@} \xdef\first@{\first@@ @} \numbercolor@ \else \expandafter\get@digit\first@ \ifx\fourth@\ampers@nd \else \expandafter\xdef\csname number@col\fourth@\endcsname{\third@} \numbercolor@ \fi \fi} \def\killseq@{% \expandafter\check@letter\first@ \ifletter \expandafter\get@item\first@ \xdef\first@{\fourth@} \get@name@number \ifnum\first@>\seq@count \else \ifnum\killseq@count>1 \xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill} \ifx\third@\second@ \else \expandafter\xdef\csname hide@seq\first@\endcsname{kill} \expandafter\xdef\csname hide@@@seq\first@\endcsname{kill} \ifnum\first@=\cons@num \xdef\cons@num{0} \fi \advance\killseq@count by -1 \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 \fi \fi\fi \killseq@ \fi \fi} \def\kill@loop{% \advance\innerloopcount by 1 \xdef\first@{\csname hide@seq\the\innerloopcount\endcsname} \ifx\first@\second@ \kill@loop \fi} \def\kill@seqnow{% \xdef\first@{\csname hide@seq\the\loopcount\endcsname} \xdef\second@{kill} \innerloopcount=\loopcount \ifx\first@\second@ \kill@loop \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{% \csname hide@seq\the\innerloopcount\endcsname} \expandafter\xdef\csname seqname\the\loopcount\endcsname{% \csname seqname\the\innerloopcount\endcsname} \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% \csname newseqname\the\innerloopcount\endcsname} \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{% \csname seq@gap\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{% \csname stack@reg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{% \csname stack@tintreg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{% \csname stack@emphreg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{% \csname stack@lowerreg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{% \csname stack@framereg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{% \csname stack@shadingreg\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{% \csname stack@top\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{% \csname stack@ttop\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{% \csname stack@tttop\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{% \csname stack@ttttop\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{% \csname stack@bottom\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{% \csname stack@bbottom\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{% \csname stack@bbbottom\the\innerloopcount\endcsname} \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{% \csname stack@bbbbottom\the\innerloopcount\endcsname} \expandafter\xdef\csname res@count\the\loopcount\endcsname{% \csname res@count\the\innerloopcount\endcsname} \expandafter\xdef\csname hide@seq\the\innerloopcount\endcsname{kill} \ifnum\loopcount=\rule@num \hideruler \fi \fi \expandafter\xdef\csname @rd\the\innerloopcount\endcsname{\the\loopcount} \advance\loopcount by 1 \ifnum\loopcount>\killseq@count \ifnum\rule@num>0\xdef\rule@num{\csname @rd\rule@num\endcsname}\fi \ifnum\cons@num>0\xdef\cons@num{\csname @rd\cons@num\endcsname}\fi \else \kill@seqnow \fi} \def\get@sim#1#2@{\xdef\sim@char{#1} \xdef\last@{#2 &@}} \def\getsim@char{% \advance\innerloopcount by 1 \ifnum\innerloopcount>\m@x \else \expandafter\get@sim\last@ \ifx\second@\sim@char \xdef\third@{2} \innerloopcount=\m@x \fi \getsim@char \fi} \def\get@count(#1)#2@{\xdef\last@{#2 &@} \xdef\m@x{#1}} \def\get@nums#1..#2@{\xdef\first@{#1} \xdef\second@{#2}} \def\func@shading#1{% \clearfuncgroups \xdef\temp@{#1} \xdef\second@{charge} \ifx\temp@\second@ \ifgerm@n \funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up} \funcgroup{basisch ($+$)}{KRH}{White}{Blue}{upper}{up} \else \ifsp@nish \funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up} \funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up} \else \funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up} \funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up} \fi \fi \else \xdef\second@{hydropathy} \ifx\temp@\second@ \ifgerm@n \funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up} \funcgroup{basisch ($+$)}{KRH}{White}{Blue}{upper}{up} \funcgroup{polar ungeladen}{YSTGNQC}{Black}{Yellow}{upper}{up} \funcgroup{hydrophob unpolar}{AFPMWVIL}{White}{Green}{upper}{up} \else \ifsp@nish \funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up} \funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up} \funcgroup{polar sin carga}{YSTGNQC}{Black}{Yellow}{upper}{up} \funcgroup{hidrof\'obico no polar}{AFPMWVIL}{White}{Green}{upper}{up} \else \funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up} \funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up} \funcgroup{polar uncharged}{YSTGNQC}{Black}{Yellow}{upper}{up} \funcgroup{hydrophobic nonpolar}{AFPMWVIL}{White}{Green}{upper}{up} \fi \fi \else \xdef\second@{chemical} \ifx\temp@\second@ \ifgerm@n \funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up} \funcgroup{aliphatisch}{AGVIL}{White}{Black}{upper}{up} \funcgroup{aliphatisch (klein)}{AG}{White}{Gray}{upper}{up} \funcgroup{Amid}{NQ}{White}{Green}{upper}{up} \funcgroup{aromatisch}{FYW}{White}{Brown}{upper}{up} \funcgroup{basisch (+)}{KRH}{White}{Blue}{upper}{up} \funcgroup{Hydroxyl}{ST}{Black}{Magenta}{upper}{up} \funcgroup{Imin}{P}{Black}{Orange}{upper}{up} \funcgroup{Schwefel}{CM}{Black}{Yellow}{upper}{up} \else \ifsp@nish \funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up} \funcgroup{alif\'atico}{AGVIL}{White}{Black}{upper}{up} \funcgroup{alif\'atico (parvo)}{AG}{White}{Gray}{upper}{up} \funcgroup{amida}{NQ}{White}{Green}{upper}{up} \funcgroup{arom\'atico}{FYW}{White}{Brown}{upper}{up} \funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up} \funcgroup{hidr\'oxido}{ST}{Black}{Magenta}{upper}{up} \funcgroup{imino}{P}{Black}{Orange}{upper}{up} \funcgroup{azufre}{CM}{Black}{Yellow}{upper}{up} \else \funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up} \funcgroup{aliphatic}{AGVIL}{White}{Black}{upper}{up} \funcgroup{aliphatic (small)}{AG}{White}{Gray}{upper}{up} \funcgroup{amide}{NQ}{White}{Green}{upper}{up} \funcgroup{aromatic}{FYW}{White}{Brown}{upper}{up} \funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up} \funcgroup{hydroxyl}{ST}{Black}{Magenta}{upper}{up} \funcgroup{imino}{P}{Black}{Orange}{upper}{up} \funcgroup{sulfur}{CM}{Black}{Yellow}{upper}{up} \fi \fi \else \xdef\second@{structure} \ifx\temp@\second@ \ifgerm@n \funcgroup{extern}{DEHKNQR}{Black}{Orange}{upper}{up} \funcgroup{ambivalent}{ACGPSTWY}{Black}{Yellow}{upper}{up} \funcgroup{intern}{FILMV}{White}{Green}{upper}{up} \else \ifsp@nish \funcgroup{externo}{DEHKNQR}{Black}{Orange}{upper}{up} \funcgroup{ambivalente}{ACGPSTWY}{Black}{Yellow}{upper}{up} \funcgroup{interno}{FILMV}{White}{Green}{upper}{up} \else \funcgroup{external}{DEHKNQR}{Black}{Orange}{upper}{up} \funcgroup{ambivalent}{ACGPSTWY}{Black}{Yellow}{upper}{up} \funcgroup{internal}{FILMV}{White}{Green}{upper}{up} \fi \fi \else \xdef\second@{standard area} \ifx\temp@\second@ \ifgerm@n \funcgroup{\ 88,1 (G); Standard Seitenkettenfl\"ache % (\AA$^2$)}% {G}{Black}{BrickRed}{upper}{up} \funcgroup{118,2 (A); 129,8 (S)}{AS}{Black}{Orange}{upper}{up} \funcgroup{146,1 (C); 146,8 (P)}% {CP}{Black}{Yellow}{upper}{up} \funcgroup{152,5 (T); 158,7 (D); 164,5 (V); 165,5 (N)}% {TDVN}{Black}{YellowGreen}{upper}{up} \funcgroup{181,0 (I); 186,2 (E)}{IE}{White}{PineGreen}{upper}{up} \funcgroup{193,1 (L); 193,2 (Q); 202,5 (H); 203,3 (M)}% {LQHM}{Black}{SkyBlue}{upper}{up} \funcgroup{222,8 (F); 225,8 (K)}{FK}{White}{RoyalPurple}{upper}{up} \funcgroup{238,8 (Y)}{Y}{White}{RedViolet}{upper}{up} \funcgroup{256,0 (R); 266,2 (W)}{RW}{White}{Black}{upper}{up} \else \ifsp@nish \funcgroup{\ 88.1 (G); Superficie est\'andar de la cadena lateral (\AA$^2$)}% {G}{Black}{BrickRed}{upper}{up} \funcgroup{118.2 (A); 129.8 (S)}{AS}{Black}{Orange}{upper}{up} \funcgroup{146.1 (C); 146.8 (P)}% {CP}{Black}{Yellow}{upper}{up} \funcgroup{152.5 (T); 158.7 (D); 164.5 (V); 165.5 (N)}% {TDVN}{Black}{YellowGreen}{upper}{up} \funcgroup{181.0 (I); 186.2 (E)}{IE}{White}{PineGreen}{upper}{up} \funcgroup{193.1 (L); 193.2 (Q); 202.5 (H); 203.3 (M)}% {LQHM}{Black}{SkyBlue}{upper}{up} \funcgroup{222.8 (F); 225.8 (K)}{FK}{White}{RoyalPurple}{upper}{up} \funcgroup{238.8 (Y)}{Y}{White}{RedViolet}{upper}{up} \funcgroup{256.0 (R); 266.2 (W)}{RW}{White}{Black}{upper}{up} \else \funcgroup{\ 88.1 (G); Standard sidechain area (\AA$^2$)}% {G}{Black}{BrickRed}{upper}{up} \funcgroup{118.2 (A); 129.8 (S)}{AS}{Black}{Orange}{upper}{up} \funcgroup{146.1 (C); 146.8 (P)}% {CP}{Black}{Yellow}{upper}{up} \funcgroup{152.5 (T); 158.7 (D); 164.5 (V); 165.5 (N)}% {TDVN}{Black}{YellowGreen}{upper}{up} \funcgroup{181.0 (I); 186.2 (E)}{IE}{White}{PineGreen}{upper}{up} \funcgroup{193.1 (L); 193.2 (Q); 202.5 (H); 203.3 (M)}% {LQHM}{Black}{SkyBlue}{upper}{up} \funcgroup{222.8 (F); 225.8 (K)}{FK}{White}{RoyalPurple}{upper}{up} \funcgroup{238.8 (Y)}{Y}{White}{RedViolet}{upper}{up} \funcgroup{256.0 (R); 266.2 (W)}{RW}{White}{Black}{upper}{up} \fi \fi \else \xdef\second@{accessible area} \ifx\temp@\second@ \ifgerm@n \funcgroup{\ 13,9 (C); Zug\"angliche Seitenkettenfl\"ache % (\AA$^2$)}% {CIV}{Black}{BrickRed}{upper}{up} \funcgroup{\ 23,0 (I); 23,5 (V); 25,2 (G)}% {IVG}{Black}{Orange}{upper}{up} \funcgroup{\ 28,7 (F); 29,0 (L); 30,5 (M); 31,5 (A)}% {FLMA}{Black}{Yellow}{upper}{up} \funcgroup{\ 41,7 (W); 44,2 (S); 46,0 (T); 46,7 (H)}% {WSTH}{Black}{YellowGreen}{upper}{up} \funcgroup{\ 53,7 (P)}{P}{White}{PineGreen}{upper}{up} \funcgroup{\ 59,1 (Y); 60,9 (D); 62,2 (N)}% {YDN}{Black}{SkyBlue}{upper}{up} \funcgroup{\ 72,3 (E); 74,0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up} \funcgroup{\ 93,8 (R)}{R}{White}{RedViolet}{upper}{up} \funcgroup{110,3 (K)}{K}{White}{Black}{upper}{up} \else \ifsp@nish \funcgroup{\ 13.9 (C); Superficie accesible de la cadena lateral (\AA$^2$)}% {CIV}{Black}{BrickRed}{upper}{up} \funcgroup{\ 23.0 (I); 23.5 (V); 25.2 (G)}% {IVG}{Black}{Orange}{upper}{up} \funcgroup{\ 28.7 (F); 29.0 (L); 30.5 (M); 31.5 (A)}% {FLMA}{Black}{Yellow}{upper}{up} \funcgroup{\ 41.7 (W); 44.2 (S); 46.0 (T); 46.7 (H)}% {WSTH}{Black}{YellowGreen}{upper}{up} \funcgroup{\ 53.7 (P)}{P}{White}{PineGreen}{upper}{up} \funcgroup{\ 59.1 (Y); 60.9 (D); 62.2 (N)}% {YDN}{Black}{SkyBlue}{upper}{up} \funcgroup{\ 72.3 (E); 74.0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up} \funcgroup{\ 93.8 (R)}{R}{White}{RedViolet}{upper}{up} \funcgroup{110.3 (K)}{K}{White}{Black}{upper}{up} \else \funcgroup{\ 13.9 (C); Accessible sidechain area (\AA$^2$)}% {CIV}{Black}{BrickRed}{upper}{up} \funcgroup{\ 23.0 (I); 23.5 (V); 25.2 (G)}% {IVG}{Black}{Orange}{upper}{up} \funcgroup{\ 28.7 (F); 29.0 (L); 30.5 (M); 31.5 (A)}% {FLMA}{Black}{Yellow}{upper}{up} \funcgroup{\ 41.7 (W); 44.2 (S); 46.0 (T); 46.7 (H)}% {WSTH}{Black}{YellowGreen}{upper}{up} \funcgroup{\ 53.7 (P)}{P}{White}{PineGreen}{upper}{up} \funcgroup{\ 59.1 (Y); 60.9 (D); 62.2 (N)}% {YDN}{Black}{SkyBlue}{upper}{up} \funcgroup{\ 72.3 (E); 74.0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up} \funcgroup{\ 93.8 (R)}{R}{White}{RedViolet}{upper}{up} \funcgroup{110.3 (K)}{K}{White}{Black}{upper}{up} \fi \fi \else \xdef\second@{rasmol} \ifx\temp@\second@ \funcgroup{Asp, Glu}{DE}{Red}{White}{upper}{up} \funcgroup{Arg, Lys, His}{KRH}{Blue}{White}{upper}{up} \funcgroup{Phe, Tyr, Trp}{FYW}{MidnightBlue}{White}{upper}{up} \funcgroup{Ala, Gly}{AG}{Gray}{White}{upper}{up} \funcgroup{Cys, Met}{CM}{Yellow}{White}{upper}{up} \funcgroup{Ser, Thr}{ST}{Orange}{White}{upper}{up} \funcgroup{Asn, Gln}{NQ}{Cyan}{White}{upper}{up} \funcgroup{Leu, Val, Ile}{LVI}{Green}{White}{upper}{up} \funcgroup{Pro}{P}{Apricot}{White}{upper}{up} \else \message{} \fi\fi\fi\fi\fi\fi\fi } \def\shadeallresidues{\all@fshadetrue} \def\get@fromstack#1;#2;#3;#4;#5@{% \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\fourth@{#4} \xdef\last@{#5@} } \def\getregion@fromstack#1{% \xdef\temp@{#1} \xdef\first@{\csname stack@reg\temp@\endcsname} \expandafter\get@fromstack\first@ \expandafter\xdef\csname style\temp@\endcsname{\first@} \expandafter\xdef\csname start\temp@\endcsname{\second@} \expandafter\xdef\csname stop\temp@\endcsname{\third@} \expandafter\xdef\csname all\temp@\endcsname{\fourth@} \expandafter\xdef\csname stack@reg\temp@\endcsname{\last@} } \def\sort@stack{% \expandafter\get@fromstack\last@ \ifx\first@\ampers@nd \xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;&;&;&;&;@} \else \ifnum\st@rt<\second@ \xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;% \first@;\second@;\third@;\fourth@;\last@} \else \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@stack \fi\fi } \def\get@regions#1..#2,#3@{% \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} \xdef\last@{\csname stack@reg\seq@\endcsname} \xdef\tmpstack{} \sort@stack \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack} } \def\get@fromemphstack#1;#2;#3;#4@{% \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\last@{#4@} } \def\getregion@fromemphstack#1{% \xdef\temp@{#1} \xdef\first@{\csname stack@emphreg\temp@\endcsname} \expandafter\get@fromemphstack\first@ \expandafter\xdef\csname emphstart\temp@\endcsname{\first@} \expandafter\xdef\csname emphstop\temp@\endcsname{\second@} \expandafter\xdef\csname emphall\temp@\endcsname{\third@} \expandafter\xdef\csname stack@emphreg\temp@\endcsname{\last@} } \def\sort@emphstack{% \expandafter\get@fromemphstack\last@ \ifx\first@\ampers@nd \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@} \else \ifnum\st@rt<\second@ \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@} \else \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@emphstack \fi\fi } \def\get@emphregions#1..#2,#3@{% \regionalemphtrue \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} \xdef\last@{\csname stack@emphreg\seq@\endcsname} \xdef\tmpstack{} \sort@emphstack \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack} } \def\getregion@fromlowerstack#1{% \xdef\temp@{#1} \xdef\first@{\csname stack@lowerreg\temp@\endcsname} \expandafter\get@fromemphstack\first@ \expandafter\xdef\csname lowerstart\temp@\endcsname{\first@} \expandafter\xdef\csname lowerstop\temp@\endcsname{\second@} \expandafter\xdef\csname lowerall\temp@\endcsname{\third@} \expandafter\xdef\csname stack@lowerreg\temp@\endcsname{\last@} } \def\sort@lowerstack{% \expandafter\get@fromemphstack\last@ \ifx\first@\ampers@nd \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@} \else \ifnum\st@rt<\second@ \xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@} \else \xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@lowerstack \fi\fi } \def\get@lowerregions#1..#2,#3@{% \regionallowertrue \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} \xdef\last@{\csname stack@lowerreg\seq@\endcsname} \xdef\tmpstack{} \sort@lowerstack \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack} } \def\get@fromdomstack#1;#2;#3@{% \xdef\first@{#1} \xdef\second@{#2} \xdef\last@{#3@} } \def\sort@domstack{% \expandafter\get@fromdomstack\last@ \ifx\first@\ampers@nd \xdef\tmpstack{\tmpstack\st@rt;\st@p;&;&;@} \else \ifnum\st@rt<\second@ \xdef\tmpstack{\tmpstack\st@rt;\st@p;\first@;\second@;\last@} \else \xdef\tmpstack{\tmpstack\first@;\second@;} \sort@domstack \fi\fi } \def\get@domainregions#1..#2,#3@{% \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} \xdef\last@{\stack@dom} \xdef\tmpstack{} \sort@domstack \xdef\stack@dom{\tmpstack} } \def\get@domain{% \expandafter\get@fromdomstack\last@ \ifx\first@\ampers@nd \else \loopcount=\first@ \loop \xdef\domain@num@list{\domain@num@list \the\loopcount,} \advance\loopcount by 1 \ifnum\loopcount>\second@\else\repeat \get@domain \fi } \def\getregion@fromtintstack#1{% \xdef\temp@{#1} \xdef\first@{\csname stack@tintreg\temp@\endcsname} \expandafter\get@fromemphstack\first@ \expandafter\xdef\csname tintstart\temp@\endcsname{\first@} \expandafter\xdef\csname tintstop\temp@\endcsname{\second@} \expandafter\xdef\csname tintall\temp@\endcsname{\third@} \expandafter\xdef\csname stack@tintreg\temp@\endcsname{\last@} } \def\get@tintregions#1..#2,#3@{% \regionaltinttrue \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} \xdef\last@{\csname stack@tintreg\seq@\endcsname} \xdef\tmpstack{} \sort@emphstack \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} } \def\getregion@fromframestack#1{% \xdef\temp@{#1} \xdef\first@{\csname stack@framereg\temp@\endcsname} \expandafter\get@fromemphstack\first@ \expandafter\xdef\csname framestart\temp@\endcsname{\first@} \expandafter\xdef\csname framestop\temp@\endcsname{\second@} \expandafter\xdef\csname framestyle\temp@\endcsname{\third@} \expandafter\xdef\csname stack@framereg\temp@\endcsname{\last@} } \def\get@frameregions#1..#2,#3@{% \frame@true \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} \xdef\last@{\csname stack@framereg\seq@\endcsname} \xdef\tmpstack{} \sort@emphstack \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack} } \def\getregion@fromshadingstack#1{% \xdef\temp@{#1} \xdef\first@{\csname stack@shadingreg\temp@\endcsname} \expandafter\get@fromemphstack\first@ \expandafter\xdef\csname shadingstart\temp@\endcsname{\first@} \expandafter\xdef\csname shadingstop\temp@\endcsname{\second@} \expandafter\xdef\csname shadingstyle\temp@\endcsname{\third@} \expandafter\xdef\csname stack@shadingreg\temp@\endcsname{\last@} } \def\get@shadingregions#1..#2,#3@{% \shading@true \xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3} \xdef\last@{\csname stack@shadingreg\seq@\endcsname} \xdef\tmpstack{} \sort@emphstack \expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack} } \def\getregion@fromfstack#1{% \xdef\temp@{#1} \xdef\first@{\csname stack@\bottop@\temp@\endcsname} \expandafter\get@fromstack\first@ \expandafter\xdef\csname text\bottop@\temp@\endcsname{\first@} \expandafter\xdef\csname start\bottop@\temp@\endcsname{\second@} \expandafter\xdef\csname stop\bottop@\temp@\endcsname{\third@} \ifx\fourth@\ampers@nd \xdef\fourth@{///} \fi \expandafter\xdef\csname style\bottop@\temp@\endcsname{\fourth@} \expandafter\xdef\csname stack@\bottop@\temp@\endcsname{\last@} } \def\sort@fstack{% \expandafter\get@fromstack\last@ \ifx\first@\ampers@nd \xdef\tmpstack{\tmpstack\f@text@;\st@rt;\st@p;\style@;&;&;&;&;@} \else \ifnum\st@rt<\second@ \xdef\tmpstack{\tmpstack\f@text@;\st@rt;\st@p;\style@;% \first@;\second@;\third@;\fourth@;\last@} \else \xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;} \sort@fstack \fi\fi } \def\get@fregions#1..#2,#3@{% \xdef\st@rt{#1} \ifx\temp@\y@ \xdef\st@p{#1} \else \xdef\st@p{#2} \fi \xdef\list@{#3} \xdef\last@{\csname stack@\bottop@\seq@\endcsname} \xdef\tmpstack{} \sort@fstack \expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack} } \def\getarrow@shape#1#2#3#4&{% \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}\xdef\fourth@@{#4} \ifx\temp@@\y@ \if\first@@ ` \xdef\first@@{a} \else \if\first@@ ' \xdef\first@@{a} \else \if\first@@ , \xdef\first@@{b} \else \if\first@@ S \xdef\first@@{c} \xdef\second@@{-} \fi\fi\fi\fi \if\third@@ ` \xdef\third@@{a} \else \if\third@@ ' \xdef\third@@{a} \else \if\third@@ , \xdef\third@@{b} \else \if\third@@ S \xdef\third@@{c} \xdef\second@@{-} \fi\fi\fi\fi \xdef\style@{\first@@ -\third@@\fourth@@} \fi \if\first@@ S \xdef\style@{\first@@ -\third@@\fourth@@} \else \if\first@@ v \if\second@@ = \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi \else \if\third@@ S \xdef\style@{\first@@ -\third@@\fourth@@} \else \if\third@@ v \if\second@@ = \else \xdef\style@{\first@@ v\third@@\fourth@@} \fi \fi\fi\fi\fi } \def\get@shape#1#2#3{% \xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}% \if\second@@ v \xdef\second@@{arrow}% \fi% \if\second@@ = \xdef\second@@{doublearrow}% \fi% } \def\getstyle@left#1#2#3#4@{% \ifstop@ \xdef\style@@{\csname fstyle\bottop@\the\loopcount\endcsname} \else \xdef\style@@{#2} \xdef\temp@{-} \ifx\style@@\temp@ \xdef\style@@{#1#2-#4} \else \xdef\temp@{v} \ifx\style@@\temp@ \xdef\style@@{#1#2-#4} \else \xdef\temp@{=} \ifx\style@@\temp@ \xdef\style@@{#1#2=#4} \else \xdef\style@@{\csname fstyle\bottop@\the\loopcount\endcsname} \fi\fi\fi\fi } \def\getstyle@right#1#2#3#4@{% \xdef\style@@{#2} \xdef\temp@{-} \ifx\style@@\temp@ \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{-#2#3#4} \fi \xdef\temp@{v} \ifx\style@@\temp@ \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{-#2#3#4} \fi \xdef\temp@{=} \ifx\style@@\temp@ \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{=#2#3#4} \fi } \def\opt@color#1[#2]#3&{\xdef\fourth@{#1}\xdef\f@color{#2}} \def\graph@opt@color#1[#2]:#3[#4][#5]#6&{% \xdef\fourth@{#1} \xdef\f@color{#2} \xdef\ffourth@{#3} \xdef\ff@color{#4} \xdef\fffourth@{#5}} \def\arrow@col@width#1[#2][#3]#4&{\xdef\fourth@{#1}\xdef\f@color{#2}\xdef\rule@@thick{#3}} \def\second@color#1,&{\xdef\back@color{#1}} \def\two@opt@color#1,#2@{% \xdef\sixth@{#1}% \xdef\seventh@{#2}% \ifx\first@\ampers@nd% \else% \xdef\frame@color{#1}% \ifx\seventh@\ampers@nd% \xdef\back@color{#1}% \xdef\backtext@color{White}% \else% \expandafter\second@color\seventh@% \fi% \fi% } \def\test@get#1#2@{% \xdef\temp@{#1} \xdef\third@@{#2@} \ifx\temp@\ampers@nd \else \if \temp@ X \xdef\temp@{\second@@} \fi \ifx\temp@\second@@ \xdef\third@@{\second@@} \else \expandafter\test@get\third@@ \fi \fi } \def\get@@second@#1#2@{\xdef\second@@{#1}\xdef\first@@{#2@}} \def\get@@third@#1]#2@{\xdef\third@@{#1&@}\xdef\fifth@@{#2@}} \def\get@third@#1#2@{\xdef\third@@{#1}\xdef\fifth@@{#2@}} \def\find@motif{% \expandafter\get@@second@\first@@ \ifx\second@@\ampers@nd \else \ifx\second@@\d@t \else \advance\temp@count by 1 \if \third@@ X \xdef\third@@{\second@@} \fi \ifx\third@@\br@cket \expandafter\get@@third@\fifth@@ \expandafter\test@get\third@@ \fi \ifx\second@@\third@@ \ifx\nineth@@\n@ \xdef\st@rt{\the\temp@count} \xdef\st@p{n} \fi \xdef\nineth@@{y} \expandafter\get@third@\fifth@@ \ifx\third@@\ampers@nd \xdef\st@p{\the\temp@count} \xdef\list@{} \xdef\tmpstack{} \xdef\temp@{shade} \ifx\temp@\temp@@ \xdef\last@{\csname stack@reg\seq@\endcsname} \loopcount=\style@ \sort@stack \expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack} \else \xdef\temp@{emph} \ifx\temp@\temp@@ \regionalemphtrue \xdef\last@{\csname stack@emphreg\seq@\endcsname} \sort@emphstack \expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack} \else \xdef\temp@{lower} \ifx\temp@\temp@@ \regionallowertrue \xdef\last@{\csname stack@lowerreg\seq@\endcsname} \sort@lowerstack \expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack} \else \xdef\temp@{tint} \ifx\temp@\temp@@ \regionaltinttrue \xdef\last@{\csname stack@tintreg\seq@\endcsname} \sort@emphstack \expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack} \else \xdef\temp@{frame} \ifx\temp@\temp@@ \frame@true \xdef\last@{\csname stack@framereg\seq@\endcsname} \sort@emphstack \expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack} \else \xdef\temp@{shading} \ifx\temp@\temp@@ \shading@true \xdef\last@{\csname stack@shadingreg\seq@\endcsname} \sort@emphstack \expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack} \else \xdef\temp@{ttttop} \ifx\temp@\temp@@ \xdef\last@{\csname stack@ttttop\seq@\endcsname} \sort@fstack \expandafter\xdef\csname stack@ttttop\seq@\endcsname{\tmpstack} \else \xdef\temp@{tttop} \ifx\temp@\temp@@ \xdef\last@{\csname stack@tttop\seq@\endcsname} \sort@fstack \expandafter\xdef\csname stack@tttop\seq@\endcsname{\tmpstack} \else \xdef\temp@{ttop} \ifx\temp@\temp@@ \xdef\last@{\csname stack@ttop\seq@\endcsname} \sort@fstack \expandafter\xdef\csname stack@ttop\seq@\endcsname{\tmpstack} \else \xdef\temp@{top} \ifx\temp@\temp@@ \xdef\last@{\csname stack@top\seq@\endcsname} \sort@fstack \expandafter\xdef\csname stack@top\seq@\endcsname{\tmpstack} \else \xdef\temp@{bottom} \ifx\temp@\temp@@ \xdef\last@{\csname stack@bottom\seq@\endcsname} \sort@fstack \expandafter\xdef\csname stack@bottom\seq@\endcsname{\tmpstack} \else \xdef\temp@{bbottom} \ifx\temp@\temp@@ \xdef\last@{\csname stack@bbottom\seq@\endcsname} \sort@fstack \expandafter\xdef\csname stack@bbottom\seq@\endcsname{\tmpstack} \else \xdef\temp@{bbbottom} \ifx\temp@\temp@@ \xdef\last@{\csname stack@bbbottom\seq@\endcsname} \sort@fstack \expandafter\xdef\csname stack@bbbottom\seq@\endcsname{\tmpstack} \else \xdef\temp@{bbbbottom} \ifx\temp@\temp@@ \xdef\last@{\csname stack@bbbbottom\seq@\endcsname} \sort@fstack \expandafter\xdef\csname stack@bbbbottom\seq@\endcsname{\tmpstack} \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@ \xdef\nineth@@{n} \fi \else \ifx\nineth@@\y@ \xdef\first@@{\second@@\first@@} \advance\temp@count by -1 \fi \xdef\nineth@@{n} \xdef\st@p{n} \xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@ \fi \fi \find@motif \fi } \def\prep@motif{% \def\get@motif@specs##1,##2,##3,##4,##5,&{% \xdef\seq@{##1} \xdef\temp@@{##2} \xdef\@ll{##3} \def\fourth@@{##4} \xdef\fifth@@{##5&@} } \loopcount=0 \loop \advance\loopcount by 1 \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{\csname style\the\loopcount\endcsname;% \csname start\the\loopcount\endcsname;% \csname stop\the\loopcount\endcsname;% \csname all\the\loopcount\endcsname;% \csname stack@reg\the\loopcount\endcsname} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{\csname emphstart\the\loopcount\endcsname;% \csname emphstop\the\loopcount\endcsname;% \csname emphall\the\loopcount\endcsname;% \csname stack@emphreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{\csname lowerstart\the\loopcount\endcsname;% \csname lowerstop\the\loopcount\endcsname;% \csname lowerall\the\loopcount\endcsname;% \csname stack@lowerreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{\csname tintstart\the\loopcount\endcsname;% \csname tintstop\the\loopcount\endcsname;% \csname tintall\the\loopcount\endcsname;% \csname stack@tintreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{\csname framestart\the\loopcount\endcsname;% \csname framestop\the\loopcount\endcsname;% \csname framestyle\the\loopcount\endcsname;% \csname stack@framereg\the\loopcount\endcsname} \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{\csname shadingstart\the\loopcount\endcsname;% \csname shadingstop\the\loopcount\endcsname;% \csname shadingstyle\the\loopcount\endcsname;% \csname stack@shadingreg\the\loopcount\endcsname} \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{\csname textttttop\the\loopcount\endcsname;% \csname startttttop\the\loopcount\endcsname;% \csname stopttttop\the\loopcount\endcsname;% \csname stylettttop\the\loopcount\endcsname;% \csname stack@ttttop\the\loopcount\endcsname} \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{\csname texttttop\the\loopcount\endcsname;% \csname starttttop\the\loopcount\endcsname;% \csname stoptttop\the\loopcount\endcsname;% \csname styletttop\the\loopcount\endcsname;% \csname stack@tttop\the\loopcount\endcsname} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{\csname textttop\the\loopcount\endcsname;% \csname startttop\the\loopcount\endcsname;% \csname stopttop\the\loopcount\endcsname;% \csname stylettop\the\loopcount\endcsname;% \csname stack@ttop\the\loopcount\endcsname} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{\csname texttop\the\loopcount\endcsname;% \csname starttop\the\loopcount\endcsname;% \csname stoptop\the\loopcount\endcsname;% \csname styletop\the\loopcount\endcsname;% \csname stack@top\the\loopcount\endcsname} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{\csname textbottom\the\loopcount\endcsname;% \csname startbottom\the\loopcount\endcsname;% \csname stopbottom\the\loopcount\endcsname;% \csname stylebottom\the\loopcount\endcsname;% \csname stack@bottom\the\loopcount\endcsname} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{\csname textbbottom\the\loopcount\endcsname;% \csname startbbottom\the\loopcount\endcsname;% \csname stopbbottom\the\loopcount\endcsname;% \csname stylebbottom\the\loopcount\endcsname;% \csname stack@bbottom\the\loopcount\endcsname} \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{\csname textbbbottom\the\loopcount\endcsname;% \csname startbbbottom\the\loopcount\endcsname;% \csname stopbbbottom\the\loopcount\endcsname;% \csname stylebbbottom\the\loopcount\endcsname;% \csname stack@bbbottom\the\loopcount\endcsname} \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{\csname textbbbbottom\the\loopcount\endcsname;% \csname startbbbbottom\the\loopcount\endcsname;% \csname stopbbbbottom\the\loopcount\endcsname;% \csname stylebbbbottom\the\loopcount\endcsname;% \csname stack@bbbbottom\the\loopcount\endcsname} \ifnum\loopcount<\seq@num\repeat \temp@@count=0 \loop \advance\temp@@count by 1 \xdef\first@@{\csname motif\the\temp@@count\endcsname} \expandafter\get@motif@specs\first@@ \xdef\first@@{\csname sequence\seq@\endcsname &@} \temp@count=\csname res@count\seq@\endcsname \xdef\f@text@{\@ll} \xdef\style@{\fourth@@} \xdef\m@tif{\fifth@@} \expandafter\get@third@\fifth@@ \xdef\nineth@@{n} \xdef\st@p{n} \find@motif \ifnum\temp@@count<\motif@num\repeat \loopcount=0 \loop \advance\loopcount by 1 \expandafter\getregion@fromstack{\the\loopcount} \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromlowerstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} \expandafter\getregion@fromshadingstack{\the\loopcount} \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \ifnum\loopcount<\seq@num\repeat } \def\test@motif#1#2@{% \xdef\temp@{shade} \ifx\temp@\temp@@ \xdef\style@{\the\loopcount} \fi \xdef\temp@{emph} \ifx\temp@\temp@@ \xdef\style@{0} \fi \xdef\temp@{lower} \ifx\temp@\temp@@ \xdef\style@{0} \fi \xdef\temp@{tint} \ifx\temp@\temp@@ \xdef\style@{0} \fi \xdef\temp@{frame} \ifx\temp@\temp@@ \xdef\style@{0} \fi \xdef\temp@{shading} \ifx\temp@\temp@@ \xdef\style@{0} \fi \xdef\temp@{#1#2} \xdef\first@{#1} \ifx\first@\br@cket \xdef\label@motif{y} \temp@count=\motif@num \advance\temp@count by 1 \xdef\motif@num{\the\temp@count} \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@} \xdef\list@{&} \else \expandafter\check@char\first@ \ifletter \xdef\label@motif{y} \temp@count=\motif@num \advance\temp@count by 1 \xdef\motif@num{\the\temp@count} \expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@} \xdef\list@{&} \fi \fi } \def\test@PDB#1:#2,#3,#4,#5,#6@{% \xdef\last@{#1[,]&}\expandafter\opt@color\last@ \xdef\PDB@distance{no} \ifx\f@color\comm@ \else \xdef\f@color{\f@color .&&@} \expandafter\coord@get\f@color \xdef\temp@{\c@@rd @} \expandafter\check@letter\temp@ \ifletter \else \temp@count=\c@@rd \multiply\temp@count by \temp@count \xdef\PDB@distance{\the\temp@count} \fi \fi \xdef\PDB@hitpos{0} \xdef\PDB@stack{} \xdef\PDB@name{#2} \xdef\PDB@type{point} \ifx\fourth@\PDB@type \xdef\PDB@{y} \xdef\last@{#3[,]&}\expandafter\opt@color\last@ \xdef\PDB@refnum@a{\fourth@} \ifx\f@color\C@lpha \xdef\PDB@back@side@a{CA} \else \xdef\PDB@back@side@a{side} \fi \xdef\PDB@refnum@b{0} \xdef\PDB@back@side@b{x} \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x} \ifx\PDB@distance\n@ \xdef\PDB@distance{3600}\fi \load@PDB \expandafter\get@item\PDB@stack \xdef\list@{\first@@} \else \xdef\PDB@type{line} \ifx\fourth@\PDB@type \xdef\PDB@{y} \xdef\last@{#3[,]&}\expandafter\opt@color\last@ \xdef\PDB@refnum{\fourth@} \ifx\f@color\C@lpha \xdef\PDB@back@side{CA} \else \xdef\PDB@back@side{side} \fi \xdef\last@{#4[,]&}\expandafter\opt@color\last@ \ifnum\PDB@refnum<\fourth@ \xdef\PDB@refnum@a{\PDB@refnum} \xdef\PDB@refnum@b{\fourth@} \xdef\PDB@back@side@a{\PDB@back@side} \ifx\f@color\C@lpha \xdef\PDB@back@side@b{CA} \else \xdef\PDB@back@side@b{side} \fi \else \xdef\PDB@refnum@b{\PDB@refnum} \xdef\PDB@refnum@a{\fourth@} \xdef\PDB@back@side@b{\PDB@back@side} \ifx\f@color\C@lpha \xdef\PDB@back@side@a{CA} \else \xdef\PDB@back@side@a{side} \fi \fi \xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x} \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi \load@PDB \expandafter\get@item\PDB@stack \xdef\list@{\first@@} \else \xdef\PDB@type{plane} \ifx\fourth@\PDB@type \xdef\PDB@{y} \xdef\last@{#3[,]&}\expandafter\opt@color\last@ \xdef\PDB@refnum{\fourth@} \ifx\f@color\C@lpha \xdef\PDB@back@side{CA} \else \xdef\PDB@back@side{side} \fi \xdef\last@{#4[,]&}\expandafter\opt@color\last@ \ifnum\PDB@refnum<\fourth@ \xdef\PDB@refnum@a{\PDB@refnum} \xdef\PDB@refnum@b{\fourth@} \xdef\PDB@back@side@a{\PDB@back@side} \ifx\f@color\C@lpha \xdef\PDB@back@side@b{CA} \else \xdef\PDB@back@side@b{side} \fi \else \xdef\PDB@refnum@b{\PDB@refnum} \xdef\PDB@refnum@a{\fourth@} \xdef\PDB@back@side@b{\PDB@back@side} \ifx\f@color\C@lpha \xdef\PDB@back@side@a{CA} \else \xdef\PDB@back@side@a{side} \fi \fi \xdef\last@{#5[,]&}\expandafter\opt@color\last@ \xdef\PDB@refnum{\fourth@} \ifx\f@color\C@lpha \xdef\PDB@back@side{CA} \else \xdef\PDB@back@side{side} \fi \ifnum\PDB@refnum>\PDB@refnum@b \xdef\PDB@refnum@c{\PDB@refnum} \xdef\PDB@back@side@c{\PDB@back@side} \else \ifnum\PDB@refnum>\PDB@refnum@a \xdef\PDB@refnum@c{\PDB@refnum@b} \xdef\PDB@back@side@c{\PDB@back@side@b} \xdef\PDB@refnum@b{\PDB@refnum} \xdef\PDB@back@side@b{\PDB@back@side} \else \xdef\PDB@refnum@c{\PDB@refnum@b} \xdef\PDB@back@side@c{\PDB@back@side@b} \xdef\PDB@refnum@b{\PDB@refnum@a} \xdef\PDB@back@side@b{\PDB@back@side@a} \xdef\PDB@refnum@a{\PDB@refnum} \xdef\PDB@back@side@a{\PDB@back@side} \fi \fi \ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi \load@PDB \expandafter\get@item\PDB@stack \xdef\list@{\first@@} \else \xdef\temp@{\list@ @} \expandafter\test@motif\temp@ \fi \fi \fi } \def\test@fill#1:#2:#3&{% \xdef\last@{#1[,][,]&}\expandafter\arrow@col@width\last@% \xdef\second@@{\fourth@}% \xdef\last@{///}% \ifx\fourth@\last@% \xdef\second@@{empty}% \else \xdef\last@{translate}% \ifx\fourth@\last@% \xdef\second@@{translate}% \xdef\fill@char{#2[,]&}% \expandafter\opt@color\fill@char% \xdef\fill@char{\fourth@}% \else \xdef\last@{fill}% \ifx\fourth@\last@ \xdef\second@@{fill}% \xdef\fill@char{#2[,]&}% \expandafter\opt@color\fill@char% \xdef\fill@char{\fourth@}% \else \xdef\last@{bar}% \ifx\fourth@\last@ \xdef\second@@{bar}% \xdef\b@r{bar}% \ifx\f@color\comm@ \xdef\g@min{,}\xdef\g@max{,}% \else \xdef\f@color{\f@color @}% \expandafter\get@item\f@color% \xdef\g@min{\fourth@} \xdef\g@max{\first@@}% \xdef\pm@shift{\fourth@}% \fi% \xdef\fill@char{#2[,]&}% \expandafter\opt@color\fill@char% \ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi% \xdef\fill@char{\fourth@}% \xdef\box@color{\f@color,&@}% \expandafter\two@opt@color\box@color% \else \xdef\last@{color}% \ifx\fourth@\last@ \xdef\second@@{color}% \ifx\f@color\comm@ \xdef\g@min{,}\xdef\g@max{,}% \else \xdef\f@color{\f@color @}% \expandafter\get@item\f@color% \xdef\g@min{\fourth@} \xdef\g@max{\first@@}% \fi% \xdef\fill@char{#2[,]&}% \expandafter\opt@color\fill@char% \ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi% \xdef\fill@char{\fourth@}% \else \xdef\last@{box}% \ifx\fourth@\last@% \xdef\second@@{box}% \ifx\f@color\comm@\xdef\f@color{White}\fi% \xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@% \ifnumber% \ifx\rule@@thick\comm@% \xdef\rule@@thick{\f@color}% \xdef\box@color{White,&@}% \else% \xdef\seventh@{\rule@@thick}% \xdef\rule@@thick{\f@color}% \xdef\box@color{\seventh@,&@}% \fi% \else% \xdef\box@color{\f@color,&@}% \fi% \expandafter\two@opt@color\box@color% \xdef\fill@char{#2[,]&}% \expandafter\opt@color\fill@char% \xdef\fill@char{\fourth@}% \else \xdef\last@{plotcolor}% \ifx\fourth@\last@% \xdef\second@@{plotcolor}% \ifx\f@color\comm@% \xdef\pm@shift{0}% \else% \xdef\pm@shift{\f@color}% \fi% \xdef\fill@char{#2[,]&}% \expandafter\opt@color\fill@char% \xdef\fill@char{\fourth@}% \else \xdef\last@{plotbar}% \ifx\fourth@\last@% \xdef\second@@{plotbar}% \xdef\b@r{bar}% \ifx\f@color\comm@ \xdef\pm@shift{0}% \else \xdef\pm@shift{\f@color}% \fi% \xdef\fill@char{#2[,]&}% \expandafter\opt@color\fill@char% \ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi% \xdef\fill@char{\fourth@}% \xdef\box@color{\f@color,&@}% \expandafter\two@opt@color\box@color% \else \xdef\arrow@color{\f@color}% \ifx\arrow@color\comm@\xdef\arrow@color{Black}\fi% \xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@% \ifnumber% \ifx\rule@@thick\comm@% \xdef\rule@@thick{\f@color}% \xdef\arrow@color{Black}% \else% \xdef\seventh@{\rule@@thick}% \xdef\rule@@thick{\f@color}% \xdef\arrow@color{\seventh@}% \fi% \fi% \xdef\fill@char{#2[,]&}% \expandafter\opt@color\fill@char% \xdef\fill@char{\fourth@}% \ifx\f@color\comm@\xdef\f@color{Black,White}\fi% \xdef\backtext@color{White}% \xdef\f@color{\f@color,&@}% \expandafter\two@opt@color\f@color% \xdef\f@color{\arrow@color}% \fi \fi \fi \fi \fi \fi \fi \fi \xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@% \ifnumber% \ifx\rule@@thick\comm@% \xdef\rule@@thick{\f@color}% \xdef\f@color{Black}% \else% \xdef\seventh@{\rule@@thick}% \xdef\rule@@thick{\f@color}% \xdef\f@color{\seventh@}% \fi% \fi% \ifx\rule@@thick\comm@\xdef\rule@@thick{\the\rule@thick}\fi% \ifx\f@color\comm@\xdef\f@color{Black}\fi} \def\clear@groups{% \expandafter\xdef\csname \prfx grpA\endcsname{ -1} \expandafter\xdef\csname \prfx grpB\endcsname{ -2} \expandafter\xdef\csname \prfx grpC\endcsname{ -3} \expandafter\xdef\csname \prfx grpD\endcsname{ -4} \expandafter\xdef\csname \prfx grpE\endcsname{ -5} \expandafter\xdef\csname \prfx grpF\endcsname{ -6} \expandafter\xdef\csname \prfx grpG\endcsname{ -7} \expandafter\xdef\csname \prfx grpH\endcsname{ -8} \expandafter\xdef\csname \prfx grpI\endcsname{ -9} \expandafter\xdef\csname \prfx grpJ\endcsname{-10} \expandafter\xdef\csname \prfx grpK\endcsname{-11} \expandafter\xdef\csname \prfx grpL\endcsname{-12} \expandafter\xdef\csname \prfx grpM\endcsname{-13} \expandafter\xdef\csname \prfx grpN\endcsname{-14} \expandafter\xdef\csname \prfx grpO\endcsname{-15} \expandafter\xdef\csname \prfx grpP\endcsname{-16} \expandafter\xdef\csname \prfx grpQ\endcsname{-17} \expandafter\xdef\csname \prfx grpR\endcsname{-18} \expandafter\xdef\csname \prfx grpS\endcsname{-19} \expandafter\xdef\csname \prfx grpT\endcsname{-20} \expandafter\xdef\csname \prfx grpU\endcsname{-21} \expandafter\xdef\csname \prfx grpV\endcsname{-22} \expandafter\xdef\csname \prfx grpW\endcsname{-23} \expandafter\xdef\csname \prfx grpX\endcsname{-24} \expandafter\xdef\csname \prfx grpY\endcsname{-25} \expandafter\xdef\csname \prfx grpZ\endcsname{-26} \expandafter\xdef\csname \prfx grp-\endcsname{-999} \expandafter\xdef\csname \prfx grp.\endcsname{-999} \expandafter\xdef\csname \prfx grp=\endcsname{-999} } \def\inactivate@chars{% \catcode`\#=12 \catcode`\"=12 \catcode`\~=12 \catcode`\^=12 \catcode`\_=12 } \def\numcount{\the\loopcount} \def\Alphacount{\@Alph\loopcount} \def\alphacount{\@alph\loopcount} \def\romancount{\@roman\loopcount} \def\Romancount{\@Roman\loopcount} \def\cut@name#1.#2@{\global\xdef\file@n@me{#1}} \def\coord@get#1.#2#3@{% \xdef\temp@{#2} \ifx\temp@\ampers@nd \xdef\temp@{0} \fi \xdef\c@@rd{#1\temp@} } \def\struc@get#1 #2 #3 #4 #5 #6 #7 #8 #9@{% \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\fourth@{#4} \xdef\fifth@{#5} \xdef\sixth@{#6} \xdef\seventh@{#7}\xdef\eighth@{#8} \xdef\nineth@{#9}} \def\get@PHD#1|#2|#3@{\xdef\PHD@line{\PHD@line #2}} \def\write@PHDsec{% \expandafter\get@sim\last@ \ifx\sim@char\c@mp \def\end@{\the\innerloopcount} \advance\innerloopcount by 1 \else \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi \if\c@mp . \else \if\c@mp L \else \if\c@mp H \ifx\show@Hsec\yes \loopcount=\first@ \advance\loopcount by 1 \xdef\first@{\the\loopcount} \ifx\m@p\yes \immediate\write\featurefile{% \string\feature{\bottop@Hsec}{\begin@..\end@}% {\label@Hsec}{\text@Hsec}} \else \immediate\write\featurefile{% \string\feature{\bottop@Hsec}{\st@rt}{\begin@..\end@}% {\label@Hsec}{\text@Hsec}}\fi \fi \else \if\c@mp E \ifx\show@Esec\yes \loopcount=\second@ \advance\loopcount by 1 \xdef\second@{\the\loopcount} \ifx\m@p\yes \immediate\write\featurefile{% \string\feature{\bottop@Esec}{\begin@..\end@}% {\label@Esec}{\text@Esec}} \else \immediate\write\featurefile{% \string\feature{\bottop@Esec}{\st@rt}{\begin@..\end@}% {\label@Esec}{\text@Esec}}\fi \fi \fi\fi\fi\fi \xdef\c@mp{\sim@char} \advance\innerloopcount by 1 \xdef\begin@{\the\innerloopcount} \fi \ifx\sim@char\ampers@nd\else\write@PHDsec\fi } \def\write@PHDtopo{% \expandafter\get@sim\last@ \ifx\sim@char\c@mp \def\end@{\the\innerloopcount} \advance\innerloopcount by 1 \else \ifnum\end@<\begin@ \xdef\end@{\begin@}\fi \if\c@mp . \else \if\c@mp L \else \if\c@mp T \ifx\show@TMtop\yes \loopcount=\first@ \advance\loopcount by 1 \xdef\first@{\the\loopcount} \ifx\m@p\yes \immediate\write\featurefile{% \string\feature{\bottop@TMtop}{\begin@..\end@}% {\label@TMtop}{\text@TMtop}} \else \immediate\write\featurefile{% \string\feature{\bottop@TMtop}{\st@rt}{\begin@..\end@}% {\label@TMtop}{\text@TMtop}}\fi \fi \else \if\c@mp i \ifx\show@itop\yes \loopcount=\second@ \advance\loopcount by 1 \xdef\second@{\the\loopcount} \ifx\m@p\yes \immediate\write\featurefile{% \string\feature{\bottop@itop}{\begin@..\end@}% {\label@itop}{\text@itop}} \else \immediate\write\featurefile{% \string\feature{\bottop@itop}{\st@rt}{\begin@..\end@}% {\label@itop}{\text@itop}}\fi \fi \else \if\c@mp o \ifx\show@etop\yes \loopcount=\second@ \advance\loopcount by 1 \xdef\second@{\the\loopcount} \ifx\m@p\yes \immediate\write\featurefile{% \string\feature{\bottop@etop}{\begin@..\end@}% {\label@etop}{\text@etop}} \else \immediate\write\featurefile{% \string\feature{\bottop@etop}{\st@rt}{\begin@..\end@}% {\label@etop}{\text@etop}}\fi \fi \fi\fi\fi\fi\fi \xdef\c@mp{\sim@char} \advance\innerloopcount by 1 \xdef\begin@{\the\innerloopcount} \fi \ifx\sim@char\ampers@nd\else\write@PHDtopo\fi } \def\include@T@coffee{% \bgroup \immediate\openin\structurefile = \TC@first@\relax \ifeof\structurefile \PackageError{TeXshade} {File `\TC@first@' not found} {\MessageBreak The file you specified is missing or you have \MessageBreak misspelled it. \MessageBreak\MessageBreak No T-Coffee shading will be displayed (using "similar"). \MessageBreak Type to proceed. \MessageBreak Type X to quit. \MessageBreak } \immediate\closein\structurefile\egroup \simmodetrue \funcmodefalse \T@coffeefalse \else \message{} \xdef\first@{} \xdef\temp@{*} \loop \read\structurefile to \readline \xdef\test@{\expandafter\string\readline} \ifx\test@\par@ \else \xdef\structureline{\readline & & & & & & & & &@} \expandafter\struc@get\structureline \ifx\first@\temp@ \xdef\temp@{y} \read\structurefile to \readline \read\structurefile to \readline \fi \fi \ifx\temp@\y@ \else\repeat \loopcount=0 \xdef\temp@{cons} \loop \read\structurefile to \readline \xdef\test@{\expandafter\string\readline} \ifx\test@\par@ \else \xdef\structureline{\readline & & & & & & & & &@} \expandafter\struc@get\structureline \if\second@ : \advance\loopcount by 1\relax \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} \fi \fi \ifx\first@\temp@\expandafter\xdef\csname T@coffee0\endcsname{} \else\repeat \xdef\temp@{\the\loopcount} \loopcount=0 \loop \read\structurefile to \readline \xdef\test@{\expandafter\string\readline} \ifx\test@\par@ \else \xdef\structureline{\readline & & & & & & & & &@} \expandafter\struc@get\structureline \advance\loopcount by 1 \ifnum\loopcount=\temp@ \loopcount=0 \fi \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname \third@} \fi \ifeof\structurefile \else\repeat \closein\structurefile \loopcount=0 \loop \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} \advance\loopcount by 1 \ifnum\loopcount=\temp@ \else\repeat \egroup \def\n@m@tch{{$\bullet$}} \expandafter\def\csname fg@color0\endcsname{TC0} \expandafter\def\csname fg@color1\endcsname{TC1} \expandafter\def\csname fg@color2\endcsname{TC2} \expandafter\def\csname fg@color3\endcsname{TC3} \expandafter\def\csname fg@color4\endcsname{TC4} \expandafter\def\csname fg@color5\endcsname{TC5} \expandafter\def\csname fg@color6\endcsname{TC6} \expandafter\def\csname fg@color7\endcsname{TC7} \expandafter\def\csname fg@color8\endcsname{TC8} \expandafter\def\csname fg@color9\endcsname{TC9} \expandafter\def\csname fg@textcolor0\endcsname{Black} \expandafter\def\csname fg@textcolor1\endcsname{Black} \expandafter\def\csname fg@textcolor2\endcsname{Black} \expandafter\def\csname fg@textcolor3\endcsname{Black} \expandafter\def\csname fg@textcolor4\endcsname{Black} \expandafter\def\csname fg@textcolor5\endcsname{Black} \expandafter\def\csname fg@textcolor6\endcsname{Black} \expandafter\def\csname fg@textcolor7\endcsname{Black} \expandafter\def\csname fg@textcolor8\endcsname{Black} \expandafter\def\csname fg@textcolor9\endcsname{Black} \fi } \def\include@DSSP{% \xdef\first@{\csname optiondssp\the\loopcount\endcsname} \xdef\bottop@{\csname bottopdssp\the\loopcount\endcsname} \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@dom@count#1,#2@{\res@count=#1 \xdef\temp@{#2 @}} \def\get@name@number{% \xdef\second@{n} \loopcount=0 \loop \advance\loopcount by 1 \expandafter\ifx\csname newseqname\the\loopcount\endcsname\first@ \xdef\first@{\the\loopcount} \loopcount=\seq@count \xdef\second@{y} \fi \ifnum\loopcount=\seq@count \else \repeat \ifx\second@\n@ \message{} \xdef\first@{1} \fi } \def\get@name@number@table{% \xdef\second@{n}% \loopcount=0% \loop% \advance\loopcount by 1% \expandafter\ifx\csname newseqname\the\loopcount\endcsname\first@% \xdef\first@{\the\loopcount}\loopcount=\seq@num% \xdef\second@{y}% \fi% \ifnum\loopcount=\seq@num\else\repeat% \ifx\second@\n@% \message{}% \xdef\first@{1}% \fi% } \def\calc@distance@point{% \loopcount=\xref@coord@a \advance\loopcount by -\x@coord\relax \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount} \loopcount=\yref@coord@a \advance\loopcount by -\y@coord\relax \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount} \loopcount=\zref@coord@a \advance\loopcount by -\z@coord\relax \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount} \advance\loopcount by \y@distance\relax \advance\loopcount by \x@distance\relax \ifnum\loopcount > \PDB@distance \else \loopcount=\PDB@hitpos \advance\loopcount by 1 \ifnum\loopcount=\PDB@pos \else \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..} \fi \xdef\PDB@hitpos{\PDB@pos} \fi } \def\calc@distance@line{% \loopcount=\x@coord\relax \multiply\loopcount by \x@orient \temp@count=\y@coord \relax \multiply\temp@count by \y@orient \advance\loopcount by \temp@count \temp@count=\z@coord \relax \multiply\temp@count by \z@orient \advance\loopcount by \temp@count \advance\loopcount by -\c@nst@ \xdef\z@hler{\the\loopcount} \multiply\loopcount by \x@orient \divide\loopcount by \f@ct@r \advance\loopcount by \xref@coord@a \advance\loopcount by -\x@coord \multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount} \loopcount=\z@hler \multiply\loopcount by \y@orient \divide\loopcount by \f@ct@r \advance\loopcount by \yref@coord@a \advance\loopcount by -\y@coord \multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount} \loopcount=\z@hler \multiply\loopcount by \z@orient \divide\loopcount by \f@ct@r \advance\loopcount by \zref@coord@a \advance\loopcount by -\z@coord \multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount} \advance\loopcount by \y@distance\relax \advance\loopcount by \x@distance\relax \ifnum\loopcount > \PDB@distance \else \loopcount=\PDB@hitpos \advance\loopcount by 1 \ifnum\loopcount=\PDB@pos \else \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..} \fi \xdef\PDB@hitpos{\PDB@pos} \fi } \def\intr@@t{% \loopcount=\r@@t \temp@count=1 \loop \advance\loopcount by \temp@count \divide\loopcount by 2 \temp@count=\r@@t \divide\temp@count by \loopcount \ifnum\loopcount>\temp@count\repeat } \def\calc@distance@plane{% \loopcount=\x@coord\relax \multiply\loopcount by \x@orient \temp@count=\y@coord \relax \multiply\temp@count by \y@orient \advance\loopcount by \temp@count \temp@count=\z@coord \relax \multiply\temp@count by \z@orient \advance\loopcount by \temp@count \advance\loopcount by \c@nst@ \divide\loopcount by \f@ct@r \multiply\loopcount by \loopcount \ifnum\loopcount > \PDB@distance \else \loopcount=\PDB@hitpos \advance\loopcount by 1 \ifnum\loopcount=\PDB@pos \else \xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..} \fi \xdef\PDB@hitpos{\PDB@pos} \fi } \def\load@PDB{% \bgroup \immediate\openin\structurefile = \PDB@name\relax \ifeof\structurefile \PackageError{TeXshade} {File `\PDB@name' not found} {\MessageBreak The file you specified is missing or you have \MessageBreak misspelled it. \MessageBreak\MessageBreak No PDB domain labeling will be displayed. \MessageBreak Type to proceed. \MessageBreak Type X to quit. \MessageBreak } \immediate\closein\structurefile\egroup \else \message{} \xdef\first@{} \loop \read\structurefile to \readline \xdef\test@{\expandafter\string\readline} \ifx\test@\par@ \else \xdef\structureline{\readline & & & & & & & & &@} \expandafter\struc@get\structureline \ifx\first@\@TOM \ifx\PDB@back@side@a\C@lpha \ifx\third@\C@lpha \xdef\temp@@@{\fifth@ &&@} \expandafter\check@letter\temp@@@ \ifnumber \ifnum\fifth@=\PDB@refnum@a \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd} \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd} \fi \else \ifnum\sixth@=\PDB@refnum@a \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd} \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd} \fi \fi \fi \else \xdef\temp@@@{\fifth@ &&@} \expandafter\check@letter\temp@@@ \ifnumber \ifnum\fifth@=\PDB@refnum@a \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd} \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd} \fi \else \ifnum\sixth@=\PDB@refnum@a \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd} \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd} \fi \fi \fi \ifx\PDB@back@side@b\C@lpha \ifx\third@\C@lpha \xdef\temp@@@{\fifth@ &&@} \expandafter\check@letter\temp@@@ \ifnumber \ifnum\fifth@=\PDB@refnum@b \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd} \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd} \fi \else \ifnum\sixth@=\PDB@refnum@b \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd} \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd} \fi \fi \fi \else \xdef\temp@@@{\fifth@ &&@} \expandafter\check@letter\temp@@@ \ifnumber \ifnum\fifth@=\PDB@refnum@b \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd} \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd} \fi \else \ifnum\sixth@=\PDB@refnum@b \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd} \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd} \fi \fi \fi \ifx\PDB@back@side@c\C@lpha \ifx\third@\C@lpha \xdef\temp@@@{\fifth@ &&@} \expandafter\check@letter\temp@@@ \ifnumber \ifnum\fifth@=\PDB@refnum@c \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd} \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd} \fi \else \ifnum\sixth@=\PDB@refnum@c \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd} \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd} \fi \fi \fi \else \xdef\temp@@@{\fifth@ &&@} \expandafter\check@letter\temp@@@ \ifnumber \ifnum\fifth@=\PDB@refnum@c \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd} \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd} \fi \else \ifnum\sixth@=\PDB@refnum@c \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd} \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd} \fi \fi \fi \fi \fi \ifeof\structurefile \else\repeat \closein\structurefile \ifx\PDB@type\@line@ \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient{\the\loopcount} \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient{\the\loopcount} \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient{\the\loopcount} \loopcount=\xref@coord@a \multiply\loopcount by \x@orient \temp@count=\yref@coord@a \multiply\temp@count by \y@orient \advance\loopcount by \temp@count \temp@count=\zref@coord@a \multiply\temp@count by \z@orient \advance\loopcount by \temp@count \xdef\c@nst@{\the\loopcount} \loopcount=\x@orient \multiply\loopcount by \x@orient \temp@count=\y@orient \multiply\temp@count by \y@orient \advance\loopcount by \temp@count \temp@count=\z@orient \multiply\temp@count by \z@orient \advance\loopcount by \temp@count \xdef\f@ct@r{\the\loopcount} \fi \ifx\PDB@type\@plane@ \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient@r{\the\loopcount} \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient@r{\the\loopcount} \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient@r{\the\loopcount} \loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@c \xdef\x@orient@s{\the\loopcount} \loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@c \xdef\y@orient@s{\the\loopcount} \loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@c \xdef\z@orient@s{\the\loopcount} \loopcount=\y@orient@r \multiply\loopcount by \z@orient@s \temp@count=\z@orient@r \multiply\temp@count by \y@orient@s \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\x@orient{\the\loopcount} \loopcount=\z@orient@r \multiply\loopcount by \x@orient@s \temp@count=\x@orient@r \multiply\temp@count by \z@orient@s \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\y@orient{\the\loopcount} \loopcount=\x@orient@r \multiply\loopcount by \y@orient@s \temp@count=\y@orient@r \multiply\temp@count by \x@orient@s \advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\z@orient{\the\loopcount} \loopcount=\x@orient \multiply\loopcount by \xref@coord@a \temp@count=\y@orient \multiply\temp@count by \yref@coord@a \advance\loopcount by \temp@count \temp@count=\z@orient \multiply\temp@count by \zref@coord@a \advance\loopcount by \temp@count \multiply\loopcount by -1\relax \xdef\c@nst@{\the\loopcount} \loopcount=\x@orient \multiply\loopcount by \loopcount \temp@count=\y@orient \multiply\temp@count by \temp@count \advance\loopcount by \temp@count \temp@count=\z@orient \multiply\temp@count by \temp@count \advance\loopcount by \temp@count \xdef\r@@t{\the\loopcount} \intr@@t \xdef\f@ct@r{\the\loopcount} \fi \immediate\openin\structurefile = \PDB@name\relax \xdef\first@{} \loop \read\structurefile to \readline \xdef\test@{\expandafter\string\readline} \ifx\test@\par@ \else \xdef\structureline{\readline & & & & & & & & &@} \expandafter\struc@get\structureline \ifx\first@\@TOM \xdef\temp@@@{\fifth@ &&@} \expandafter\check@letter\temp@@@ \ifnumber \xdef\PDB@pos{\fifth@} \xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\x@coord{\c@@rd} \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\y@coord{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\z@coord{\c@@rd} \else \xdef\PDB@pos{\sixth@} \xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\x@coord{\c@@rd} \xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\y@coord{\c@@rd} \xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\z@coord{\c@@rd} \fi \ifnum\PDB@hitpos=\PDB@pos \else \ifx\PDB@type\@point@ \calc@distance@point \else \ifx\PDB@type\@line@ \calc@distance@line \else \ifx\PDB@type\@plane@ \calc@distance@plane \fi \fi \fi \fi \fi \fi \ifeof\structurefile \xdef\PDB@stack{\PDB@stack\PDB@hitpos,&@} \else\repeat \closein\structurefile \fi \egroup } %%%%% Definition of user commands \def\clearfuncgroups{\xdef\prfx{func} \clear@groups \xdef\fgroup@num{0}} \clearfuncgroups \def\germanlanguage{\germ@ntrue \sp@nishfalse \def\cons@name{Konsensus}} \def\spanishlanguage{\germ@nfalse \sp@nishtrue \def\cons@name{consenso}} \def\englishlanguage{\germ@nfalse \sp@nishfalse \def\cons@name{consensus}} \def\showlegend{\legend@true} \def\hidelegend{\legend@false} \def\movelegend#1#2{% \setlength\hspace@legend{#1} \setlength\vspace@legend{#2} } \newcommand{\showcaption}[2][bottom]{\def\cap@pos{#1}\def\c@p{#2}} \def\shortcaption#1{\def\c@pshort{#1}} \def\funcgroup#1#2#3#4#5#6{% \xdef\first@{#1} \loopcount=0 \innerloopcount=0 \loop \advance\loopcount by 1 \ifx\csname fgroup@name\the\loopcount\endcsname\first@ \innerloopcount=\loopcount \loopcount=\fgroup@num \fi \ifnum\loopcount<\fgroup@num \repeat \ifnum\innerloopcount=0 \ifnum\fgroup@num<9 \innerloopcount=\fgroup@num \advance\innerloopcount by 1 \xdef\fgroup@num{\the\innerloopcount} \else \message{} \fi \fi \ifnum\innerloopcount>0 \expandafter\xdef\csname fgroup@name\the\innerloopcount\endcsname{\first@} \expandafter\xdef\csname fg@textcolor\the\innerloopcount\endcsname{#3} \expandafter\xdef\csname fg@color\the\innerloopcount\endcsname{#4} \expandafter\xdef\csname funcm@tch\the\innerloopcount\endcsname{#5} \expandafter\def\csname func@style\the\innerloopcount\endcsname{% \csname text#6\endcsname} \xdef\prfx{func} \xdef\third@{#2&,@} \loopcount=\innerloopcount \expandafter\group@get\third@ \fi} \def\pepgroups#1{% \xdef\prfx{pep} \clear@groups \xdef\third@{#1&,@} \loopcount=0 \loop \expandafter\group@get\third@ \advance\loopcount by 1 \ifnum\loopcount<10 \repeat} \def\DNAgroups#1{% \xdef\prfx{DNA} \clear@groups \xdef\third@{#1&,@} \loopcount=0 \loop \expandafter\group@get\third@ \advance\loopcount by 1 \ifnum\loopcount<10 \repeat} \def\pepsims#1#2{\xdef\prfx{pep} \def\sim@set{\expandafter\residue@get\second@ \ifx\first@\ampers@nd \else \advance\innerloopcount by 1 \expandafter\xdef\csname simpair\third@\first@\endcsname{1} \expandafter\xdef\csname simpair\first@\third@\endcsname{1} \xdef\second@{\csname sequence\the\loopcount\endcsname} \sim@set \fi} \xdef\first@{#1} \make@upper \xdef\third@{\first@} \xdef\last@{#2} \xdef\second@{#2 &@} \innerloopcount=0 \sim@set \expandafter\xdef\csname \prfx sim\third@\endcsname{% (\the\innerloopcount)\last@}} \def\DNAsims#1#2{\xdef\prfx{DNA} \def\sim@set{\expandafter\residue@get\second@ \ifx\first@\ampers@nd \else \advance\innerloopcount by 1 \xdef\second@{\csname sequence\the\loopcount\endcsname} \sim@set \fi} \xdef\first@{#1} \make@upper \xdef\third@{\first@} \xdef\last@{#2} \xdef\second@{#2 &@} \innerloopcount=0 \sim@set \expandafter\xdef\csname \prfx sim\third@\endcsname{% (\the\innerloopcount)\last@}} \def\fingerprint#1{% \ifnum #1 >0 \residuesperline*{#1} \def\finger@linenum{#1} \shownames{left} \hidenumbering \rulersteps{100} \nomatchresidues{}{Gray10}{}{} \loopcount=0 \loop \advance\loopcount by 1 \separationline{\the\loopcount} \ifnum\loopcount<\seq@count\repeat \fi} \def\printPDBlist#1{% \xdef\list@{} \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@ \xdef\first@{\list@ &} \ifx\first@\ampers@nd \else \xdef\first@{\list@ @} \loop \expandafter\get@item\first@ \fourth@ \ifx\first@@\ampers@nd\else{,\ }\repeat \fi } \def\messagePDBlist#1{% \xdef\list@{} \xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@ \xdef\first@{\list@ &} \ifx\first@\ampers@nd \else \message{(#1:} \xdef\first@{\list@ @}% \loop% \expandafter\get@item\first@% \message{\fourth@}% \ifx\first@@\ampers@nd\else\repeat% \message{)} \fi } \def\shaderegion#1#2#3#4{% \regionalshadetrue \xdef\seq@{#1} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ \xdef\first@{\seq@} \ifletter \get@name@number \xdef\seq@{\first@} \fi \ifnum\seq@>\seq@count \message{} \else \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi \loopcount=\seq@regions \advance\loopcount by 1 \xdef\seq@regions{\the\loopcount} \expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3} \expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4} \xdef\list@{#2,&} \xdef\temp@@{shade} \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ \ifx\list@\ampers@nd \else \loop \xdef\list@{\list@ @} \expandafter\get@regions\list@ \ifx\list@\ampers@nd\else\repeat \fi \fi } \def\shadeblock#1#2#3#4{% \xdef\seq@{#1} \xdef\@ll{yes} \shaderegion{#1}{#2}{#3}{#4} \xdef\@ll{} } \def\tintregion#1#2{% \xdef\seq@{#1} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ \xdef\first@{\seq@} \ifletter \get@name@number \xdef\seq@{\first@} \fi \ifnum\seq@>\seq@count \message{} \else \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi \xdef\list@{#2,&} \xdef\temp@@{tint} \loopcount=0 \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ \ifx\list@\ampers@nd \else \loop \xdef\list@{\list@ @} \expandafter\get@tintregions\list@ \ifx\list@\ampers@nd\else\repeat \fi \fi } \def\tintblock#1#2{% \xdef\seq@{#1} \xdef\@ll{yes} \tintregion{#1}{#2} \xdef\@ll{} } \def\tintdefault#1{% \xdef\first@{#1} \xdef\second@{strong} \ifx\first@\second@ \xdef\light@{LightLightLight} \else \xdef\second@{medium} \ifx\first@\second@ \xdef\light@{LightLight} \else \xdef\second@{weak} \ifx\first@\second@ \xdef\light@{Light} \else \xdef\light@{LightLight} \fi\fi\fi } \def\lowerregion#1#2{% \xdef\seq@{#1} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ \xdef\first@{\seq@} \ifletter \get@name@number \xdef\seq@{\first@} \fi \ifnum\seq@>\seq@count \message{} \else \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi \xdef\list@{#2,&} \xdef\temp@@{lower} \loopcount=0 \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ \ifx\list@\ampers@nd \else \loop \xdef\list@{\list@ @} \expandafter\get@lowerregions\list@ \ifx\list@\ampers@nd\else\repeat \fi \fi } \def\lowerblock#1#2{% \xdef\seq@{#1} \xdef\@ll{yes} \lowerregion{#1}{#2} \xdef\@ll{} } \def\emphregion#1#2{% \xdef\seq@{#1} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ \xdef\first@{\seq@} \ifletter \get@name@number \xdef\seq@{\first@} \fi \ifnum\seq@>\seq@count \message{} \else \ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi \xdef\list@{#2,&} \xdef\temp@@{emph} \loopcount=0 \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ \ifx\list@\ampers@nd \else \loop \xdef\list@{\list@ @} \expandafter\get@emphregions\list@ \ifx\list@\ampers@nd\else\repeat \fi \fi } \def\emphblock#1#2{% \xdef\seq@{#1} \xdef\@ll{yes} \emphregion{#1}{#2} \xdef\@ll{} } \def\emphdefault#1{\def\res@style{\csname text#1\endcsname}} \def\frameblock#1#2#3{% \xdef\seq@{#1} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ \xdef\first@{\seq@} \ifletter \get@name@number \xdef\seq@{\first@} \fi \ifnum\seq@>\seq@count \message{} \else \xdef\@ll{#3} \xdef\list@{#2,&} \xdef\temp@@{frame} \loopcount=0 \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ \ifx\list@\ampers@nd \else \loop \xdef\list@{\list@ @} \expandafter\get@frameregions\list@ \ifx\list@\ampers@nd\else\repeat \fi \fi } \def\changeshadingcolors#1#2#3{% \xdef\seq@{#1} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ \xdef\first@{\seq@} \ifletter \get@name@number \xdef\seq@{\first@} \fi \ifnum\seq@>\seq@count \message{} \else \xdef\@ll{#3} \xdef\list@{#2,&} \xdef\temp@@{shading} \loopcount=0 \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ \ifx\list@\ampers@nd \else \loop \xdef\list@{\list@ @} \expandafter\get@shadingregions\list@ \ifx\list@\ampers@nd\else\repeat \fi \fi } \def\bargraphstretch#1{\def\b@r@stretch{#1}} \def\colorscalestretch#1{\def\sc@le@stretch{#1}} \def\rm@@measure#1#2@{% \xdef\test@{#1} \ifx\test@\ampers@nd \else \expandafter\check@char\test@ \ifnumber\xdef\first@{\first@ #1} \xdef\second@{#2 &@} \expandafter\rm@@measure\second@ \fi \fi } \def\rm@measure#1.#2@{\xdef\first@{#1.}\xdef\second@{#2 @}\xdef\third@{#1}\expandafter\rm@@measure\second@} \def\pm@calc{% \temp@@length=100000sp \temp@@length=\g@min\temp@@length \innerloopcount=\temp@@length \xdef\min@{\the\innerloopcount} \arrow@height=\temp@@length \temp@@length=100000sp \temp@@length=\g@max\temp@@length \advance\temp@@length by -\arrow@height \innerloopcount=\temp@@length \divide\innerloopcount by 100 \ifnum\innerloopcount=0 \innerloopcount=1 \fi \xdef\m@x{\the\innerloopcount} \xdef\test@{\g@min pt} \setlength\arrow@width{\test@} \xdef\test@{\g@max pt} \setlength\arrow@height{\test@} \advance\arrow@height by -\arrow@width \ifdim\arrow@width<0pt\temp@@length=-\arrow@width\xdef\test@{y}\else\temp@@length=\arrow@width\xdef\test@{n}\fi \ifdim\arrow@height>0pt \ifx\test@\n@ \xdef\test@{y} \else \xdef\test@{n} \fi \ifdim\temp@@length<\arrow@height\temp@@length=\arrow@height\fi \else \ifdim\temp@@length>-\arrow@height\temp@@length=\arrow@height\fi \fi \ifdim\temp@@length<100pt\arrow@width=100\arrow@width\arrow@height=100\arrow@height\else \ifdim\temp@@length<10pt\arrow@width=1000\arrow@width\arrow@height=1000\arrow@height\else \ifdim\temp@@length<1pt\arrow@width=10000\arrow@width\arrow@height=10000\arrow@height\else \ifdim\temp@@length<0.1pt\arrow@width=100000\arrow@width\arrow@height=100000\arrow@height\else \ifdim\temp@@length<0.01pt\arrow@width=1000000\arrow@width \arrow@height=1000000\arrow@height\else \ifdim\temp@@length<0.001pt\arrow@width=10000000\arrow@width \arrow@height=10000000\arrow@height\else \ifdim\temp@@length<0.0001pt\arrow@width=100000000\arrow@width \arrow@height=100000000\arrow@height\else \ifdim\temp@@length<0.00001pt\arrow@width=1000000000\arrow@width \arrow@height=1000000000\arrow@height \fi\fi\fi\fi\fi\fi\fi\fi \ifx\test@\y@ \xdef\pm@{0} \else \xdef\test@{-\the\arrow@height @} \expandafter\rm@measure\test@ \divide\arrow@width by \third@ \xdef\pm@{\the\arrow@width @} \expandafter\rm@measure\pm@ \xdef\pm@{\first@} \fi } \def\read@graph{% \bgroup \immediate\openin\structurefile = \fill@char\relax \ifeof\structurefile \PackageError{TeXshade} {File `\fill@char' not found} {\MessageBreak The file you specified is missing or you have \MessageBreak misspelled it. \MessageBreak\MessageBreak No feature graph will be displayed. \MessageBreak Type 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@{tttop} \ifx\bottop@\temp@ \tttopfeaturetrue\fi \xdef\temp@{ttttop} \ifx\bottop@\temp@ \ttttopfeaturetrue\fi \xdef\temp@{bottom} \ifx\bottop@\temp@ \bottomfeaturetrue\fi \xdef\temp@{bbottom} \ifx\bottop@\temp@ \bbottomfeaturetrue\fi \xdef\temp@{bbbottom} \ifx\bottop@\temp@ \bbbottomfeaturetrue\fi \xdef\temp@{bbbbottom} \ifx\bottop@\temp@ \bbbbottomfeaturetrue\fi \xdef\seq@{#2} \xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi \xdef\first@{\seq@ @} \expandafter\check@letter\first@ \xdef\first@{\seq@} \ifletter \get@name@number \xdef\seq@{\first@} \fi \ifnum\seq@>\seq@count \message{} \else \ifnum\seq@>-1 \xdef\temp@{#4::&}\expandafter\test@fill\temp@ \xdef\last@{bar} \ifx\second@@\last@ \xdef\last@{hydrophobicity} \ifx\last@\fourth@ \xdef\second@@{bh} \else \xdef\last@{molweight} \ifx\last@\fourth@ \xdef\second@@{bm} \else \xdef\last@{charge} \ifx\last@\fourth@ \xdef\second@@{bc} \else \xdef\last@{conservation} \ifx\last@\fourth@ \xdef\second@@{bcons} \fi \fi \fi \fi \fi \xdef\last@{color} \ifx\second@@\last@ \xdef\last@{hydrophobicity} \ifx\last@\fourth@ \xdef\second@@{ch} \else \xdef\last@{molweight} \ifx\last@\fourth@ \xdef\second@@{cm} \else \xdef\last@{charge} \ifx\last@\fourth@ \xdef\second@@{cc} \else \xdef\last@{conservation} \ifx\last@\fourth@ \xdef\second@@{ccons} \fi \fi \fi \fi \fi \xdef\last@{bar} \ifx\second@@\last@ \xdef\list@{#3,&} \xdef\style@{#4} \def\f@text@{#5} \do@bargraph \xdef\temp@{bottom} \ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi \xdef\temp@{bbottom} \ifx\bottop@\temp@ \xdef\bbottom@stretch{y}\fi \xdef\temp@{bbbottom} \ifx\bottop@\temp@ \xdef\bbbottom@stretch{y}\fi \xdef\temp@{bbbbottom} \ifx\bottop@\temp@ \xdef\bbbbottom@stretch{y}\fi \else \xdef\last@{color} \ifx\second@@\last@ \xdef\list@{#3,&} \xdef\style@{#4} \def\f@text@{#5} \do@colorgraph \else \xdef\f@@color{\f@color} \def\f@text@{#5} \xdef\f@color{\f@@color} \xdef\temp@{#4&} \ifx\temp@\ampers@nd \xdef\list@{#3,&} \xdef\style@{&} \def\f@text@{#5} \else \xdef\last@{restriction} \ifx\second@@\last@ \xdef\temp@{\bottop@ @} \expandafter\firstchar@get\temp@ \xdef\temp@{y} \if\first@ t \xdef\style@{fill:\kern0.9\box@width$\blacktriangledown$[\f@color]} \else \xdef\style@{fill:\kern0.9\box@width$\blacktriangle$[\f@color]} \fi \xdef\f@text@{\kern0.9\box@width#5} \else \xdef\last@{bh} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi \xdef\style@{plot[bar]:Hydro[\f@color][-53]} \else \xdef\last@{bm} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi \xdef\style@{plot[bar]:molw[\f@color][0]} \else \xdef\last@{bc} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi \xdef\style@{plot[bar]:charge[\f@color][-50]} \else \xdef\last@{bcons} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi \xdef\last@{T-Coffee} \ifx\f@color\last@ \xdef\T@coffee@bcons{y} \xdef\f@color{Gray50} \fi \xdef\style@{cons[bar]:cons[\f@color][0]} \else \xdef\last@{ch} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{RedGreen}\fi \xdef\style@{plot[color]:Hydro[\f@color][-53]} \else \xdef\last@{cm} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{Gray}\fi \xdef\style@{plot[color]:molw[\f@color][0]} \else \xdef\last@{cc} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{RedBlue}\fi \xdef\style@{plot[color]:charge[\f@color][-50]} \else \xdef\last@{ccons} \ifx\second@@\last@ \ifx\f@color\gr@ydef@ult\xdef\f@color{ColdHot}\fi \xdef\last@{T-Coffee} \ifx\f@color\last@ \xdef\T@coffee@ccons{y} \xdef\f@color{TC} \fi \xdef\style@{cons[color]:cons[\f@color][0]} \else \xdef\style@{#4} \xdef\temp@@{n} \expandafter\get@firstfill\temp@ \if\second@@ ^ \xdef\second@@{_} \fi \if\second@@ _ \xdef\temp@{\fill@char} \xdef\temp@@{y}\fi \expandafter\getarrow@shape\temp@ \fi \fi \fi \fi \fi \fi \fi \fi \fi \xdef\list@{#3,&} \xdef\@ll{\f@text@} \xdef\temp@@{\bottop@} \xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@ \fi \loopcount=0 \ifx\list@\ampers@nd \else \loop \advance\loopcount by 1\relax \xdef\list@{\list@ @} \expandafter\get@fregions\list@ \ifx\list@\ampers@nd\else\repeat \fi \fi\fi\fi \fi } \def\showfeaturename#1#2{\expandafter\xdef\csname featuretextn@me#1\endcsname{#2}} \def\showfeaturestylename#1#2{\expandafter\xdef\csname featurestylesn@me#1\endcsname{#2}} \def\hidefeaturename#1{\expandafter\xdef\csname featuretextn@me#1\endcsname{}} \def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{} \xdef\featuretextn@metttop{}\xdef\featuretextn@mettttop{}\xdef\featuretextn@mebbbbottom{}\xdef\featuretextn@mebbbottom{}} \def\hidefeaturestylename#1{\expandafter\xdef\csname featurestylesn@me#1\endcsname{}} \def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{} \xdef\featurestylesn@metttop{}\xdef\featurestylesn@mettttop{}\xdef\featurestylesn@mebbbbottom{}\xdef\featurestylesn@mebbbottom{}} \def\seqtype#1{\xdef\seq@type{#1} \if\seq@type P \xdef\prefix@{pep} \else \if\seq@type p \xdef\seq@type{P} \xdef\prefix@{pep} \else \xdef\seq@type{N} \xdef\prefix@{DNA} \fi\fi} \def\nameseq#1#2{% \xdef\first@{#1 @} \expandafter\check@letter\first@ \xdef\first@{#1} \ifletter \get@name@number \fi \expandafter\xdef\csname newseqname\first@\endcsname{#2} } \newcommand\threshold[2][n]{% \xdef\first@{#1} \ifx\first@\n@ \xdef\thresh@ld{#2} \else \all@shadetrue \ifnum\first@>#2 \xdef\thresh@ld{#2} \xdef\all@thresh@ld{#1} \else \xdef\thresh@ld{#1} \xdef\all@thresh@ld{#2} \fi \fi } \def\constosingleseq#1{% \xdef\first@{#1 @} \expandafter\check@letter\first@ \xdef\first@{#1} \ifletter \get@name@number \fi \ifnum\first@>\seq@count \message{} \else \ifnum\first@>0 \xdef\cons@num{\first@} \hideconsensus\fi\fi } \def\constoallseqs{\xdef\cons@num{0}} \def\residuesperline{% \def\@rplfix*##1{% \res@perline=##1 \ifnum\res@perline<1 \res@perline=1\fi \rpl@fixtrue} \def\@rplvar ##1{% \res@perline=##1 \ifnum\res@perline<5 \res@perline=5\fi \rpl@fixfalse} \def\decide@{\ifx\l@@k * \let\next\@rplfix \else \let\next\@rplvar \fi \next} \futurelet\l@@k\decide@} \def\numberingwidth#1{\def\num@width{#1}} \def\charstretch#1{% \def\char@stretch{#1} \xdef\temp@{\char@stretch .00@} \expandafter\coord@get\temp@ \loopcount=\c@@rd \multiply \loopcount by 7 \divide \loopcount by 10 \ifnum\loopcount<10 \xdef\temp@{0\the\loopcount @} \else \xdef\temp@{\the\loopcount @} \fi \expandafter\decimal@B\temp@ \ifnum\loopcount>99 \xdef\char@stretch@W{#1} \else \xdef\char@stretch@W{\temp@} \fi } \def\linestretch#1{\def\line@stretch{#1}} \def\logostretch#1{% \def\logo@stretch{#1} \setlength\temp@@length{1000sp} \setlength\temp@@length{\logo@stretch\temp@@length} \loopcount=\temp@@length \xdef\logo@stretch@IOOO{\the\loopcount} } \def\noblockskip{\def\block@skip{\vspace{0pt}}} \def\smallblockskip{\def\block@skip{\vspace{\baselineskip}}} \def\medblockskip{\def\block@skip{\vspace{1.5\baselineskip}}} \def\bigblockskip{\def\block@skip{\vspace{2\baselineskip}}} \def\vblockspace#1{\def\block@skip{\vspace{#1}}} \def\topspace#1{\def\t@sp@ce{#1}} \def\ttopspace#1{\def\tt@sp@ce{#1}} \def\tttopspace#1{\def\ttt@sp@ce{#1}} \def\ttttopspace#1{\def\tttt@sp@ce{#1}} \def\bottomspace#1{\def\b@sp@ce{#1}} \def\bbottomspace#1{\def\bb@sp@ce{#1}} \def\bbbottomspace#1{\def\bbb@sp@ce{#1}} \def\bbbbottomspace#1{\def\bbbb@sp@ce{#1}} \def\rulerspace#1{\def\ruler@sp@ce{#1}} \def\fixblockspace{\fix@true} \def\flexblockspace{\fix@false} \def\nosepline{\def\seq@skip{\relax}} \def\smallsepline{\def\seq@skip{\vspace{3pt}}\def\sep@space{3pt}} \def\medsepline{\def\seq@skip{\vspace{6pt}}\def\sep@space{6pt}} \def\bigsepline{\def\seq@skip{\vspace{12pt}}\def\sep@space{12pt}} \def\vsepspace#1{\def\seq@skip{\vspace{#1}}\xdef\sep@space{#1}} \def\separationline#1{% \xdef\first@@{#1} \xdef\first@{#1 @} \expandafter\check@letter\first@ \xdef\first@{#1} \ifletter \get@name@number \xdef\first@@{\first@} \fi \ifnum\first@@>\seq@count \xdef\first@@{1} \else \ifnum\first@@<0 \xdef\first@@{1} \else \expandafter\def\csname seq@gap\first@@\endcsname{yes} \loopcount=\seq@gap@num \advance\loopcount by 1 \xdef\seq@gap@num{\the\loopcount} \fi \fi} \newcommand{\shadingmode}[2][-1]{% \T@coffeefalse \xdef\last@{#2} \xdef\first@{identical} \ifx\first@\last@ \simmodefalse \funcmodefalse \xdef\second@{#1 @} \expandafter\check@letter\second@ \ifnumber \all@shadetrue \ifnum#1<0 \all@shadefalse \else \ifnum#1>100 \xdef\all@thresh@ld{100} \else \xdef\all@thresh@ld{#1} \fi\fi \else \xdef\last@{#1} \xdef\first@{allmatchspecial} \ifx\last@\first@ \xdef\all@thresh@ld{100} \all@shadetrue \fi \fi \else \xdef\first@{similar} \ifx\first@\last@ \simmodetrue \funcmodefalse \xdef\second@{#1 @} \expandafter\check@letter\second@ \ifnumber \all@shadetrue \ifnum#1<0 \all@shadefalse \else \ifnum#1>100 \xdef\all@thresh@ld{100} \else \xdef\all@thresh@ld{#1} \fi\fi \else \xdef\last@{#1} \xdef\first@{allmatchspecial} \ifx\last@\first@ \xdef\all@thresh@ld{100} \all@shadetrue \fi \fi \else \xdef\first@{functional} \ifx\first@\last@ \if\seq@type N \message{} \else \simmodefalse \funcmodetrue \func@shading{#1} \xdef\seq@type{P} \xdef\prefix@{pep} \fi \else \xdef\first@{T-Coffee} \ifx\first@\last@ \simmodefalse \funcmodefalse \T@coffeetrue \xdef\second@{#1 @} \expandafter\check@letter\second@ \ifletter \xdef\TC@first@{#1}\include@T@coffee\fi \else \xdef\first@{diverse} \ifx\first@\last@ \xdef\last@{#1} \ifnum\last@>\seq@count \xdef\last@{1}\fi \ifnum\last@<1 \xdef\last@{1}\fi \simmodetrue \funcmodefalse \threshold{0} \xdef\divref@{\last@} \constosingleseq{\last@} \nomatchresidues{Black}{White}{lower}{up} \similarresidues{Black}{White}{lower}{up} \conservedresidues{Black}{White}{{.}}{up} \allmatchresidues{Black}{White}{{.}}{up} \gapchar{-} \hideconsensus \else \message{} \simmodetrue \funcmodefalse \fi\fi\fi\fi\fi} \def\hideallmatchpositions{\xdef\all@out{y}} \def\showallmatchpositions{\xdef\all@out{n}} \newcommand\allmatchspecial[1][100]{% \ifnum#1<0 \xdef\all@thresh@ld{0} \else \ifnum#1>100 \xdef\all@thresh@ld{100} \else \xdef\all@thresh@ld{#1} \fi\fi \all@shadetrue} \def\allmatchspecialoff{\all@shadefalse} \def\stopchar#1{\def\st@p@char{#1}} \def\gapchar#1{% \xdef\first@{rule}\xdef\second@{#1} \ifx\first@\second@\def\gap@char{o} \else\def\gap@char{#1}\fi} \def\gaprule#1{\def\gap@rulethick{#1}} \def\domaingaprule#1{\def\domgap@rulethick{#1}} \newcommand{\setends}[3][&]{% \xdef\start@seq{#2} \xdef\temp@{consensus} \ifx\start@seq\temp@ %%% \message{<\noexpand\setends does not accept `consensus'>} \xdef\start@seq{0} %%%%%%%%%% \xdef\second@{#3@} \expandafter\get@nums\second@ \xdef\start@num{\first@} \xdef\end@num{\second@} \ifnum\start@num<1 \xdef\start@num{1}\fi \ifnum\end@num<\start@num \xdef\end@num{\start@num}\fi \loopcount=\end@num \advance\loopcount by 1 \advance\loopcount by -\start@num \xdef\end@num{\the\loopcount} \start@false %%%%%%%%%% \else \xdef\first@{\start@seq @} \expandafter\check@letter\first@ \xdef\first@{\start@seq} \ifletter \get@name@number \xdef\start@seq{\first@} \fi \ifnum\start@seq>\seq@count \message{<\noexpand\setends{} error: sequence `#2' not defined>} \xdef\start@seq{0} \else \ifnum\start@seq<1 \message{<\noexpand\setends{} error: sequence `#2' not defined>} \xdef\start@seq{0} \else \xdef\second@{#3@} \expandafter\get@nums\second@ \xdef\start@num{\first@} \xdef\end@num{\second@} \ifnum\start@num=0 \xdef\allow@zero{y}\fi \ifnum\end@num=0 \xdef\allow@zero{y}\fi \start@false \fi \fi \fi \xdef\first@{#1}\ifx\first@\ampers@nd\else\startnumber{#2}{#1}\fi } \newcommand{\startnumber}[3][&]{% \xdef\first@{#2} \xdef\second@{consensus} \ifx\first@\second@ \ifnum#3=0 \xdef\allow@zero{y} \fi \expandafter\xdef\csname seq@start0\endcsname{#2} \cons@count=#3 \advance\cons@count by -1\relax \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} \else \xdef\first@{#2 @} \expandafter\check@letter\first@ \xdef\first@{#2} \ifletter \get@name@number \fi \ifnum\first@>\seq@count \message{} \else \xdef\second@{#3} \ifnum\second@=0 \xdef\allow@zero{y} \fi \expandafter\xdef\csname seq@start\first@\endcsname{\second@} \res@count=\second@ \advance\res@count by -1 \expandafter\xdef\csname res@count\first@\endcsname{\the\res@count} \fi \fi \xdef\first@{#1}\ifx\first@\ampers@nd\else\setends{#2}{#1}\fi } \def\seqlength#1#2{% \xdef\first@{#1 @} \expandafter\check@letter\first@ \xdef\first@{#1} \ifletter \get@name@number \fi \ifnum\first@>\seq@count \message{} \else \xdef\second@{#2} \ifnum\second@<0 \xdef\second@{1} \fi \expandafter\xdef\csname seq@len\first@\endcsname{\second@} \fi} \newcommand\shownumbering[2][n]{% \xdef\first@{#1}\ifx\first@\n@\else\xdef\numbering@fg{#1}\fi \xdef\first@{#2} \xdef\second@{left} \ifx\first@\second@ \numbers@lefttrue \numbers@rightfalse \numbers@true \fi \xdef\second@{right} \ifx\first@\second@ \numbers@leftfalse \numbers@righttrue \numbers@true \fi \xdef\second@{leftright} \ifx\first@\second@ \numbers@lefttrue \numbers@righttrue \numbers@true \fi } \def\hidenumbering{\numbers@false} \def\hidenumber#1{\xdef\first@{#1,&,@} \hidenumber@} \newcommand\shownames[2][n]{% \xdef\first@{#1}\ifx\first@\n@\else\xdef\names@fg{#1}\fi \xdef\first@{#2} \xdef\second@{left} \ifx\first@\second@ \names@rightfalse \else \names@righttrue \fi \names@true} \def\hidenames{\names@false} \def\hidename#1{\xdef\first@{#1,&,@} \hidename@} \def\hideresidues{\hidechartrue} \def\showresidues{\hidecharfalse} \def\alignment#1{% \xdef\first@{#1} \xdef\temp@{left} \ifx\first@\temp@ \xdef\c@factor{0} \else \xdef\temp@{center} \ifx\first@\temp@ \xdef\c@factor{0.5} \else \xdef\temp@{right} \ifx\first@\temp@ \xdef\c@factor{1} \fi\fi\fi} \def\donotshade#1{% \xdef\temp@{consensus} \xdef\first@{#1} \ifx\first@\temp@ \consensuscolors{Black}{White}{Black}{White}{Black}{White} \else \xdef\first@{#1,&,@} \donot@shade \fi} \def\hideseqs{\xdef\hide@seqs{y}} \def\showseqs{\xdef\hide@seqs{n}} \def\hideseq#1{\xdef\first@{#1,&,@} \hideseq@} \def\killseq#1{\xdef\first@{#1,&,@} \killseq@} \def\hidesequencelogo{\show@logofalse} \def\hidesubfamilylogo{\show@sublogofalse} \def\logo@group@get#1#2@{% \xdef\first@{#1}\xdef\third@{#2@} \ifx\first@\ampers@nd \else \ifnum`#1>96 \make@upper\fi \expandafter\xdef\csname logo@col\first@\endcsname{\second@} \expandafter\logo@group@get\third@ \fi } \def\logocolor#1#2{% \xdef\logo@colors@set{yes} \xdef\second@{#2} \xdef\third@{#1&@} \expandafter\logo@group@get\third@ } \newcommand\clearlogocolors[1][Black]{% \logocolor{ABCDEFGHIJKLMNOPQRSTUVWXYZ}{#1} } \def\dofrequencycorrection{\xdef\do@freq@correction{y}} \def\undofrequencycorrection{\xdef\do@freq@correction{n}} \newcommand\showlogoscale[2][Black]{\xdef\logo@scalecol{#1}\xdef\show@logoscale{#2}} \def\hidelogoscale{\xdef\show@logoscale{n}} \def\hidenegatives{\xdef\hide@negatives{y}\xdef\sublogo@tint{}} \newcommand\shownegatives[1][medium]{% \xdef\hide@negatives{n} \xdef\first@{#1} \xdef\second@{full} \ifx\first@\second@ \xdef\sublogo@tint{} \else \xdef\second@{strong} \ifx\first@\second@ \xdef\sublogo@tint{Light} \else \xdef\second@{medium} \ifx\first@\second@ \xdef\sublogo@tint{LightLight} \else \xdef\second@{weak} \ifx\first@\second@ \xdef\sublogo@tint{LightLightLight} \else \xdef\sublogo@tint{LightLight} \fi\fi\fi\fi } \def\set@logocolors{% \xdef\second@{undefined} \ifx\first@\second@ \if\logo@colors@set\n@ \xdef\first@{standard} \fi \fi \xdef\second@{standard} \ifx\first@\second@ \if\seq@type A \xdef\logo@colors@set{n} \else \if\seq@type P \xdef\first@{rasmol} \else \xdef\first@{nucleotide} \fi \fi \fi \xdef\second@{nucleotide} \ifx\first@\second@ \clearlogocolors \logocolor{G}{Black} \logocolor{A}{Green} \logocolor{TU}{Red} \logocolor{C}{Blue} \else \xdef\second@{rasmol} \ifx\first@\second@ \clearlogocolors \logocolor{DE}{Red} \logocolor{CM}{Yellow} \logocolor{KR}{Blue} \logocolor{ST}{Orange} \logocolor{FY}{MidnightBlue} \logocolor{NQ}{Cyan} \logocolor{G}{LightGray} \logocolor{LVI}{Green} \logocolor{A}{DarkGray} \logocolor{W}{CarnationPink} \logocolor{H}{CornflowerBlue} \logocolor{P}{Apricot} \logocolor{BZ}{LightMagenta} \else \xdef\second@{chemical} \ifx\first@\second@ \clearlogocolors \logocolor{DE}{Red} \logocolor{VIL}{Black} \logocolor{AG}{Gray} \logocolor{NQ}{Green} \logocolor{FYW}{Brown} \logocolor{KRH}{Blue} \logocolor{ST}{Magenta} \logocolor{P}{Orange} \logocolor{CM}{Yellow} \else \xdef\second@{hydropathy} \ifx\first@\second@ \clearlogocolors \logocolor{DE}{Red} \logocolor{KRH}{Blue} \logocolor{YSTGNQC}{Yellow} \logocolor{AFPMWVIL}{Green} \else \xdef\second@{structure} \ifx\first@\second@ \clearlogocolors \logocolor{DEHKNQR}{Orange} \logocolor{ACGPSTWY}{Yellow} \logocolor{FILMV}{Green} \else \xdef\second@{standard area} \ifx\first@\second@ \clearlogocolors \logocolor{G}{BrickRed} \logocolor{AS}{Orange} \logocolor{CP}{Yellow} \logocolor{TDVN}{YellowGreen} \logocolor{IE}{PineGreen} \logocolor{LQHM}{SkyBlue} \logocolor{FK}{RoyalPurple} \logocolor{Y}{RedViolet} \logocolor{RW}{Black} \else \xdef\second@{accessible area} \ifx\first@\second@ \clearlogocolors \logocolor{C}{BrickRed} \logocolor{IVG}{Orange} \logocolor{FLMA}{Yellow} \logocolor{WSTH}{YellowGreen} \logocolor{P}{PineGreen} \logocolor{YDN}{SkyBlue} \logocolor{EQ}{RoyalPurple} \logocolor{R}{RedViolet} \logocolor{K}{Black} \fi\fi\fi\fi\fi\fi\fi } \newcommand\findsubfamily[2][n]{% \xdef\first@{#1} \ifx\first@\n@ \else \xdef\subfamily@threshold{#1} \fi \xdef\subfamily@seq{#2} } \def\setsubfamily#1{% \xdef\sub@family@setting{#1} \loopcount=1 \loop \expandafter\xdef\csname subfamily@num\the\loopcount\endcsname{1} \advance\loopcount by 1 \ifnum\loopcount>\seq@count\else\repeat \xdef\subfamily@count{2} \res@count=0 \xdef\first@{#1,&,@} \setsubfamily@ \clear@res@nums{1} \clear@res@nums{2} \expandafter\xdef\csname group@num2\endcsname{\the\res@count} \loopcount=\seq@count \advance\loopcount by -\res@count \expandafter\xdef\csname group@num1\endcsname{\the\loopcount} } \def\subfamilythreshold#1{\xdef\subfamily@threshold{#1}} \newcommand\showsubfamilylogo[2][undefined]{% \xdef\first@{#1} \set@logocolors \xdef\first@{#2} \xdef\last@{top} \ifx\first@\last@\xdef\sublogo@top{0}\else\xdef\sublogo@top{1}\fi \show@sublogotrue } \def\relevance#1{% \def\sig@max{#1} \setlength\temp@@length{1000sp} \setlength\temp@@length{\sig@max\temp@@length} \loopcount=\temp@@length \xdef\sig@max{\the\loopcount} } \newcommand\showrelevance[2][Black]{\def\sig@color{#1}\def\sig@char{#2}\xdef\hide@sig{n}} \def\hiderelevance{\xdef\hide@sig{y}} \newcommand\showsequencelogo[2][undefined]{% \xdef\first@{#1} \set@logocolors \xdef\first@{#2} \xdef\last@{top} \ifx\first@\last@\xdef\logo@top{0}\else\xdef\logo@top{1}\fi \show@logotrue } \newcommand\showconsensus[2][n]{% \xdef\text@scale{n} \xdef\box@scale{n} \xdef\first@{#1} \ifx\first@\n@ \xdef\collect@cons@colors{no} \else \xdef\first@{#1,&,@} \expandafter\get@item\first@ \xdef\c@nsc@l{\fourth@} \xdef\first@@{Gray} \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else \xdef\first@@{RedBlue} \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else \xdef\first@@{BlueRed} \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else \xdef\first@@{RedGreen} \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else \xdef\first@@{GreenRed} \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else \xdef\first@@{ColdHot} \ifx\c@nsc@l\first@@\xdef\text@scale{y}\else \xdef\first@@{HotCold} \ifx\c@nsc@l\first@@\xdef\text@scale{y} \fi\fi\fi\fi\fi\fi\fi \expandafter\get@item\first@ \ifx\fourth@\ampers@nd \xdef\c@nssc@le{White} \else \xdef\c@nssc@le{\fourth@} \xdef\first@{Gray} \ifx\c@nssc@le\first@\xdef\box@scale{y}\else \xdef\first@{RedBlue} \ifx\c@nssc@le\first@\xdef\box@scale{y}\else \xdef\first@{BlueRed} \ifx\c@nssc@le\first@\xdef\box@scale{y}\else \xdef\first@{RedGreen} \ifx\c@nssc@le\first@\xdef\box@scale{y}\else \xdef\first@{GreenRed} \ifx\c@nssc@le\first@\xdef\box@scale{y}\else \xdef\first@{ColdHot} \ifx\c@nssc@le\first@\xdef\box@scale{y}\else \xdef\first@{HotCold} \ifx\c@nssc@le\first@\xdef\box@scale{y}\else \fi\fi\fi\fi\fi\fi\fi \fi \xdef\collect@cons@colors{y} \fi \xdef\first@{#2} \xdef\last@{top} \ifx\first@\last@\xdef\cons@top{0}\else\xdef\cons@top{1}\fi \show@construe} \def\consensuscolors#1#2#3#4#5#6{% \xdef\last@{\ampers@nd} \xdef\first@{#1&}\xdef\second@{#2&} \ifx\first@\last@\else\def\ConsTextNomatch{#1}\fi \ifx\second@\last@\else\def\ConsNomatch{#2}\fi \xdef\first@{#3&}\xdef\second@{#4&} \ifx\first@\last@\else\def\ConsTextMatch{#3}\fi \ifx\second@\last@\else\def\ConsMatch{#4}\fi \xdef\first@{#5&}\xdef\second@{#6&} \ifx\first@\last@\else\def\ConsTextAllmatch{#5}\fi \ifx\second@\last@\else\def\ConsAllmatch{#6}\fi } \def\defconsensus#1#2#3{% \xdef\second@{#1&} \ifx\second@\ampers@nd \else \def\n@m@tch{#1}\fi \xdef\second@{#2&} \ifx\second@\ampers@nd \else \def\m@tch{#2}\fi \xdef\second@{#3&} \ifx\second@\ampers@nd \else \def\@llm@tch{#3}\fi} \def\hideconsensus{\show@consfalse} \def\nameconsensus#1{\def\cons@name{#1}} \def\namesequencelogo#1{\def\logo@name@user{#1}} \newcommand\namesubfamilylogo[2][]{\def\sublogo@name@neg{#1}\def\sublogo@name@user{#2}} \def\hideleadinggaps{\sh@wg@psfalse} \def\showleadinggaps{\sh@wg@pstrue} \newcommand\showruler[3][n]{% \xdef\first@{#1} \ifx\first@\n@\else\xdef\ruler@fg{#1}\fi \xdef\first@{consensus} \xdef\second@{#3} \xdef\third@{bottom} \xdef\fourth@{#2} \ifx\third@\fourth@ \xdef\rule@top{1}\else\xdef\rule@top{0}\fi \ifx\first@\second@ \xdef\rule@num{0} \else \xdef\first@{#3 @} \expandafter\check@letter\first@ \xdef\first@{#3} \ifletter \get@name@number \fi \ifnum\first@>\seq@count \else \ifnum\first@>0 \xdef\rule@num{\first@} \fi \fi \fi \xdef\ruler@{}} \def\hideruler{\xdef\rule@num{-1}} \def\allowzero{\xdef\allow@zero{y}} \def\disallowzero{\xdef\allow@zero{n}} \def\rulersteps#1{% \xdef\ruler@step{#1} \ifnum#1<4 \xdef\ruler@rot{90}\fi } \def\rotateruler{\xdef\ruler@rot{90}} \def\unrotateruler{\xdef\ruler@rot{0}} \def\namerulerpos#1#2{% \expandafter\xdef\csname alt@ruler#1\endcsname{#2} } \def\featurerule#1{\setlength\rule@thick{#1}} \def\orderseqs#1{% \def\order@loop{% \expandafter\check@letter\first@ \ifletter \expandafter\get@item\first@ \xdef\first@{\fourth@} \get@name@number \xdef\seq@order{\seq@order,\first@} \xdef\first@{\first@@ @} \order@loop \else \expandafter\get@digit\first@ \ifx\fourth@\ampers@nd \else \xdef\seq@order{\seq@order,\fourth@} \order@loop \fi \fi} \xdef\first@{#1,&,@} \xdef\seq@order{} \order@loop \xdef\seq@order{\seq@order @} \expandafter\get@item\seq@order \xdef\seq@order{\first@@,@} } \def\setfamily#1#2{% \xdef\second@{#2&} \ifx\second@\ampers@nd \else \xdef\first@{#1} \xdef\second@{#2} \xdef\temp@{rm} \ifx\second@\temp@ \xdef\third@{\rmdefault} \else \xdef\temp@{sf} \ifx\second@\temp@ \xdef\third@{\sfdefault} \else \xdef\temp@{tt} \ifx\second@\temp@ \xdef\third@{\ttdefault} \else \xdef\third@{\second@} \fi\fi\fi \xdef\temp@{featurenames} \ifx\first@\temp@ \xdef\ftext@family{\third@} \else \xdef\temp@{featurestylenames} \ifx\first@\temp@ \xdef\fstyles@family{\third@} \else \xdef\temp@{features} \ifx\first@\temp@ \xdef\featuretext@family{\third@} \else \xdef\temp@{featurestyles} \ifx\first@\temp@ \xdef\featurestyles@family{\third@} \else \xdef\temp@{numbering} \ifx\first@\temp@ \xdef\numbertext@family{\third@} \else \xdef\temp@{names} \ifx\first@\temp@ \xdef\namestext@family{\third@} \else \xdef\temp@{residues} \ifx\first@\temp@ \xdef\residues@family{\third@} \else \xdef\temp@{legend} \ifx\first@\temp@ \xdef\legend@family{\third@} \else \xdef\temp@{labels} \ifx\first@\temp@ \xdef\label@family{\third@} \else \xdef\temp@{ruler} \ifx\first@\temp@ \xdef\ruler@family{\second@} \else \xdef\temp@{all} \ifx\first@\temp@ \xdef\ftext@family{\third@} \xdef\fstyles@family{\third@} \xdef\featuretext@family{\third@} \xdef\featurestyles@family{\third@} \xdef\numbertext@family{\third@} \xdef\namestext@family{\third@} \xdef\residues@family{\third@} \xdef\legend@family{\third@} \xdef\label@family{\third@} \xdef\ruler@family{\second@} \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi \fi } \def\setseries#1#2{% \xdef\second@{#2&} \ifx\second@\ampers@nd \else \xdef\first@{#1} \xdef\second@{#2} \xdef\temp@{bf} \ifx\second@\temp@ \xdef\third@{\bfdefault} \else \xdef\temp@{md} \ifx\second@\temp@ \xdef\third@{\mddefault} \else \xdef\third@{\second@} \fi\fi \xdef\temp@{featurenames} \ifx\first@\temp@ \xdef\ftext@series{\third@} \else \xdef\temp@{featurestylenames} \ifx\first@\temp@ \xdef\fstyles@series{\third@} \else \xdef\temp@{features} \ifx\first@\temp@ \xdef\featuretext@series{\third@} \else \xdef\temp@{featurestyles} \ifx\first@\temp@ \xdef\featurestyles@series{\third@} \else \xdef\temp@{numbering} \ifx\first@\temp@ \xdef\numbertext@series{\third@} \else \xdef\temp@{names} \ifx\first@\temp@ \xdef\namestext@series{\third@} \else \xdef\temp@{residues} \ifx\first@\temp@ \xdef\residues@series{\third@} \else \xdef\temp@{legend} \ifx\first@\temp@ \xdef\legend@series{\third@} \else \xdef\temp@{labels} \ifx\first@\temp@ \xdef\label@series{\third@} \else \xdef\temp@{all} \ifx\first@\temp@ \xdef\ftext@series{\third@} \xdef\fstyles@series{\third@} \xdef\featuretext@series{\third@} \xdef\featurestyles@series{\third@} \xdef\numbertext@series{\third@} \xdef\namestext@series{\third@} \xdef\residues@series{\third@} \xdef\legend@series{\third@} \xdef\label@series{\third@} \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi \fi } \def\setshape#1#2{% \xdef\second@{#2&} \ifx\second@\ampers@nd \else \xdef\first@{#1} \xdef\second@{#2} \xdef\temp@{it} \ifx\second@\temp@ \xdef\third@{\itdefault} \else \xdef\temp@{sl} \ifx\second@\temp@ \xdef\third@{\sldefault} \else \xdef\temp@{sc} \ifx\second@\temp@ \xdef\third@{\scdefault} \else \xdef\temp@{up} \ifx\second@\temp@ \xdef\third@{\updefault} \else \xdef\third@{\second@} \fi\fi\fi\fi \xdef\temp@{featurenames} \ifx\first@\temp@ \xdef\ftext@shape{\third@} \else \xdef\temp@{featurestylenames} \ifx\first@\temp@ \xdef\fstyles@shape{\third@} \else \xdef\temp@{features} \ifx\first@\temp@ \xdef\featuretext@shape{\third@} \else \xdef\temp@{featurestyles} \ifx\first@\temp@ \xdef\featurestyles@shape{\third@} \else \xdef\temp@{numbering} \ifx\first@\temp@ \xdef\numbertext@shape{\third@} \else \xdef\temp@{names} \ifx\first@\temp@ \xdef\namestext@shape{\third@} \else \xdef\temp@{residues} \ifx\first@\temp@ \xdef\residues@shape{\third@} \else \xdef\temp@{legend} \ifx\first@\temp@ \xdef\legend@shape{\third@} \else \xdef\temp@{labels} \ifx\first@\temp@ \xdef\label@shape{\third@} \else \xdef\temp@{all} \ifx\first@\temp@ \xdef\ftext@shape{\third@} \xdef\fstyles@shape{\third@} \xdef\featuretext@shape{\third@} \xdef\featurestyles@shape{\third@} \xdef\numbertext@shape{\third@} \xdef\namestext@shape{\third@} \xdef\residues@shape{\third@} \xdef\legend@shape{\third@} \xdef\label@shape{\third@} \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi \fi } \def\setsize#1#2{% \xdef\second@{#2&} \ifx\second@\ampers@nd \else \xdef\first@{#1} \xdef\temp@{features} \ifx\first@\temp@ \def\featuretext@size{\csname #2\endcsname} \else \xdef\temp@{featurestyles} \ifx\first@\temp@ \def\featurestyles@size{\csname #2\endcsname} \else \xdef\temp@{featurenames} \ifx\first@\temp@ \def\ftext@size{\csname #2\endcsname} \else \xdef\temp@{featurestylenames} \ifx\first@\temp@ \def\fstyles@size{\csname #2\endcsname} \else \xdef\temp@{numbering} \ifx\first@\temp@ \def\numbertext@size{\csname #2\endcsname} \else \xdef\temp@{names} \ifx\first@\temp@ \def\namestext@size{\csname #2\endcsname} \else \xdef\temp@{legend} \ifx\first@\temp@ \def\legend@size{\csname #2\endcsname} \else \xdef\temp@{labels} \ifx\first@\temp@ \def\label@size{\csname #2\endcsname} \else \xdef\temp@{residues} \ifx\first@\temp@ \def\residues@size{\csname #2\endcsname} \xdef\res@size{#2} \else \xdef\temp@{all} \ifx\first@\temp@ \def\featuretext@size{\csname #2\endcsname} \def\featurestyles@size{\csname #2\endcsname} \def\ftext@size{\csname #2\endcsname} \def\fstyles@size{\csname #2\endcsname} \def\numbertext@size{\csname #2\endcsname} \def\namestext@size{\csname #2\endcsname} \def\legend@size{\csname #2\endcsname} \def\label@size{\csname #2\endcsname} \def\residues@size{\csname #2\endcsname} \xdef\res@size{#2} \fi\fi\fi\fi\fi\fi\fi\fi\fi\fi \xdef\temp@{Huge} \ifx\temp@\res@size \def\bottomruler@size{\csname Large\endcsname} \else \xdef\temp@{huge} \ifx\temp@\res@size \def\bottomruler@size{\csname large\endcsname} \else \xdef\temp@{LARGE} \ifx\temp@\res@size \def\bottomruler@size{\csname normalsize\endcsname} \else \xdef\temp@{Large} \ifx\temp@\res@size \def\bottomruler@size{\csname small\endcsname} \else \xdef\temp@{large} \ifx\temp@\res@size \def\bottomruler@size{\csname footnotesize\endcsname} \else \xdef\temp@{normalsize} \ifx\temp@\res@size \def\bottomruler@size{\csname scriptsize\endcsname} \else \def\bottomruler@size{\csname tiny\endcsname} \fi\fi\fi\fi\fi\fi \fi \xdef\temp@{ruler} \ifx\first@\temp@ \def\bottomruler@size{\csname #2\endcsname} \fi } \def\setfont#1#2#3#4#5{% \setfamily{#1}{#2}\setseries{#1}{#3} \setshape{#1}{#4}\setsize{#1}{#5}} \def\featurenamesrm{\setfamily{featurenames}{rm}} \def\featurenamessf{\setfamily{featurenames}{sf}} \def\featurenamestt{\setfamily{featurenames}{tt}} \def\featurenamesmd{\setseries{featurenames}{md}} \def\featurenamesbf{\setseries{featurenames}{bf}} \def\featurenamesup{\setshape {featurenames}{up}} \def\featurenamesit{\setshape {featurenames}{it}} \def\featurenamessl{\setshape {featurenames}{sl}} \def\featurenamessc{\setshape {featurenames}{sc}} \def\featurenamestiny {\setsize{featurenames}{tiny}} \def\featurenamesscriptsize {\setsize{featurenames}{scriptsize}} \def\featurenamesfootnotesize{\setsize{featurenames}{footnotesize}} \def\featurenamessmall {\setsize{featurenames}{small}} \def\featurenamesnormalsize {\setsize{featurenames}{normalsize}} \def\featurenameslarge {\setsize{featurenames}{large}} \def\featurenamesLarge {\setsize{featurenames}{Large}} \def\featurenamesLARGE {\setsize{featurenames}{LARGE}} \def\featurenameshuge {\setsize{featurenames}{huge}} \def\featurenamesHuge {\setsize{featurenames}{Huge}} \def\featurestylenamesrm{\setfamily{featurestylenames}{rm}} \def\featurestylenamessf{\setfamily{featurestylenames}{sf}} \def\featurestylenamestt{\setfamily{featurestylenames}{tt}} \def\featurestylenamesmd{\setseries{featurestylenames}{md}} \def\featurestylenamesbf{\setseries{featurestylenames}{bf}} \def\featurestylenamesup{\setshape {featurestylenames}{up}} \def\featurestylenamesit{\setshape {featurestylenames}{it}} \def\featurestylenamessl{\setshape {featurestylenames}{sl}} \def\featurestylenamessc{\setshape {featurestylenames}{sc}} \def\featurestylenamestiny {\setsize{featurestylenames}{tiny}} \def\featurestylenamesscriptsize {\setsize{featurestylenames}{scriptsize}} \def\featurestylenamesfootnotesize{\setsize{featurestylenames}{footnotesize}} \def\featurestylenamessmall {\setsize{featurestylenames}{small}} \def\featurestylenamesnormalsize {\setsize{featurestylenames}{normalsize}} \def\featurestylenameslarge {\setsize{featurestylenames}{large}} \def\featurestylenamesLarge {\setsize{featurestylenames}{Large}} \def\featurestylenamesLARGE {\setsize{featurestylenames}{LARGE}} \def\featurestylenameshuge {\setsize{featurestylenames}{huge}} \def\featurestylenamesHuge {\setsize{featurestylenames}{Huge}} \def\featuresrm{\setfamily{features}{rm}} \def\featuressf{\setfamily{features}{sf}} \def\featurestt{\setfamily{features}{tt}} \def\featuresmd{\setseries{features}{md}} \def\featuresbf{\setseries{features}{bf}} \def\featuresup{\setshape {features}{up}} \def\featuresit{\setshape {features}{it}} \def\featuressl{\setshape {features}{sl}} \def\featuressc{\setshape {features}{sc}} \def\featurestiny {\setsize{features}{tiny}} \def\featuresscriptsize {\setsize{features}{scriptsize}} \def\featuresfootnotesize{\setsize{features}{footnotesize}} \def\featuressmall {\setsize{features}{small}} \def\featuresnormalsize {\setsize{features}{normalsize}} \def\featureslarge {\setsize{features}{large}} \def\featuresLarge {\setsize{features}{Large}} \def\featuresLARGE {\setsize{features}{LARGE}} \def\featureshuge {\setsize{features}{huge}} \def\featuresHuge {\setsize{features}{Huge}} \def\featurestylesrm{\setfamily{featurestyles}{rm}} \def\featurestylessf{\setfamily{featurestyles}{sf}} \def\featurestylestt{\setfamily{featurestyles}{tt}} \def\featurestylesmd{\setseries{featurestyles}{md}} \def\featurestylesbf{\setseries{featurestyles}{bf}} \def\featurestylesup{\setshape {featurestyles}{up}} \def\featurestylesit{\setshape {featurestyles}{it}} \def\featurestylessl{\setshape {featurestyles}{sl}} \def\featurestylessc{\setshape {featurestyles}{sc}} \def\featurestylestiny {\setsize{featurestyles}{tiny}} \def\featurestylesscriptsize {\setsize{featurestyles}{scriptsize}} \def\featurestylesfootnotesize{\setsize{featurestyles}{footnotesize}} \def\featurestylessmall {\setsize{featurestyles}{small}} \def\featurestylesnormalsize {\setsize{featurestyles}{normalsize}} \def\featurestyleslarge {\setsize{featurestyles}{large}} \def\featurestylesLarge {\setsize{featurestyles}{Large}} \def\featurestylesLARGE {\setsize{featurestyles}{LARGE}} \def\featurestyleshuge {\setsize{featurestyles}{huge}} \def\featurestylesHuge {\setsize{featurestyles}{Huge}} \def\numberingrm{\setfamily{numbering}{rm}} \def\numberingsf{\setfamily{numbering}{sf}} \def\numberingtt{\setfamily{numbering}{tt}} \def\numberingmd{\setseries{numbering}{md}} \def\numberingbf{\setseries{numbering}{bf}} \def\numberingup{\setshape {numbering}{up}} \def\numberingit{\setshape {numbering}{it}} \def\numberingsl{\setshape {numbering}{sl}} \def\numberingsc{\setshape {numbering}{sc}} \def\numberingtiny {\setsize{numbering}{tiny}} \def\numberingscriptsize {\setsize{numbering}{scriptsize}} \def\numberingfootnotesize{\setsize{numbering}{footnotesize}} \def\numberingsmall {\setsize{numbering}{small}} \def\numberingnormalsize {\setsize{numbering}{normalsize}} \def\numberinglarge {\setsize{numbering}{large}} \def\numberingLarge {\setsize{numbering}{Large}} \def\numberingLARGE {\setsize{numbering}{LARGE}} \def\numberinghuge {\setsize{numbering}{huge}} \def\numberingHuge {\setsize{numbering}{Huge}} \def\namesrm{\setfamily{names}{rm}} \def\namessf{\setfamily{names}{sf}} \def\namestt{\setfamily{names}{tt}} \def\namesmd{\setseries{names}{md}} \def\namesbf{\setseries{names}{bf}} \def\namesup{\setshape {names}{up}} \def\namesit{\setshape {names}{it}} \def\namessl{\setshape {names}{sl}} \def\namessc{\setshape {names}{sc}} \def\namestiny {\setsize{names}{tiny}} \def\namesscriptsize {\setsize{names}{scriptsize}} \def\namesfootnotesize{\setsize{names}{footnotesize}} \def\namessmall {\setsize{names}{small}} \def\namesnormalsize {\setsize{names}{normalsize}} \def\nameslarge {\setsize{names}{large}} \def\namesLarge {\setsize{names}{Large}} \def\namesLARGE {\setsize{names}{LARGE}} \def\nameshuge {\setsize{names}{huge}} \def\namesHuge {\setsize{names}{Huge}} \def\residuesrm{\setfamily{residues}{rm}} \def\residuessf{\setfamily{residues}{sf}} \def\residuestt{\setfamily{residues}{tt}} \def\residuesmd{\setseries{residues}{md}} \def\residuesbf{\setseries{residues}{bf}} \def\residuesup{\setshape {residues}{up}} \def\residuesit{\setshape {residues}{it}} \def\residuessl{\setshape {residues}{sl}} \def\residuessc{\setshape {residues}{sc}} \def\residuestiny {\setsize{residues}{tiny}} \def\residuesscriptsize {\setsize{residues}{scriptsize}} \def\residuesfootnotesize{\setsize{residues}{footnotesize}} \def\residuessmall {\setsize{residues}{small}} \def\residuesnormalsize {\setsize{residues}{normalsize}} \def\residueslarge {\setsize{residues}{large}} \def\residuesLarge {\setsize{residues}{Large}} \def\residuesLARGE {\setsize{residues}{LARGE}} \def\residueshuge {\setsize{residues}{huge}} \def\residuesHuge {\setsize{residues}{Huge}} \def\legendrm{\setfamily{legend}{rm}} \def\legendsf{\setfamily{legend}{sf}} \def\legendtt{\setfamily{legend}{tt}} \def\legendmd{\setseries{legend}{md}} \def\legendbf{\setseries{legend}{bf}} \def\legendup{\setshape {legend}{up}} \def\legendit{\setshape {legend}{it}} \def\legendsl{\setshape {legend}{sl}} \def\legendsc{\setshape {legend}{sc}} \def\legendtiny {\setsize{legend}{tiny}} \def\legendscriptsize {\setsize{legend}{scriptsize}} \def\legendfootnotesize{\setsize{legend}{footnotesize}} \def\legendsmall {\setsize{legend}{small}} \def\legendnormalsize {\setsize{legend}{normalsize}} \def\legendlarge {\setsize{legend}{large}} \def\legendLarge {\setsize{legend}{Large}} \def\legendLARGE {\setsize{legend}{LARGE}} \def\legendhuge {\setsize{legend}{huge}} \def\legendHuge {\setsize{legend}{Huge}} \def\rulerrm{\setfamily{ruler}{rm}} \def\rulersf{\setfamily{ruler}{sf}} \def\rulertt{\setfamily{ruler}{tt}} \def\rulertiny {\setsize{ruler}{tiny}} \def\rulerscriptsize {\setsize{ruler}{scriptsize}} \def\rulerfootnotesize{\setsize{ruler}{footnotesize}} \def\rulersmall {\setsize{ruler}{small}} \def\rulernormalsize {\setsize{ruler}{normalsize}} \def\rulerlarge {\setsize{ruler}{large}} \def\rulerLarge {\setsize{ruler}{Large}} \def\rulerLARGE {\setsize{ruler}{LARGE}} \def\rulerhuge {\setsize{ruler}{huge}} \def\rulerHuge {\setsize{ruler}{Huge}} \def\funcshadingstyle#1#2#3#4#5{% \xdef\temp@{nomatch} \xdef\first@{#1} \ifx\temp@\first@ \xdef\first@{0} \else \xdef\first@{\csname funcgrp#1\endcsname} \fi \ifnum\first@>-1 \expandafter\xdef\csname fg@textcolor\first@\endcsname{#2} \expandafter\xdef\csname fg@color\first@\endcsname{#3} \expandafter\xdef\csname funcm@tch\first@\endcsname{#4} \expandafter\def\csname func@style\first@\endcsname{\csname text#5\endcsname} \fi} \def\defshadingcolors#1{% \expandafter\xdef\csname TextNomatch@#1\endcsname{\TextNomatch} \expandafter\xdef\csname Nomatch@#1\endcsname{\Nomatch} \expandafter\xdef\csname resn@m@tch@#1\endcsname{\resn@m@tch} \expandafter\xdef\csname TextSimilar@#1\endcsname{\TextSimilar} \expandafter\xdef\csname Similar@#1\endcsname{\Similar} \expandafter\xdef\csname ressimm@tch@#1\endcsname{\ressimm@tch} \expandafter\xdef\csname TextIdentical@#1\endcsname{\TextIdentical} \expandafter\xdef\csname Identical@#1\endcsname{\Identical} \expandafter\xdef\csname resm@tch@#1\endcsname{\resm@tch} \expandafter\xdef\csname TextAllmatch@#1\endcsname{\TextAllmatch} \expandafter\xdef\csname Allmatch@#1\endcsname{\Allmatch} \expandafter\xdef\csname res@llm@tch@#1\endcsname{\res@llm@tch} \expandafter\xdef\csname gap@fg@#1\endcsname{\gap@fg} \expandafter\xdef\csname gap@bg@#1\endcsname{\gap@bg} } \def\shadingcolors#1{% \gapcolors{Black}{White} \nomatchresidues{Black}{White}{upper}{up} \xdef\first@{#1} \xdef\second@{blues} \ifx\first@\second@ \similarresidues{Black}{Magenta}{upper}{up} \conservedresidues{White}{RoyalBlue}{upper}{up} \allmatchresidues{Goldenrod}{RoyalPurple}{upper}{up} \else \xdef\second@{greens} \ifx\first@\second@ \similarresidues{Black}{GreenYellow}{upper}{up} \conservedresidues{White}{PineGreen}{upper}{up} \allmatchresidues{YellowOrange}{OliveGreen}{upper}{up} \else \xdef\second@{reds} \ifx\first@\second@ \similarresidues{Black}{YellowOrange}{upper}{up} \conservedresidues{White}{BrickRed}{upper}{up} \allmatchresidues{YellowGreen}{Mahagony}{upper}{up} \else \xdef\second@{black} \ifx\first@\second@ \similarresidues{Black}{White}{upper}{sl} \conservedresidues{White}{Black}{upper}{up} \allmatchresidues{White}{Black}{upper}{sl} \else \xdef\second@{grays} \ifx\first@\second@ \similarresidues{Black}{LightGray}{upper}{up} \conservedresidues{White}{DarkGray}{upper}{up} \allmatchresidues{White}{Black}{upper}{up} \else \xdef\TextNomatch{\csname TextNomatch@#1\endcsname} \xdef\Nomatch {\csname Nomatch@#1\endcsname} \xdef\resn@m@tch {\csname resn@m@tch@#1\endcsname} \xdef\TextSimilar{\csname TextSimilar@#1\endcsname} \xdef\Similar {\csname Similar@#1\endcsname} \xdef\ressimm@tch{\csname ressimm@tch@#1\endcsname} \xdef\TextIdentical{\csname TextIdentical@#1\endcsname} \xdef\Identical {\csname Identical@#1\endcsname} \xdef\resm@tch {\csname resm@tch@#1\endcsname} \xdef\TextAllmatch{\csname TextAllmatch@#1\endcsname} \xdef\Allmatch {\csname Allmatch@#1\endcsname} \xdef\res@llm@tch {\csname res@llm@tch@#1\endcsname} \xdef\gap@fg {\csname gap@fg@#1\endcsname} \xdef\gap@bg {\csname gap@bg@#1\endcsname} \xdef\domgap@fg {\csname domgap@fg@#1\endcsname} \xdef\domgap@bg {\csname domgap@bg@#1\endcsname} \fi\fi\fi\fi\fi \xdef\first@{#1} \expandafter\defshadingcolors{\first@} } \def\nomatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} \xdef\last@{\ampers@nd} \ifx\first@\last@\else\def\TextNomatch{#1} \expandafter\def\csname fg@textcolor0\endcsname{#1} \fi \ifx\second@\last@\else\gdef\Nomatch{#2} \expandafter\def\csname fg@color0\endcsname{#2} \fi \ifx\third@\last@\else\def\resn@m@tch{#3} \fi \xdef\first@{#4&} \ifx\first@\last@\else \def\no@style{\csname text#4\endcsname} \expandafter\def\csname func@style0\endcsname% {\csname text#4\endcsname}\fi} \def\similarresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} \xdef\last@{\ampers@nd} \ifx\first@\last@\else\def\TextSimilar{#1}\fi \ifx\second@\last@\else\gdef\Similar{#2}\fi \ifx\third@\last@\else\def\ressimm@tch{#3}\fi \xdef\first@{#4&} \ifx\first@\last@\else \def\sim@style{\csname text#4\endcsname}\fi} \def\conservedresidues#1#2#3#4{\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} \xdef\last@{\ampers@nd} \ifx\first@\last@\else\def\TextIdentical{#1}\fi \ifx\second@\last@\else\gdef\Identical{#2}\fi \ifx\third@\last@\else\def\resm@tch{#3}\fi \xdef\first@{#4&} \ifx\first@\last@\else \def\id@style{\csname text#4\endcsname}\fi} \def\allmatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&} \xdef\last@{\ampers@nd} \ifx\first@\last@\else\def\TextAllmatch{#1}\fi \ifx\second@\last@\else\gdef\Allmatch{#2}\fi \ifx\third@\last@\else\def\res@llm@tch{#3}\fi \xdef\first@{#4&} \ifx\first@\last@\else \def\all@style{\csname text#4\endcsname}\fi} \def\gapcolors#1#2 {\xdef\first@{#1&}\xdef\second@{#2&} \xdef\last@{\ampers@nd} \ifx\first@\last@\else\def\gap@fg{#1} \expandafter\def\csname fg@textcolor*\endcsname{#1}\fi \ifx\second@\last@\else\def\gap@bg{#2} \expandafter\def\csname fg@color*\endcsname{#2}\fi} \def\domaingapcolors#1#2 {\xdef\first@{#1&}\xdef\second@{#2&} \xdef\last@{\ampers@nd} \ifx\first@\last@\else\def\domgap@fg{#1} \expandafter\def\csname fg@textcolor!\endcsname{#1}\fi \ifx\second@\last@\else\def\domgap@bg{#2} \expandafter\def\csname fg@color!\endcsname{#2}\fi} \def\shadebox#1{% \xdef\first@{White}% \xdef\third@{#1}% \xdef\second@{nomatch}% \ifx\second@\third@ \ifx\Nomatch\first@\white@box\else\textcolor{\Nomatch}{\box@rule}\fi% \else \xdef\second@{similar}% \ifx\second@\third@ \ifx\Similar\first@\white@box\else\textcolor{\Similar}{\box@rule}\fi% \else \xdef\second@{conserved}% \ifx\second@\third@ \ifx\Identical\first@\white@box\else\textcolor{\Identical}{\box@rule}\fi% \else \xdef\second@{allmatch}% \ifx\second@\third@ \ifx\Allmatch\first@\white@box\else\textcolor{\Allmatch}{\box@rule}\fi% \else \ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi \fi\fi\fi\fi} \def\featurenamescolor#1{% \expandafter\xdef\csname ftext@fg@ttttop\endcsname{#1} \expandafter\xdef\csname ftext@fg@tttop\endcsname{#1} \expandafter\xdef\csname ftext@fg@ttop\endcsname{#1} \expandafter\xdef\csname ftext@fg@top\endcsname{#1} \expandafter\xdef\csname ftext@fg@bottom\endcsname{#1} \expandafter\xdef\csname ftext@fg@bbottom\endcsname{#1} \expandafter\xdef\csname ftext@fg@bbbottom\endcsname{#1} \expandafter\xdef\csname ftext@fg@bbbbottom\endcsname{#1} } \def\featurestylenamescolor#1{% \expandafter\xdef\csname fstyles@fg@ttttop\endcsname{#1} \expandafter\xdef\csname fstyles@fg@tttop\endcsname{#1} \expandafter\xdef\csname fstyles@fg@ttop\endcsname{#1} \expandafter\xdef\csname fstyles@fg@top\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bottom\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bbottom\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bbbottom\endcsname{#1} \expandafter\xdef\csname fstyles@fg@bbbbottom\endcsname{#1} } \def\featurenamecolor#1#2{\expandafter\xdef\csname ftext@fg@#1\endcsname{#2}} \def\featurestylenamecolor#1#2{\expandafter\xdef\csname fstyles@fg@#1\endcsname{#2}} \def\namescolor#1{\xdef\names@fg{#1}} \def\namecolor#1#2{% \xdef\first@{consensus} \xdef\second@{#1} \ifx\first@\second@ \expandafter\xdef\csname name@col0\endcsname{#2} \else \xdef\first@{featurenames} \xdef\second@{#1} \ifx\first@\second@ \xdef\ftext@fg{#2} \else \xdef\first@{featurestylenames} \xdef\second@{#1} \ifx\first@\second@ \xdef\fstyles@fg{#2} \else \xdef\first@{#1,&,@} \xdef\third@{#2} \namecolor@ \fi\fi\fi } \def\numberingcolor#1{\xdef\numbering@fg{#1}} \def\numbercolor#1#2{% \xdef\first@{consensus} \xdef\second@{#1} \ifx\first@\second@ \expandafter\xdef\csname number@col0\endcsname{#2} \else \xdef\first@{#1,&,@} \xdef\third@{#2} \numbercolor@ \fi } \def\legendcolor#1{\xdef\legend@fg{#1}} \def\rulercolor#1{\xdef\ruler@fg{#1}} \def\molweight#1#2{% \xdef\temp@{Da}% \xdef\second@{#2}% \ifx\second@\temp@\xdef\third@{Da}\else\xdef\third@{kDa}\fi% \xdef\first@{#1 @} \expandafter\check@letter\first@ \xdef\first@{#1} \ifletter \get@name@number \fi \xdef\first@{\csname @rd\first@\endcsname}% \loopcount=\csname mol@weight\first@\endcsname% \divide\loopcount by 10\relax% \innerloopcount=\loopcount% \hbox{% \ifnum\loopcount>1000% \divide\loopcount by 1000\relax% \pos@count=\loopcount% \multiply\loopcount by 1000\relax% \advance\innerloopcount by -\loopcount% \loopcount=\innerloopcount% \ifnum\loopcount>949\advance\pos@count by 1\relax\fi% \the\pos@count% \ifx\temp@\second@\ifgerm@n .\else {,}\fi\fi% \else% \ifx\second@\temp@ \else 0\fi% \fi% \ifx\second@\temp@% \the\loopcount% \loopcount=\csname mol@weight\first@\endcsname% \innerloopcount=\loopcount% \divide\loopcount by 10\relax% \multiply\loopcount by 10\relax% \advance\innerloopcount by -\loopcount\relax% \else% \divide\innerloopcount by 10\relax% \advance\innerloopcount by 5\relax% \divide\innerloopcount by 10\relax% \fi% \ifnum\innerloopcount>9\relax\innerloopcount=0\relax\fi% \ifgerm@n {,}\else .\fi% \the\innerloopcount~\third@}} \newcommand\charge[2][o]{% \xdef\temp@{pep}% \ifx\prefix@\temp@% \xdef\first@{#2 @} \expandafter\check@letter\first@ \xdef\first@{#2} \ifletter \get@name@number \fi \xdef\second@{\csname @rd\first@\endcsname}% \loopcount=\csname ch@rge\second@\endcsname% \xdef\first@{#1}\make@lower% \if\first@ i\fi% \if\first@ o\advance\loopcount by \chargeNterm% \advance\loopcount by \chargeCterm\fi% \if\first@ n\advance\loopcount by \chargeNterm\fi% \if\first@ c\advance\loopcount by \chargeCterm\fi% \hbox{\ensuremath{% \ifnum\loopcount>0 +% \else\ifnum\loopcount=0 \pm% \else -\multiply\loopcount by -1\relax% \fi\fi% \innerloopcount=\loopcount% \divide\loopcount by 1000\relax% \the\loopcount% \multiply\loopcount by 1000\relax% \advance\innerloopcount by -\loopcount\relax% \divide\innerloopcount by 10\relax% \ifnum\innerloopcount=0% \else% \ifgerm@n {,}\else .\fi% \ifnum\innerloopcount<10 0\fi% \the\innerloopcount% \fi}}% \fi} \def\TeXshade{% \setbox1=\hbox{\texttt{H}}% \def\logo@rule{\vrule depth0.25\ht1 height1.25\ht1 width\wd1}% \TeX% \logo@rule\kern-\wd1\textcolor{White}{\texttt{s}}% \logo@rule\kern-\wd1\textcolor{White}{\texttt{h}}% \texttt{a}% \logo@rule\kern-\wd1\textcolor{White}{\texttt{d}}% \texttt{e}} \def\includeTCoffee#1{% \xdef\TC@first@{#1}\include@T@coffee} \def\firstcolumnDSSP{\xdef\fc@DSSP{y}} \def\secondcolumnDSSP{\xdef\fc@DSSP{n}} \newcommand{\includeDSSP}[3][existing]{% \temp@count=\dssp@num \advance\temp@count by 1 \xdef\dssp@num{\the\temp@count} \xdef\first@{#1} \xdef\temp@{existing} \ifx\first@\temp@ \else\xdef\first@{make new}\fi \expandafter\xdef\csname optiondssp\the\temp@count\endcsname{\first@} \xdef\first@{#2 @} \expandafter\check@letter\first@ \xdef\first@{#2} \ifletter \get@name@number \fi \expandafter\xdef\csname doseqdssp\the\temp@count\endcsname{\first@} \expandafter\xdef\csname filenamedssp\the\temp@count\endcsname{#3} \expandafter\ifnum\csname doseqdssp\the\temp@count\endcsname>\seq@count \message{} \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 } \newcommand\exportconsensus[2][export.txt]{% \ifx\exp@rt\n@ \xdef\first@{#2 @} \expandafter\check@letter\first@ \xdef\first@{#2} \ifletter \get@name@number \fi \xdef\exp@rt@num{\first@} \xdef\exp@rt{y} \immediate\openout\exp@rtfile = #1 \fi } \def\setdomain#1#2{% \xdef\first@{#1} \xdef\temp@{consensus} \ifx\first@\temp@ \xdef\domain@seq{0} \else \xdef\first@{#1 @} \expandafter\check@letter\first@ \xdef\first@{#1} \ifletter \get@name@number \fi \xdef\domain@seq{\csname @rd\first@\endcsname}% \fi \xdef\list@{#2,&} \xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@ \loop \xdef\list@{\list@ @} \expandafter\get@domainregions\list@ \ifx\list@\ampers@nd\else\repeat \xdef\dom@in{y} } \def\decimal@IOO#1#2#3{#1#2\temp@#3} \def\decimal@IO#1#2{#1\temp@#2} \def\decimal@I#1{0\temp@#1} \def\percentsimilarity#1#2{% \xdef\first@{#2@}\expandafter\check@letter\first@% \xdef\first@{#2}\xdef\second@@{#2}% \ifletter\get@name@number@table\xdef\second@@{\first@}\fi% \xdef\first@{#1@}\expandafter\check@letter\first@% \xdef\first@{#1}\xdef\first@@{#1}% \ifletter\get@name@number@table\xdef\first@@{\first@}\fi% \ifnum\first@@<\second@@% \loopcount=\csname simcount\first@@ @\second@@\endcsname% \temp@count=\csname poscount\first@@ @\second@@\endcsname% \else% \ifnum\first@@=\second@@ \loopcount=1 \temp@count=1% \else% \loopcount=\csname simcount\second@@ @\first@@\endcsname% \temp@count=\csname poscount\second@@ @\first@@\endcsname% \fi% \fi% \multiply\loopcount by 1000% \divide\loopcount by \temp@count% \xdef\first@{\the\loopcount}% \ifgerm@n\xdef\temp@{,}\else\xdef\temp@{.}\fi% \ifnum\first@=1000 100\temp@0% \else% \ifnum\first@>99 \expandafter\decimal@IOO\first@% \else% \ifnum\first@>9 \expandafter\decimal@IO\first@% \else% \ifnum\first@>0 \expandafter\decimal@I\first@% \else 0\temp@0% \fi% \fi% \fi% \fi% } \def\percentidentity#1#2{% \xdef\first@{#2@}\expandafter\check@letter\first@% \xdef\first@{#2}\xdef\second@@{#2}% \ifletter\get@name@number@table\xdef\second@@{\first@}\fi% \xdef\first@{#1@}\expandafter\check@letter\first@% \xdef\first@{#1}\xdef\first@@{#1}% \ifletter\get@name@number@table\xdef\first@@{\first@}\fi% \ifnum\first@@<\second@@% \loopcount=\csname identcount\first@@ @\second@@\endcsname% \temp@count=\csname poscount\first@@ @\second@@\endcsname% \else% \ifnum\first@@=\second@@ \loopcount=1 \temp@count=1% \else% \loopcount=\csname identcount\second@@ @\first@@\endcsname% \temp@count=\csname poscount\second@@ @\first@@\endcsname% \fi% \fi% \multiply\loopcount by 1000% \divide\loopcount by \temp@count% \xdef\first@{\the\loopcount}% \ifgerm@n\xdef\temp@{,}\else\xdef\temp@{.}\fi% \ifnum\first@=1000 100\temp@0% \else% \ifnum\first@>99 \expandafter\decimal@IOO\first@% \else% \ifnum\first@>9 \expandafter\decimal@IO\first@% \else% \ifnum\first@>0 \expandafter\decimal@I\first@% \else 0\temp@0% \fi% \fi% \fi% \fi% } \def\similaritytable{% \def\name@loop{% \advance\outerloopcount by 1 \ifnum\outerloopcount>\seq@num\relax \else \immediate\write\exp@rtfile{&\string\multicolumn{1}{c}{\string\kern1ex\string\begin{rotopo}{90}\csname newseqname\the\outerloopcount\endcsname\string\end{rotopo}}} \name@loop\fi } \def\inner@loop{% \advance\innerloopcount by 1 \ifnum\innerloopcount>\seq@num\relax \else \ifnum\innerloopcount=\outerloopcount\relax \immediate\write\exp@rtfile{& {---\hss}}\fi \ifnum\innerloopcount>\outerloopcount\relax \immediate\write\exp@rtfile{& \string\percentsimilarity{\the\outerloopcount}{\the\innerloopcount}}\fi \ifnum\innerloopcount<\outerloopcount\relax \immediate\write\exp@rtfile{& \string\percentidentity{\the\outerloopcount}{\the\innerloopcount}}\fi \inner@loop\fi } \def\outer@loop{% \advance\outerloopcount by 1 \ifnum\outerloopcount>\seq@num\relax \else \immediate\write\exp@rtfile{\csname newseqname\the\outerloopcount\endcsname} \innerloopcount=0 \inner@loop \immediate\write\exp@rtfile{&\string\\} \outer@loop\fi } \xdef\temp@{l|} \outerloopcount=0 \loop \advance\outerloopcount by 1 \xdef\temp@{\temp@ r} \ifnum\outerloopcount<\seq@num\repeat \advance\outerloopcount by 1 \xdef\seq@num@plus{\the\outerloopcount} \advance\outerloopcount by 1 \xdef\seq@num@plus@plus{\the\outerloopcount} \ifnum\seq@num<3 \xdef\temp@@{$\approx$} \else \ifnum\seq@num<5 \xdef\temp@@{simil.}\ifgerm@n\def\temp@@{\string\"{A}hnl.}\fi\ifsp@nish\xdef\temp@@{simil.}\fi\else \xdef\temp@@{similarity} \ifgerm@n\ifnum\seq@num=5\def\temp@@{\string\"{A}hnlichk.}\else\def\temp@@{\string\"{A}hnlichkeit}\fi\fi\ifsp@nish\xdef\temp@@{similitud}\fi\fi \fi \xdef\temp@@@{identity}\ifgerm@n\def\temp@@@{Identit\string\"{a}t}\fi\ifsp@nish\xdef\temp@@@{identidad}\fi \immediate\openout\exp@rtfile = simtable.tmp \immediate\write\exp@rtfile{\string\begin{tabular}{\temp@ |r}} \immediate\write\exp@rtfile{\string\multicolumn{\seq@num@plus@plus}{c}{}\string\\[\name@@width]} \immediate\write\exp@rtfile{\string\multicolumn{1}{c}{}} \outerloopcount=0 \name@loop \immediate\write\exp@rtfile{&\string\\ \string\cline{2-\seq@num@plus}} \immediate\write\exp@rtfile{&\string\multicolumn{\seq@num}{|c|}{}&\string\\[-2ex]} \outerloopcount=0 \outer@loop \immediate\write\exp@rtfile{\string\cline{2-\seq@num@plus}} \immediate\write\exp@rtfile{\string\multicolumn{\seq@num@plus}{c}{}&} \immediate\write\exp@rtfile{\string\multicolumn{1}{r}{\string\kern1.5ex\string\begin{rotopo}{90}\kern1em\% \temp@@\string\end{rotopo}}\string\\[-2ex]} \immediate\write\exp@rtfile{\string\multicolumn{1}{c}{}&\string\multicolumn{\seq@num}{l}{\% \temp@@@}&\string\\} \immediate\write\exp@rtfile{\string\end{tabular}} \immediate\closeout\exp@rtfile \input{simtable.tmp} } \def\identitytable{\similaritytable} %%%%% Calculate consensus \def\check@sim{% \xdef\first@{\csname res\the\loopcount\endcsname} \xdef\first@{\csname \prefix@ grp\first@\endcsname} \newrestrue \ifnum\first@<0 \newresfalse \else \innerloopcount=\loopcount \ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi \ifnum\innerloopcount<\seq@count \loop \advance\innerloopcount by 1 \xdef\second@{\csname res\the\innerloopcount\endcsname} \expandafter\ifx\csname \prefix@ grp\second@\endcsname\first@ \newresfalse \innerloopcount=\seq@count \fi \ifnum\innerloopcount<\seq@count \repeat \fi \fi \ifnewres \pos@sum=0 \innerloopcount=0 \loop \advance\innerloopcount by 1 \xdef\second@{\csname res\the\innerloopcount\endcsname} \expandafter\ifx\csname \prefix@ grp\second@\endcsname\first@ \advance\pos@sum by 1 \fi \ifnum\innerloopcount<\seq@count \repeat \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum} \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@ \else \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x \xdef\m@x{\csname pos\the\loopcount\endcsname} \xdef\cons@seq{\the\loopcount} \xdef\match@case{\c@se} \xdef\simgroup@{\first@} \else \expandafter\ifnum\csname pos\the\loopcount\endcsname=\m@x \xdef\match@case{0} \fi \fi \fi \fi \ifnum\loopcount=\cons@num \loopcount=1 \fi \advance\loopcount by -1 \ifnum\loopcount>0 \check@sim \fi} \def\check@ident{% \xdef\first@{\csname res\the\loopcount\endcsname} \newrestrue \expandafter\check@char\first@ \ifletter \innerloopcount=\loopcount \ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi \ifnum\innerloopcount<\seq@count \loop \advance\innerloopcount by 1 \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ \newresfalse \innerloopcount=\seq@count \fi \ifnum\innerloopcount<\seq@count \repeat \fi \else \newresfalse \fi \ifnewres \pos@sum=0 \innerloopcount=0 \loop \advance\innerloopcount by 1 \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ \advance\pos@sum by 1 \fi \ifnum\innerloopcount<\seq@count \repeat \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum} \expandafter\ifnum\csname pos\the\loopcount\endcsname=\seq@count \xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \loopcount=1 \else \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum} \expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld@ \else \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x \xdef\m@x{\csname pos\the\loopcount\endcsname} \expandafter\ifnum\csname pos\the\loopcount\endcsname<\all@thresh@ld@ \xdef\cons@seq{\the\loopcount} \xdef\match@case{1} \else \xdef\cons@seq{\the\loopcount} \xdef\match@case{2} \fi \else \expandafter\ifnum\csname pos\the\loopcount\endcsname=\m@x \xdef\match@case{0} \fi \fi \fi \fi \fi \ifnum\loopcount=\cons@num \loopcount=1 \fi \advance\loopcount by -1 \ifnum\loopcount>0 \check@ident \fi} \def\get@simchar{% \xdef\first@{\csname res\the\loopcount\endcsname} \newrestrue \expandafter\check@char\first@ \ifletter \innerloopcount=\loopcount \ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi \ifnum\innerloopcount<\seq@count \loop \advance\innerloopcount by 1 \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ \newresfalse \innerloopcount=\seq@count \fi \ifnum\innerloopcount<\seq@count \repeat \fi \else \newresfalse \fi \ifnewres \pos@sum=0 \innerloopcount=0 \loop \advance\innerloopcount by 1 \expandafter\ifx\csname res\the\innerloopcount\endcsname\first@ \xdef\second@{\csname res\the\innerloopcount\endcsname} \expandafter\ifx\csname \prefix@ grp\second@\endcsname\simgroup@ \advance\pos@sum by 1 \fi \fi \ifnum\innerloopcount<\seq@count \repeat \expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum} \expandafter\ifnum\csname pos\the\loopcount\endcsname>\m@x \xdef\m@x{\csname pos\the\loopcount\endcsname} \xdef\cons@seq{\the\loopcount} \fi \fi \ifnum\loopcount=\cons@num \loopcount=1 \fi \advance\loopcount by -1 \ifnum\loopcount>0 \get@simchar \fi} \def\unc@nserved{% \ifsimmode \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi \xdef\match@case{0} \xdef\m@x{1} \check@sim \ifnum\match@case=0 \loopcount=0 \loop \advance\loopcount by 1 \xdef\first@{noshade} \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ \expandafter\ifx\csname res\the\loopcount\endcsname\d@t \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname3\gap@char} \else \expandafter\ifx\csname res\the\loopcount\endcsname\questi@n \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname3\st@p@char} \else \expandafter\ifx\csname res\the\loopcount\endcsname\equ@l \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname!\dom@char} \xdef\g@p{y} \else \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% 3\csname res\the\loopcount\endcsname} \fi \fi \fi \else \xdef\first@{\csname res\the\loopcount\endcsname} \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \xdef\g@p{y} \else \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\gap@char} \else \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \else \ifx\first@\questi@n \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \def\first@{{}} \def\third@{8} \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\st@p@char} \else \def\first@{{}} \def\third@{8} \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \else \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\resn@m@tch\low@up \else \xdef\first@{\resn@m@tch} \fi\fi\fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname3\first@} \fi \fi \fi \fi \ifnum\loopcount<\seq@count \repeat \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else \xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else \xdef\first@{\n@m@tch} \fi\fi \expandafter\ifx\csname lower@seq0\endcsname\y@ \expandafter\xdef\csname lower@seq0\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq0\endcsname\y@ \expandafter\xdef\csname tint@seq0\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq0\endcsname\y@ \expandafter\xdef\csname emph@seq0\endcsname{n} \xdef\first@{,\first@}\fi \ifx\g@p\y@ \xdef\consensus{\consensus 8{}} \else \xdef\consensus{\consensus 4\first@} \expandafter\ifx\csname res\cons@num\endcsname\d@t \else\xdef\constopo{\constopo 0}\fi \fi \else \ifnum\cons@num>0 \xdef\tmp@{\csname res\cons@num\endcsname} \else \xdef\m@x{0} \loopcount=\seq@count \get@simchar \xdef\tmp@{\csname res\cons@seq\endcsname} \fi \xdef\second@{\csname \prefix@ grp\tmp@\endcsname} \loopcount=0 \loop \advance\loopcount by 1 \xdef\first@{noshade} \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ \xdef\first@{\csname res\the\loopcount\endcsname} \ifx\first@\d@t\def\first@{\gap@char}\fi \ifx\first@\questi@n\def\first@{\st@p@char}\fi \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname3\first@} \else \xdef\first@{\csname res\the\loopcount\endcsname} \xdef\last@{\csname res\the\loopcount\endcsname} \expandafter\ifnum\csname \prefix@ grp\last@\endcsname=\second@ \xdef\third@{2} \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\ressimm@tch\low@up \else \xdef\first@{\ressimm@tch} \fi\fi\fi \else \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \else \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\gap@char} \else \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \fi \fi \else \ifx\first@\questi@n \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \def\first@{{}} \def\third@{8} \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\st@p@char} \else \def\first@{{}} \def\third@{8} \fi \fi \else \xdef\third@{3} \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\resn@m@tch\low@up \else \xdef\first@{\resn@m@tch} \fi\fi\fi \fi \fi \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \fi \ifnum\loopcount<\seq@count \repeat \xdef\first@{\tmp@} \xdef\low@up{lower} \ifx\m@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\m@tch\low@up \else \xdef\first@{\m@tch} \fi\fi \expandafter\ifx\csname lower@seq0\endcsname\y@ \expandafter\xdef\csname lower@seq0\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq0\endcsname\y@ \expandafter\xdef\csname tint@seq0\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq0\endcsname\y@ \expandafter\xdef\csname emph@seq0\endcsname{n} \xdef\first@{,\first@}\fi \ifx\g@p\y@ \xdef\consensus{\consensus 8{}} \else \xdef\consensus{\consensus5\first@} \xdef\constopo{\constopo 1} \fi \fi \else \iffuncmode \loopcount=0 \loop \advance\loopcount by 1 \xdef\first@{\csname res\the\loopcount\endcsname} \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y} \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \else \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \ifsh@wg@ps \def\first@{\gap@char}\def\third@{*} \else \def\first@{{}} \def\third@{/} \fi \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\first@{\gap@char}\def\third@{*} \else \ifsh@wg@ps \def\first@{\gap@char}\def\third@{*} \else \def\first@{{}} \def\third@{/} \fi \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \else \ifx\first@\questi@n \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \def\first@{{}} \def\third@{/} \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\first@{\st@p@char}\def\third@{*} \else \def\first@{{}} \def\third@{/} \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\st@p@char}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\st@p@char}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\st@p@char}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \else \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\resn@m@tch\low@up \else \xdef\first@{\resn@m@tch} \fi\fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname0\first@} \fi \fi \fi \ifnum\loopcount<\seq@count \repeat \else \loopcount=0 \loop \advance\loopcount by 1 \xdef\first@{noshade} \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ \xdef\first@{\csname res\the\loopcount\endcsname} \ifx\first@\d@t\def\first@{\gap@char}\fi \ifx\first@\questi@n\def\first@{\st@p@char}\fi \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% 3\first@} \else \xdef\first@{\csname res\the\loopcount\endcsname} \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \else \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\gap@char} \else \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \else \ifx\first@\questi@n \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \def\first@{{}} \def\third@{8} \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\st@p@char} \else \def\first@{{}} \def\third@{8} \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \else \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\resn@m@tch\low@up \else \xdef\first@{\resn@m@tch} \fi\fi\fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname3\first@} \fi \fi \fi \fi \ifnum\loopcount<\seq@count \repeat \xdef\low@up{lower} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else \xdef\low@up{upper} \ifx\n@m@tch\low@up \xdef\first@{{ }} \else \xdef\first@{\n@m@tch} \fi\fi \expandafter\ifx\csname lower@seq0\endcsname\y@ \expandafter\xdef\csname lower@seq0\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq0\endcsname\y@ \expandafter\xdef\csname tint@seq0\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq0\endcsname\y@ \expandafter\xdef\csname emph@seq0\endcsname{n} \xdef\first@{,\first@}\fi \ifx\g@p\y@ \xdef\consensus{\consensus 8{}} \else \xdef\consensus{\consensus 4\first@} \xdef\constopo{\constopo 0} \fi \fi\fi} \def\c@nserved{% \xdef\tmp@{\csname res\cons@seq\endcsname} \loopcount=0 \loop \advance\loopcount by 1 \xdef\first@{noshade} \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ \xdef\first@{\csname res\the\loopcount\endcsname} \ifx\first@\d@t\def\first@{\gap@char}\fi \ifx\first@\questi@n\def\first@{\st@p@char}\fi \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% 3\first@} \else \xdef\second@{\csname res\the\loopcount\endcsname} \ifx\tmp@\second@ \xdef\third@{1} \else \xdef\third@{3} \ifsimmode \xdef\last@{\csname \prefix@ sim\tmp@\endcsname &@} \expandafter\get@count\last@ \innerloopcount=0 \getsim@char \fi \fi \xdef\first@{\csname res\the\loopcount\endcsname} \ifcase\third@ \or \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\resm@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\resm@tch\low@up \else \xdef\first@{\resm@tch} \fi\fi\fi \or \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\ressimm@tch\low@up \else \xdef\first@{\ressimm@tch} \fi\fi\fi \else \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\resn@m@tch\low@up \else \xdef\first@{\resn@m@tch} \fi\fi\fi \fi \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \fi \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\gap@char} \else \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \fi \fi \fi \ifx\first@\questi@n \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \def\first@{{}} \def\third@{8} \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\st@p@char} \else \def\first@{{}} \def\third@{8} \fi \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \fi \ifnum\loopcount<\seq@count \repeat \xdef\first@{\csname res\cons@seq\endcsname} \xdef\second@{lower} \ifx\m@tch\second@ \make@lower \else \xdef\second@{upper} \ifx\m@tch\second@ \else \xdef\first@{\m@tch} \fi\fi \expandafter\ifx\csname lower@seq0\endcsname\y@ \expandafter\xdef\csname lower@seq0\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq0\endcsname\y@ \expandafter\xdef\csname tint@seq0\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq0\endcsname\y@ \expandafter\xdef\csname emph@seq0\endcsname{n} \xdef\first@{,\first@}\fi \ifx\g@p\y@ \xdef\consensus{\consensus 8{}} \else \xdef\consensus{\consensus 5\first@} \xdef\constopo{\constopo 2} \fi} \def\allm@tch{% \xdef\tmp@{\csname res\cons@seq\endcsname} \loopcount=0 \loop \advance\loopcount by 1 \xdef\first@{noshade} \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@ \xdef\first@{\csname res\the\loopcount\endcsname} \ifx\first@\d@t\def\first@{\gap@char}\fi \ifx\first@\questi@n\def\first@{\st@p@char}\fi \ifx\first@\equ@l\def\first@{\dom@char} \xdef\g@p{y} \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% 3\first@} \else \xdef\second@{\csname res\the\loopcount\endcsname} \ifx\tmp@\second@ \ifall@shade \xdef\third@{0} \else \xdef\third@{1} \fi \else \xdef\third@{3} \ifsimmode \xdef\last@{\csname \prefix@ sim\tmp@\endcsname &@} \expandafter\get@count\last@ \innerloopcount=0 \getsim@char \fi \fi \xdef\first@{\csname res\the\loopcount\endcsname} \ifcase\third@ \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\res@llm@tch\low@up \else \xdef\first@{\res@llm@tch} \fi\fi\fi \or \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\res@llm@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\res@llm@tch\low@up \else \xdef\first@{\res@llm@tch} \fi\fi\fi \or \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\ressimm@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\ressimm@tch\low@up \else \xdef\first@{\ressimm@tch} \fi\fi\fi \else \ifnum\divref@=\loopcount\else \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\resn@m@tch\low@up \else \xdef\first@{\resn@m@tch} \fi\fi\fi \fi \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{9} \xdef\g@p{y} \fi \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\gap@char} \else \ifsh@wg@ps \def\first@{\gap@char}\def\third@{7} \else \def\first@{{}} \def\third@{8} \fi \fi \fi \fi \ifx\first@\questi@n \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \def\first@{{}} \def\third@{8} \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\third@{7}\def\first@{\st@p@char} \else \def\first@{{}} \def\third@{8} \fi \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \fi \ifnum\loopcount<\seq@count \repeat \xdef\first@{\csname res\cons@seq\endcsname} \xdef\second@{lower} \ifx\@llm@tch\second@ \make@lower \else \xdef\second@{upper} \ifx\@llm@tch\second@ \else \xdef\first@{\@llm@tch} \fi\fi \expandafter\ifx\csname lower@seq0\endcsname\y@ \expandafter\xdef\csname lower@seq0\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq0\endcsname\y@ \expandafter\xdef\csname tint@seq0\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq0\endcsname\y@ \expandafter\xdef\csname emph@seq0\endcsname{n} \xdef\first@{,\first@}\fi \ifx\g@p\y@ \xdef\consensus{\consensus 8{}} \else \xdef\consensus{\consensus 6\first@} \xdef\constopo{\constopo 3} \fi} \def\functi@nal{% \ifnum\cons@num>0 \xdef\first@{\csname res\cons@num\endcsname} \else \xdef\first@{\csname res\cons@seq\endcsname} \fi \xdef\second@{\csname funcgrp\first@\endcsname} \loopcount=0 \loop \advance\loopcount by 1 \xdef\third@{noshade} \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ \xdef\first@{\csname res\the\loopcount\endcsname} \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% 0\first@} \else \xdef\first@{\csname res\the\loopcount\endcsname} \ifx\first@\equ@l \def\first@{\dom@char} \def\third@{!} \xdef\g@p{y} \else \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \ifsh@wg@ps \def\first@{\gap@char}\def\third@{*} \else \def\first@{{}} \def\third@{/} \fi \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\first@{\gap@char}\def\third@{*} \else \ifsh@wg@ps \def\first@{\gap@char}\def\third@{*} \else \def\first@{{}} \def\third@{/} \fi \fi \fi \else \ifx\first@\questi@n \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \def\first@{{}} \def\third@{/} \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\first@{\st@p@char}\def\third@{*} \else \def\first@{{}} \def\third@{/} \fi \fi \else \expandafter\ifnum\csname funcgrp\first@\endcsname=\second@ \xdef\low@up{lower} \expandafter\ifx\csname funcm@tch\second@\endcsname\low@up \make@lower \fi \xdef\third@{\second@} \else \xdef\third@{0} \xdef\low@up{lower} \ifx\resn@m@tch\low@up \make@lower \else \xdef\low@up{upper} \ifx\resn@m@tch\low@up \else \xdef\first@{\resn@m@tch} \fi\fi \fi \fi \fi \fi \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname\third@\first@} \fi \ifnum\loopcount<\seq@count \repeat} \def\all@funcshade{% \loopcount=0 \loop \advance\loopcount by 1 \xdef\first@{\csname res\the\loopcount\endcsname} \xdef\second@{\csname funcgrp\first@\endcsname} \ifnum\second@<0 \xdef\second@{0} \fi \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!} \xdef\g@p{y} \fi \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \ifsh@wg@ps \def\first@{\gap@char}\def\second@{*} \else \def\first@{{}} \def\second@{/} \fi \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\first@{\gap@char}\def\second@{*} \else \ifsh@wg@ps \def\first@{\gap@char}\def\second@{*} \else \def\first@{{}} \def\second@{/} \fi \fi \fi \fi \ifx\first@\questi@n \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \def\first@{{}} \def\second@{/} \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\first@{\st@p@char}\def\second@{*} \else \def\first@{{}} \def\second@{/} \fi \fi \fi \xdef\low@up{lower} \expandafter\ifx\csname funcm@tch\second@\endcsname\low@up \make@lower \fi \xdef\third@{noshade} \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% 0\first@} \else \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% \second@\first@} \fi \ifnum\loopcount<\seq@count \repeat} \def\T@coffee@shade{% \loopcount=0 \loop \advance\loopcount by 1 \xdef\first@{\csname res\the\loopcount\endcsname} \xdef\second@{\csname TC@num\the\loopcount\endcsname} \ifx\first@\equ@l \def\first@{\dom@char} \def\second@{!} \xdef\g@p{y} \fi \ifx\first@\d@t \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \ifsh@wg@ps \def\first@{\gap@char}\def\second@{*} \else \def\first@{{}} \def\second@{/} \fi \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\first@{\gap@char}\def\second@{*} \else \ifsh@wg@ps \def\first@{\gap@char}\def\second@{*} \else \def\first@{{}} \def\second@{/} \fi \fi \fi \fi \ifx\first@\questi@n \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@start\the\loopcount\endcsname \def\first@{{}} \def\second@{/} \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname% <\csname seq@len\the\loopcount\endcsname \def\first@{\st@p@char}\def\second@{*} \else \def\first@{{}} \def\second@{/} \fi \fi \fi \xdef\third@{noshade} \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\third@ \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% *\first@} \else \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \xdef\first@{,\first@}\fi \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% \second@\first@} \fi \ifnum\loopcount<\seq@count \repeat \xdef\first@{\csname res0\endcsname} \expandafter\ifx\csname lower@seq0\endcsname\y@ \expandafter\xdef\csname lower@seq0\endcsname{n} \xdef\first@{;\first@}\fi \expandafter\ifx\csname tint@seq0\endcsname\y@ \expandafter\xdef\csname tint@seq0\endcsname{n} \xdef\first@{=\first@}\fi \expandafter\ifx\csname emph@seq0\endcsname\y@ \expandafter\xdef\csname emph@seq0\endcsname{n} \xdef\first@{,\first@}\fi \xdef\second@{\csname TC@num0\endcsname} \ifx\g@p\y@ \xdef\consensus{\consensus 8{}} \else \xdef\consensus{\consensus\second@\n@m@tch} \xdef\constopo{\constopo\second@} \fi } \def\getregion@fromstack@first{% \expandafter\getregion@fromstack{\the\loopcount} \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname stop\the\loopcount\endcsname<\first@@ \getregion@fromstack@first \else \expandafter\ifx\csname all\the\loopcount\endcsname\y@ \innerloopcount=\csname style\the\loopcount\endcsname \fi \expandafter\xdef\csname shade@style\the\loopcount\endcsname{% \csname style\the\loopcount\endcsname} \fi \fi } \def\calc@regshade{% \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 \expandafter\xdef\csname shade@style\the\loopcount\endcsname{y} \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\the\loopcount\endcsname>\first@@ \else \expandafter\ifnum\csname stop\the\loopcount\endcsname<\first@@ \getregion@fromstack@first \else \expandafter\ifx\csname all\the\loopcount\endcsname\y@ \innerloopcount=\csname style\the\loopcount\endcsname \fi \expandafter\xdef\csname shade@style\the\loopcount\endcsname{% \csname style\the\loopcount\endcsname} \expandafter\ifnum\csname stop\the\loopcount\endcsname=\first@@ \expandafter\getregion@fromstack{\the\loopcount} \fi \fi \fi\fi \ifnum\loopcount<\seq@count \repeat \loopcount=0 \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@ \else \xdef\consensus{\consensus&\csname shade@style\the\loopcount\endcsname)} \fi \loop \advance\loopcount by 1 \expandafter\ifx\csname shade@style\the\loopcount\endcsname\y@ \ifnum\innerloopcount>0 \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% &\the\innerloopcount)} \fi \else \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% &\csname shade@style\the\loopcount\endcsname)} \fi \ifnum\loopcount<\seq@count \repeat } \def\getregion@fromshadingstack@first{% \expandafter\getregion@fromshadingstack{\the\loopcount} \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname<\first@@ \getregion@fromshadingstack@first \fi \fi } \def\calc@shading{% \xdef\shading@style{&} \loopcount=-1 \loop \advance\loopcount by 1 \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>\first@@ \else \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname<\first@@ \getregion@fromshadingstack@first \else \xdef\shading@style{\csname shadingstyle\the\loopcount\endcsname} \expandafter\ifnum\csname shadingstop\the\loopcount\endcsname=\first@@ \expandafter\getregion@fromshadingstack{\the\loopcount} \fi \fi \fi\fi \ifnum\loopcount<\seq@count \repeat \loopcount=0 \loop \advance\loopcount by 1 \ifx\shading@style\ampers@nd \else \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname¤\shading@style)} \fi \ifnum\loopcount<\seq@count \repeat } \def\getregion@fromemphstack@first{% \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname emphstop\the\loopcount\endcsname<\first@@ \getregion@fromemphstack@first \else \expandafter\ifx\csname emphall\the\loopcount\endcsname\y@ \innerloopcount=1 \fi \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} \fi \fi } \def\calc@regemph{% \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>\first@@ \else \expandafter\ifnum\csname emphstop\the\loopcount\endcsname<\first@@ \getregion@fromemphstack@first \else \expandafter\ifx\csname emphall\the\loopcount\endcsname\y@ \innerloopcount=1 \fi \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} \expandafter\ifnum\csname emphstop\the\loopcount\endcsname=\first@@ \expandafter\getregion@fromemphstack{\the\loopcount} \fi \fi \fi\fi \ifnum\loopcount<\seq@count \repeat \loopcount=0 \expandafter\ifx\csname emph@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} \fi \ifnum\innerloopcount>0 \loop \advance\loopcount by 1 \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{y} \ifnum\loopcount<\seq@count \repeat \fi } \def\getregion@fromlowerstack@first{% \expandafter\getregion@fromlowerstack{\the\loopcount} \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@ \getregion@fromlowerstack@first \else \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@ \innerloopcount=1 \fi \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y} \fi \fi } \def\calc@reglower{% \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>\first@@ \else \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname<\first@@ \getregion@fromlowerstack@first \else \expandafter\ifx\csname lowerall\the\loopcount\endcsname\y@ \innerloopcount=1 \fi \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y} \expandafter\ifnum\csname lowerstop\the\loopcount\endcsname=\first@@ \expandafter\getregion@fromlowerstack{\the\loopcount} \fi \fi \fi\fi \ifnum\loopcount<\seq@count \repeat \loopcount=0 \expandafter\ifx\csname lower@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y} \fi \ifnum\innerloopcount>0 \loop \advance\loopcount by 1 \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{y} \ifnum\loopcount<\seq@count \repeat \fi } \def\getregion@fromtintstack@first{% \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname tintstop\the\loopcount\endcsname<\first@@ \getregion@fromtintstack@first \else \expandafter\ifx\csname tintall\the\loopcount\endcsname\y@ \innerloopcount=1 \fi \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} \fi \fi } \def\calc@regtint{% \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>\first@@ \else \expandafter\ifnum\csname tintstop\the\loopcount\endcsname<\first@@ \getregion@fromtintstack@first \else \expandafter\ifx\csname tintall\the\loopcount\endcsname\y@ \innerloopcount=1 \fi \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} \expandafter\ifnum\csname tintstop\the\loopcount\endcsname=\first@@ \expandafter\getregion@fromtintstack{\the\loopcount} \fi \fi \fi\fi \ifnum\loopcount<\seq@count \repeat \loopcount=0 \expandafter\ifx\csname tint@seq\the\loopcount\endcsname\y@ \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} \fi \ifnum\innerloopcount>0 \loop \advance\loopcount by 1 \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{y} \ifnum\loopcount<\seq@count \repeat \fi } \def\getregion@fromframestack@first{% \expandafter\getregion@fromframestack{\the\loopcount} \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname framestop\the\loopcount\endcsname<\first@@ \getregion@fromframestack@first \else \ifnum\frame@on=0 \xdef\frame@on{1} \xdef\frame@{1} \expandafter\xdef\csname fr@style\the\loopcount\endcsname{% \csname framestyle\the\loopcount\endcsname} \innerloopcount=\pos@count \advance\innerloopcount by -\frame@pos \xdef\styleframe{\styleframe&\the\innerloopcount;&;} \xdef\frame@pos{\the\pos@count} \fi \expandafter\ifnum\csname framestop\the\loopcount\endcsname=\first@@ \expandafter\getregion@fromframestack{\the\loopcount} \ifnum\frame@on=1 \xdef\frame@on{0} \innerloopcount=\pos@count \advance\innerloopcount by 1 \advance\innerloopcount by -\frame@pos \xdef\styleframe{\styleframe&\the\innerloopcount;% \csname fr@style\the\loopcount\endcsname;} \innerloopcount=\pos@count \advance\innerloopcount by 1 \xdef\frame@pos{\the\innerloopcount} \fi \fi \ifnum\pos@count=\res@perline \ifnum\frame@on=1 \innerloopcount=\pos@count \advance\innerloopcount by 1 \advance\innerloopcount by -\frame@pos \xdef\styleframe{\styleframe&\the\innerloopcount;% \csname fr@style\the\loopcount\endcsname;} \innerloopcount=\pos@count \advance\innerloopcount by 1 \xdef\frame@pos{\the\innerloopcount} \fi \fi \expandafter\ifnum\csname res@count\the\loopcount\endcsname=\end@num\relax \ifnum\frame@on=1 \innerloopcount=\pos@count \advance\innerloopcount by 1 \advance\innerloopcount by -\frame@pos \xdef\styleframe{\styleframe&\the\innerloopcount;% \csname fr@style\the\loopcount\endcsname;} \innerloopcount=\pos@count \advance\innerloopcount by 1 \xdef\frame@pos{\the\innerloopcount} \fi \fi \fi \fi } \def\calc@frame{% \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname framestart\the\loopcount\endcsname>\first@@ \else \expandafter\ifnum\csname framestop\the\loopcount\endcsname<\first@@ \getregion@fromframestack@first \else \ifnum\frame@on=0 \xdef\frame@on{1} \xdef\frame@{1} \expandafter\xdef\csname fr@style\the\loopcount\endcsname{% \csname framestyle\the\loopcount\endcsname} \innerloopcount=\pos@count \advance\innerloopcount by -\frame@pos \xdef\styleframe{\styleframe&\the\innerloopcount;&;} \xdef\frame@pos{\the\pos@count} \fi \expandafter\ifnum\csname framestop\the\loopcount\endcsname=\first@@ \expandafter\getregion@fromframestack{\the\loopcount} \ifnum\frame@on=1 \xdef\frame@on{0} \innerloopcount=\pos@count \advance\innerloopcount by 1 \advance\innerloopcount by -\frame@pos \xdef\styleframe{\styleframe&\the\innerloopcount;% \csname fr@style\the\loopcount\endcsname;} \innerloopcount=\pos@count \advance\innerloopcount by 1 \xdef\frame@pos{\the\innerloopcount} \fi \fi \ifnum\pos@count=\res@perline \ifnum\frame@on=1 \innerloopcount=\pos@count \advance\innerloopcount by 1 \advance\innerloopcount by -\frame@pos \xdef\styleframe{\styleframe&\the\innerloopcount;% \csname fr@style\the\loopcount\endcsname;} \innerloopcount=\pos@count \advance\innerloopcount by 1 \xdef\frame@pos{\the\innerloopcount} \fi \fi \expandafter\ifnum\csname res@count\the\loopcount\endcsname=\end@num\relax \ifnum\frame@on=1 \innerloopcount=\pos@count \advance\innerloopcount by 1 \advance\innerloopcount by -\frame@pos \xdef\styleframe{\styleframe&\the\innerloopcount;% \csname fr@style\the\loopcount\endcsname;} \innerloopcount=\pos@count \advance\innerloopcount by 1 \xdef\frame@pos{\the\innerloopcount} \fi \fi \fi \fi\fi \ifnum\loopcount<\seq@count \repeat } \def\get@nextres#1#2:{% \xdef\first@{#1} \xdef\temp@{#2:} \ifx\first@\gap@char \expandafter\get@nextres\temp@ \else \if\first@ @ \xdef\temp@{} \else \xdef\temp@{+\first@} \expandafter\xdef\csname last@res\bottop@\endcsname{} \fi \fi} \def\get@@nextres#1#2:{% \xdef\first@{#1} \xdef\temp@@{#2:} \ifx\first@\gap@char \expandafter\get@@nextres\temp@@ \else \if\first@ @ \xdef\temp@@{} \else \xdef\temp@@{+\first@} \expandafter\xdef\csname last@res\bottop@\endcsname{} \fi \fi} \def\char@get#1#2@{\xdef\first@{#1} \xdef\tr@nsl@ted{#2@}} \def\trans@now#1#2@{% \xdef\first@{#1} \xdef\tr@nsl@ted{#2@} \ifx\first@\ampers@nd \else \expandafter\check@char\first@ \ifletter \xdef\triplet@{\triplet@\first@} \advance\triple@count by 1 \ifnum\triple@count=1 \xdef\out@{\out@{-}} \fi \ifnum\triple@count=3 \expandafter\ifx\csname @\triplet@\endcsname\relax \expandafter\xdef\csname @\triplet@\endcsname{?} \fi \xdef\out@{\out@\csname @\triplet@\endcsname\out@@{-}} \triple@count=0 \xdef\triplet@{} \xdef\out@@{} \fi \fi \if\first@ - \ifnum\triple@count<2 \xdef\out@{\out@{-}} \else \xdef\out@@{\out@@{-}} \fi \fi \if\first@ + \expandafter\char@get\tr@nsl@ted \xdef\triplet@{\triplet@\first@} \advance\triple@count by 1 \ifnum\triple@count=3 \expandafter\ifx\csname @\triplet@\endcsname\relax \expandafter\xdef\csname @\triplet@\endcsname{?} \fi \xdef\out@{\out@\csname @\triplet@\endcsname\out@@} \triple@count=0 \xdef\triplet@{} \xdef\out@@{} \fi \fi \if\first@ 2 \loop \expandafter\char@get\tr@nsl@ted \ifx\first@\ampers@nd \lettertrue \xdef\tr@nsl@ted{&@} \else \expandafter\check@char\first@ \fi \ifletter\else\xdef\out@{\out@{-}}\repeat \xdef\out@{\out@{-}} \fi \expandafter\trans@now\tr@nsl@ted \fi } \def\do@translation{% \xdef\triplet@{} \xdef\out@{} \xdef\out@@{} \xdef\tr@nsl@ted{\tr@nsl@ted &@} \triple@count=0 \expandafter\trans@now\tr@nsl@ted \xdef\tr@nsl@ted{\out@} } \def\trans@pep#1#2@{% \xdef\first@{#1} \xdef\tr@nsl@ted{#2@} \ifx\first@\ampers@nd \else \expandafter\check@char\first@ \ifletter \xdef\out@{\out@\csname rev@\first@\endcsname} \else \xdef\out@{\out@{-}{-}{-}} \fi \expandafter\trans@pep\tr@nsl@ted \fi } \def\rev@translation{% \xdef\out@{} \xdef\tr@nsl@ted{\tr@nsl@ted &@} \expandafter\trans@pep\tr@nsl@ted \xdef\tr@nsl@ted{\out@} } \def\sum@up{% \advance\innerloopcount by 1 \xdef\second@@@{\csname res\the\innerloopcount\endcsname} \xdef\third@@@{\csname cons\first@@@\second@@@\endcsname} \advance\temp@count by \third@@@ \ifnum\innerloopcount<\seq@count\sum@up\fi } \def\sum@up@cons{% \innerloopcount=\outerloopcount \xdef\first@@@{\csname res\the\outerloopcount\endcsname} \sum@up \advance\outerloopcount by 1\relax \ifnum\outerloopcount<\seq@count \sum@up@cons \else \innerloopcount=\seq@count \advance\innerloopcount by -1 \multiply\innerloopcount by \seq@count \multiply\temp@count by 2 \multiply\temp@count by \m@trixf@ctor \divide\temp@count by \innerloopcount \ifnum\temp@count>100 \temp@count=100 \fi \ifnum\temp@count<0 \temp@count=0 \fi \xdef\cons@val{\the\temp@count} \ifx\first@\equ@l \xdef\cons@val{N} \fi \ifx\T@coffee@bcons\y@ \xdef\cons@val{\csname TC@num0\endcsname} \if\cons@val * \xdef\cons@val{99} \fi \fi \ifx\T@coffee@ccons\y@ \xdef\cons@val{\csname TC@num0\endcsname} \if\cons@val * \xdef\cons@val{99} \fi \fi \fi } \def\collect@cons@res{% \xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname} \advance\innerloopcount by 1 \ifnum\innerloopcount>\seq@count\relax \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \else \collect@cons@res \fi } \def\sum@@up{% \advance\innerloopcount by 1 \xdef\second@@@{\csname res\the\innerloopcount\endcsname} \ifx\first@@@\d@t \else \ifx\first@@@\questi@n \else \ifx\first@@@\equ@l \else \ifx\second@@@\d@t \else \ifx\second@@@\questi@n \else \ifx\second@@@\equ@l \else \xdef\third@@@{\csname poscount\the\outerloopcount @\the\innerloopcount\endcsname} \temp@@count=\third@@@ \advance\temp@@count by 1 \expandafter\xdef\csname poscount\the\outerloopcount @\the\innerloopcount\endcsname{\the\temp@@count} \xdef\third@@@{\csname simcount\the\outerloopcount @\the\innerloopcount\endcsname} \temp@@count=\third@@@ \xdef\third@@@{\csname simpair\first@@@\second@@@\endcsname} \advance\temp@@count by \third@@@ \expandafter\xdef\csname simcount\the\outerloopcount @\the\innerloopcount\endcsname{\the\temp@@count} \ifx\first@@@\second@@@ \xdef\third@@@{\csname identcount\the\outerloopcount @\the\innerloopcount\endcsname} \temp@@count=\third@@@ \advance\temp@@count by 1 \expandafter\xdef\csname identcount\the\outerloopcount @\the\innerloopcount\endcsname{\the\temp@@count} \fi \fi \fi \fi \fi \fi \fi \ifnum\innerloopcount<\seq@count\sum@@up\fi } \def\sum@up@sim{% \innerloopcount=\outerloopcount \xdef\first@@@{\csname res\the\outerloopcount\endcsname} \sum@@up \advance\outerloopcount by 1\relax \ifnum\outerloopcount<\seq@count \sum@up@sim \fi } \def\collect@similarity{% \xdef\temp@{\temp@\csname res\the\innerloopcount\endcsname} \advance\innerloopcount by 1 \ifnum\innerloopcount>\seq@count\relax \outerloopcount=1\relax \temp@count=0\relax \sum@up@sim \else \collect@similarity \fi } \def\sum@up@bits{% \ifx\first@@@\second@@@ \ifx\first@@@\d@t \temp@count=0\relax \else \temp@count=100\relax \fi \else \temp@count=0 \fi \multiply\temp@count by \last@ \divide\temp@count by 100 \expandafter\ifx\csname info@\subfamily@seq @\the\outerloopcount\endcsname\relax \expandafter\xdef\csname info@\subfamily@seq @\the\outerloopcount\endcsname{0} \fi \xdef\third@@@{\csname info@\subfamily@seq @\the\outerloopcount\endcsname} \advance\temp@count by \third@@@ \expandafter\xdef\csname info@\subfamily@seq @\the\outerloopcount\endcsname{\the\temp@count} } \def\sum@up@info{% \ifnum\outerloopcount=\subfamily@seq \advance\outerloopcount by 1 \fi \ifnum\outerloopcount>\seq@count \else \xdef\first@@@{\csname res\the\outerloopcount\endcsname} \sum@up@bits \advance\outerloopcount by 1\relax \fi \ifnum\outerloopcount>\seq@count\else\sum@up@info\fi } \def\collect@info{% \outerloopcount=1\relax \temp@count=0\relax \xdef\second@@@{\csname res\subfamily@seq\endcsname} \sum@up@info } \def\calc@grouping{% \xdef\second@{\csname res@num\d@t\endcsname} \innerloopcount=\seq@count \advance\innerloopcount by -\second@ \xdef\second@{\the\innerloopcount} \xdef\seventh@{0} \innerloopcount=0 \outerloopcount=65 \loop \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} \xdef\first@{\csname res@num\first@@\endcsname} \ifnum\first@>0 \temp@count=\csname log2@\first@\endcsname \advance\temp@count by -\csname log2@\second@\endcsname \advance\temp@count by \csname res@corr\first@@\endcsname \multiply\temp@count by -\first@ \divide\temp@count by \second@ \advance\innerloopcount by \temp@count\relax \temp@count=\second@ %%% \advance\temp@count by -\first@ %%% \advance\temp@count by \seventh@ %%% \xdef\seventh@{\the\temp@count} %%% \fi \expandafter\xdef\csname res@num\first@@\endcsname{0} \advance\outerloopcount by 1 \ifnum\outerloopcount>90\else\repeat \expandafter\xdef\csname res@num\d@t\endcsname{0} \if\seq@type P \temp@count=\csname log2@20\endcsname \ifnum\sig@max=100000 \xdef\sig@max{2321} \fi \else \temp@count=\csname log2@4\endcsname \ifnum\sig@max=100000 \xdef\sig@max{1000} \fi \fi \xdef\bit@max{\the\temp@count} \advance\temp@count by -\innerloopcount \multiply\temp@count by \second@ \divide\temp@count by \seq@count \xdef\last@{\the\temp@count} \expandafter\xdef\csname bit@pos\the\loopcount\endcsname{\last@} \temp@count=\bit@total \advance\temp@count by \last@ \xdef\bit@total{\the\temp@count} \collect@info } \def\do@grouping{% \ifnum\loopcount>\total@pos \else \triple@count=1 \loop \xdef\first@{\csname seq\the\triple@count\endcsname} \expandafter\dis@get\first@ \ifx\first@\ampers@nd \else \innerloopcount=\csname res@num\first@\endcsname \advance\innerloopcount by 1 \expandafter\xdef\csname res@num\first@\endcsname{\the\innerloopcount} \fi \advance\triple@count by 1\relax \ifnum\triple@count>\seq@count \calc@grouping \advance\loopcount by 1 \do@grouping \else \repeat \fi } \def\total@frequency@correction{% \innerloopcount=0 \outerloopcount=65 \loop \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} \xdef\first@{\csname res@corr\first@@\endcsname} \advance\innerloopcount by \first@\relax \advance\outerloopcount by 1 \ifnum\outerloopcount>90\else\repeat \xdef\res@num@total{\the\innerloopcount} \outerloopcount=65 \loop \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} \xdef\first@{\csname res@corr\first@@\endcsname} \innerloopcount=\first@\relax \ifnum\innerloopcount>0 \multiply\innerloopcount by 1000\relax \divide\innerloopcount by \res@num@total\relax \innerloopcount=\csname log2@\the\innerloopcount\endcsname \advance\innerloopcount by -5644\relax \multiply\innerloopcount by -1\relax \fi \expandafter\xdef\csname res@corr\first@@\endcsname{\the\innerloopcount} \ifnum\the\innerloopcount>\corr@max \xdef\corr@max{\the\innerloopcount}\fi \advance\outerloopcount by 1 \ifnum\outerloopcount>90\else\repeat } \def\calc@total@frequency{% \ifnum\loopcount>\total@pos \else \triple@count=1 \loop \xdef\first@{\csname seq\the\triple@count\endcsname} \expandafter\tot@get\first@ \ifx\first@\ampers@nd \else \innerloopcount=\csname res@corr\first@\endcsname \advance\innerloopcount by 1 \expandafter\xdef\csname res@corr\first@\endcsname{\the\innerloopcount} \fi \advance\triple@count by 1\relax \ifnum\triple@count>\seq@count \advance\loopcount by 1 \calc@total@frequency \else \repeat \fi } \def\prep@logo{% \if\seq@type P \ifx\do@freq@correction\y@ \xdef\do@freq@correction{n} \loopcount=1 \loop \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} \advance\loopcount by 1 \ifnum\loopcount>\seq@count\else\repeat \xdef\corr@max{0} \loopcount=1 \calc@total@frequency \total@frequency@correction \fi \fi } \def\define@subfamilies{% \xdef\first@{\csname group@num1\endcsname} \advance\loopcount by -1 \xdef\last@{\the\loopcount} \outerloopcount=\bit@total \divide\outerloopcount by \last@ \xdef\bit@mean{\the\outerloopcount} \multiply\outerloopcount by \subfamily@threshold\relax \divide\outerloopcount by 100\relax \xdef\sub@threshold{\the\outerloopcount} \ifnum\first@=0 \clear@res@nums{1} \clear@res@nums{2} \immediate\write\featurefile{TeXshade subfamily logo data file for \alignfilename} \immediate\write\featurefile{--} \immediate\write\featurefile{Average information content [1000*bits per position]: \bit@mean} \immediate\write\featurefile{Subfamily threshold setting [percent]: \subfamily@threshold} \immediate\write\featurefile{=> \bit@mean\space * 0.\subfamily@threshold\space = \sub@threshold\space [1000*bits per position]} \immediate\write\featurefile{} \expandafter\xdef\csname subfamily@num\subfamily@seq\endcsname{2} \immediate\write\featurefile{Automatic subfamily assignment around sequence no. \subfamily@seq:} \immediate\write\featurefile{[sequence pair: average shared information *1000, subfamily number]} \temp@count=1 \outerloopcount=1 \loop \ifnum\outerloopcount=\subfamily@seq \advance\outerloopcount by 1 \fi \ifnum\outerloopcount>\seq@count \else \xdef\first@{\csname info@\subfamily@seq @\the\outerloopcount\endcsname} \loopcount=\first@\relax \divide\loopcount by \last@\relax \ifnum\loopcount>\sub@threshold \expandafter\xdef\csname subfamily@num\the\outerloopcount\endcsname{2} \advance\temp@count by 1\relax \else \expandafter\xdef\csname subfamily@num\the\outerloopcount\endcsname{1} \fi \xdef\first@@{\csname subfamily@num\the\outerloopcount\endcsname} \immediate\write\featurefile{\subfamily@seq-\the\outerloopcount:\space\the\loopcount,\space subfamily: \first@@} \advance\outerloopcount by 1 \fi \ifnum\outerloopcount>\seq@count\else\repeat \immediate\write\featurefile{} \immediate\write\featurefile{//} \ifnum\temp@count>0 \expandafter\xdef\csname group@num2\endcsname{\the\temp@count} \else \message{} \show@sublogofalse \immediate\write\featurefile{} \fi \loopcount=\seq@count \advance\loopcount by -\temp@count \ifnum\loopcount>0 \expandafter\xdef\csname group@num1\endcsname{\the\loopcount} \else \message{} \immediate\write\featurefile{} \show@sublogofalse \fi \else \immediate\write\featurefile{TeXshade subfamily logo data file for \alignfilename} \immediate\write\featurefile{--} \immediate\write\featurefile{Average information content [1000*bits per position]: \bit@mean} \immediate\write\featurefile{Subfamily threshold setting [percent]: \subfamily@threshold} \immediate\write\featurefile{=> \bit@mean\space * 0.\subfamily@threshold\space = \sub@threshold\space [1000*bits per position]} \immediate\write\featurefile{} \immediate\write\featurefile{User defined subfamily: \sub@family@setting} \immediate\write\featurefile{} \immediate\write\featurefile{//} \fi } \def\prep@sublogo{% \message{} \immediate\openout\featurefile = sublogo.txt \if\seq@type P \ifx\do@freq@correction\y@ \xdef\do@freq@correction{n} \loopcount=1 \loop \xdef\first@{\csname @rd\the\loopcount\endcsname} %%% \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\first@\endcsname &@} \advance\loopcount by 1 \ifnum\loopcount>\seq@count\else\repeat \xdef\corr@max{0} \loopcount=1 \calc@total@frequency \total@frequency@correction \fi \fi \loopcount=1 \loop \xdef\first@{\csname @rd\the\loopcount\endcsname} %%% \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\first@\endcsname &@} \advance\loopcount by 1 \ifnum\loopcount>\seq@count\else\repeat \loopcount=1 \do@grouping \define@subfamilies \ifshow@sublogo \loopcount=1 \loop \xdef\first@{\csname @rd\the\loopcount\endcsname} %%% \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\first@\endcsname &@} \advance\loopcount by 1 \ifnum\loopcount>\seq@count\else\repeat \xdef\first@{\csname group@num1\endcsname} \xdef\first@@{\csname log2@\first@\endcsname} \xdef\second@{\csname group@num2\endcsname} \xdef\second@@{\csname log2@\second@\endcsname} \loopcount=\first@ \advance\loopcount by \second@ \xdef\third@{\the\loopcount} \xdef\third@@{\csname log2@\third@\endcsname} \loopcount=\first@@ \advance\loopcount by -\third@@ \multiply\loopcount by \first@ \divide\loopcount by \third@ \xdef\first@@@{\the\loopcount} \loopcount=\second@@ \advance\loopcount by -\third@@ \multiply\loopcount by \second@ \divide\loopcount by \third@ \xdef\second@@@{\the\loopcount} \loopcount=\bit@max \advance\loopcount by \first@@@ \advance\loopcount by \second@@@ \xdef\group@correction{\the\loopcount} \loopcount=1 \total@count=0 \do@sublogo \immediate\closeout\featurefile \openin\sublogofile = sublogo.txt\relax \read@header \else \immediate\closeout\featurefile \fi } \def\read@header{% \read\sublogofile to \first@\relax \xdef\first@{\expandafter\string\first@} \ifx\first@\par@ \read@header \else \xdef\first@{\first@ @} \expandafter\seq@get\first@ \ifx\first@\he@derend \else\read@header \fi \fi } \def\read@sublogo{% \xdef\stack@sublogo{}% \loopcount=1 % \loop% \ifeof\sublogofile% \advance\loopcount by \res@perline% \else% \read\sublogofile to \first@\relax% \xdef\first@{\expandafter\string\first@}% \ifx\first@\par@% \advance\loopcount by \res@perline% \else \xdef\first@{\first@ @}% \expandafter\sublogo@get\first@% \xdef\stack@sublogo{\stack@sublogo\first@}% \advance\loopcount by 1% \fi% \fi% \ifnum\loopcount=\res@perline\else\repeat% } \def\calc@sublogo{% \xdef\seventh@{\csname res@num.2\endcsname} \xdef\first@{\csname group@num2\endcsname} \innerloopcount=\first@ \advance\innerloopcount by -\seventh@ \xdef\seventh@{\the\innerloopcount} \xdef\eighth@{\csname res@num.1\endcsname} \xdef\first@{\csname group@num1\endcsname} \innerloopcount=\first@ \advance\innerloopcount by -\eighth@ \xdef\eighth@{\the\innerloopcount} \xdef\nineth@{n} \xdef\pos@max{0} \xdef\pos@min{0} \outerloopcount=65 \loop \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} \xdef\first@{\csname res@num\first@@ 1\endcsname} \xdef\temp@{\first@} \temp@count=\first@ \ifnum\seventh@>0 \multiply\temp@count by \seventh@ \fi \xdef\first@{\the\temp@count} \xdef\second@{\csname res@num\first@@ 2\endcsname} \temp@count=\temp@ \advance\temp@count by \second@\relax \ifnum\temp@count>0 \temp@count=\second@ \ifnum\eighth@>0 \multiply\temp@count by \eighth@ \fi \advance\temp@count by -\first@ \xdef\last@{\csname bit@pos\the\loopcount\endcsname} \multiply\temp@count by \last@ \ifnum\seventh@>0 \divide\temp@count by \seventh@ \fi \ifnum\eighth@>0 \divide\temp@count by \eighth@ \fi \multiply\temp@count by \bit@max \divide\temp@count by \group@correction \ifx\hide@negatives\y@ \ifnum\temp@count>0 \else \temp@count=1 \fi% \else \ifnum\temp@count=0 \temp@count=1 \fi% \fi \expandafter\xdef\csname res@val\first@@\endcsname{\the\temp@count} \expandafter\xdef\csname res@num\first@@ 1\endcsname{0} \expandafter\xdef\csname res@num\first@@ 2\endcsname{0} \xdef\nineth@{y} \else \expandafter\xdef\csname res@val\first@@\endcsname{0} \expandafter\xdef\csname res@num\first@@ 1\endcsname{0} \expandafter\xdef\csname res@num\first@@ 2\endcsname{0} \fi \ifnum\temp@count>\pos@max \xdef\pos@max{\the\temp@count}\fi \ifnum\temp@count<\pos@min \xdef\pos@min{\the\temp@count}\fi \advance\outerloopcount by 1 \ifnum\outerloopcount>90\else\repeat \expandafter\xdef\csname res@val\d@t\endcsname{0} \expandafter\xdef\csname res@num\d@t 1\endcsname{0} \expandafter\xdef\csname res@num\d@t 2\endcsname{0} \temp@count=\pos@min\relax \multiply\temp@count by -1\relax \xdef\pos@min{\the\temp@count} \ifnum\pos@min>\pos@max \xdef\pos@max{\pos@min}\fi \temp@count=\pos@max \multiply\temp@count by 100 \relax \divide\temp@count by \bit@max \relax \xdef\sublogo@num{\sublogo@num\the\temp@count,} \ifnum\pos@max<\sig@max \xdef\sublogo@sig{\sublogo@sig n} \else \xdef\sublogo@sig{\sublogo@sig y} \fi \ifx\nineth@\y@ \xdef\tmpstack{&:&,} \outerloopcount=65 \loop \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} \xdef\second@@{\csname res@val\first@@\endcsname} \ifnum\second@@=0 \else \xdef\third@{\tmpstack @} \xdef\tmpstack{} \sort@logostack \fi \advance\outerloopcount by 1 \ifnum\outerloopcount>90 \immediate\write\featurefile{\expandafter\string\tmpstack&:&,} \else\repeat \else \immediate\write\featurefile{\expandafter\string O:0,&:&,} \fi } \def\do@sublogo{% \ifnum\loopcount>\total@pos \xdef\sublogo@sig{\sublogo@sig &@} \else \triple@count=1 \loop \xdef\first@{\csname seq\the\triple@count\endcsname} \expandafter\dis@get\first@ \ifnum\triple@count=\start@seq \ifx\first@\d@t\else \advance\total@count by 1\relax\fi \fi \ifnum\loopcount<\start@number \else \ifnum\total@count>\end@num \else \ifx\first@\ampers@nd \else \xdef\second@{\csname subfamily@num\the\triple@count\endcsname} \innerloopcount=\csname res@num\first@\second@\endcsname \advance\innerloopcount by 1 \expandafter\xdef\csname res@num\first@\second@\endcsname{\the\innerloopcount} \fi \fi \fi \advance\triple@count by 1\relax \ifnum\triple@count>\seq@count \ifnum\loopcount<\start@number \else \ifnum\total@count>\end@num \else \calc@sublogo \fi \fi \advance\loopcount by 1 \do@sublogo \else \repeat \fi } \def\calc@logo{% \xdef\second@{\csname res@num\d@t\endcsname} \innerloopcount=\seq@count \advance\innerloopcount by -\second@ \xdef\second@{\the\innerloopcount} \xdef\seventh@{0} \innerloopcount=0 \outerloopcount=65 \loop \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} \xdef\first@{\csname res@num\first@@\endcsname} \ifnum\first@>0 \temp@count=\csname log2@\first@\endcsname \advance\temp@count by -\csname log2@\second@\endcsname \advance\temp@count by \csname res@corr\first@@\endcsname %%%% correct for background freq. \multiply\temp@count by -\first@ \divide\temp@count by \second@ \advance\innerloopcount by \temp@count\relax \fi \advance\outerloopcount by 1 \ifnum\outerloopcount>90\else\repeat \if\seq@type P \temp@count=\csname log2@20\endcsname \else \temp@count=\csname log2@4\endcsname \fi \advance\temp@count by -\innerloopcount \multiply\temp@count by \second@ \divide\temp@count by \seq@count \xdef\last@{\the\temp@count} \xdef\nineth@{n} \outerloopcount=65 \loop \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} \xdef\first@{\csname res@num\first@@\endcsname} \ifnum\first@>0 \temp@count=\last@ \multiply\temp@count by \first@\relax \divide\temp@count by \second@\relax \ifnum\temp@count=0 % \temp@count=1 % \fi% \expandafter\xdef\csname res@val\first@@\endcsname{\the\temp@count} \expandafter\xdef\csname res@num\first@@\endcsname{0} \xdef\nineth@{y} \else \expandafter\xdef\csname res@val\first@@\endcsname{0} \fi \advance\outerloopcount by 1 \ifnum\outerloopcount>90\else\repeat \expandafter\xdef\csname res@val\d@t\endcsname{0} \expandafter\xdef\csname res@num\d@t\endcsname{0} \ifx\nineth@\y@ \xdef\tmpstack{&:&,} \outerloopcount=65 \loop \xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname} \xdef\second@@{\csname res@val\first@@\endcsname} \ifnum\second@@>0 \xdef\third@{\tmpstack @} \xdef\tmpstack{} \sort@logostack \fi \advance\outerloopcount by 1 \ifnum\outerloopcount>90 \xdef\stack@sequencelogo{\stack@sequencelogo\tmpstack&:&,} \else\repeat \else \xdef\stack@sequencelogo{\stack@sequencelogo O:0,&:&,} \fi } \def\get@fromlogostack#1:#2,#3@{% \xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} } \def\sort@logostack{% \expandafter\get@fromlogostack\third@ \ifx\first@\ampers@nd \xdef\tmpstack{\tmpstack\first@@:\second@@,} \else \ifnum\second@@<0 \ifnum\second@>0 \xdef\tmpstack{\tmpstack\first@@:\second@@,\first@:\second@,\third@} \else \temp@count=\second@@\relax \multiply\temp@count by -1\relax \triple@count=\second@\relax \multiply\triple@count by -1\relax \ifnum\temp@count<\triple@count \xdef\tmpstack{\tmpstack\first@@:\second@@,\first@:\second@,\third@} \else \xdef\tmpstack{\tmpstack\first@:\second@,} \xdef\third@@{\third@ .} \ifx\third@@\d@t \xdef\third@{&:&,@} \else \xdef\third@{\third@ @} \fi \sort@logostack \fi \fi \else \ifnum\second@@<\second@ \xdef\tmpstack{\tmpstack\first@@:\second@@,\first@:\second@,\third@} \else \xdef\tmpstack{\tmpstack\first@:\second@,} \xdef\third@@{\third@ .} \ifx\third@@\d@t \xdef\third@{&:&,@} \else \xdef\third@{\third@ @} \fi \sort@logostack \fi \fi \fi } \def\calc@feature{% \loopcount=-1 \innerloopcount=0 \loop \advance\loopcount by 1 \ifnum\loopcount=0 \xdef\first@@{\the\cons@count} \else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>\first@@ \else \expandafter\ifnum\csname stop\bottop@\the\loopcount\endcsname<\first@@ \expandafter\getregion@fromfstack{\the\loopcount} \else \innerloopcount=\loopcount \expandafter\ifnum\csname featureon\bottop@\endcsname=0 \expandafter\xdef\csname featureon\bottop@\endcsname{1} \expandafter\xdef\csname feature@\bottop@\endcsname{1} \expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{% \csname text\bottop@\the\loopcount\endcsname} \expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{% \csname style\bottop@\the\loopcount\endcsname} \innerloopcount=\pos@count \advance\innerloopcount by -\csname featurepos\bottop@\endcsname \expandafter\xdef\csname textfeature\bottop@\endcsname{% \csname textfeature\bottop@\endcsname% &\the\innerloopcount;{};} \expandafter\xdef\csname stylefeature\bottop@\endcsname{% \csname stylefeature\bottop@\endcsname% &\the\innerloopcount;&;} \expandafter\xdef\csname featurepos\bottop@\endcsname{\the\pos@count} \xdef\temp@@@{n} \xdef\fourth@{} \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname} \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi \xdef\fourth@{} \xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname} \xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@ \ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi \ifx\temp@@@\y@ \ifnum\loopcount=0 \message{} \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 } \def\add@to@rule@tens{% \advance\innerloopcount by \ruler@step\relax \ifnum\innerloopcount=0 \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi \fi \expandafter\ifnum\csname res@count\rule@num\endcsname>\innerloopcount \add@to@rule@tens \else \xdef\rule@tens{\the\innerloopcount} \fi } \def\c@nsensus{% \ifnum\pos@count>\res@perline \else \loopcount=0 \ifx\g@p\n@ \global\advance\cons@count by 1\relax \fi \ifnum\cons@count=0\relax \ifx\allow@zero\n@ \global\advance\cons@count by 1 \fi \fi \ifT@coffee \xdef\TC@line{\csname T@coffee0\endcsname} \expandafter\TC@get\TC@line \fi \expandafter\xdef\csname res@count0\endcsname{\the\cons@count} \loop \advance\loopcount by 1 \ifT@coffee \xdef\TC@line{\csname T@coffee\the\loopcount\endcsname} \expandafter\TC@get\TC@line \xdef\TC@first@{\csname TC@num\the\loopcount\endcsname} \fi \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\residue@get\seq@line \xdef\first@{\csname res\the\loopcount\endcsname} \innerloopcount=\csname res@num\first@\endcsname \advance\innerloopcount by 1 \expandafter\xdef\csname res@num\first@\endcsname{\the\innerloopcount} \expandafter\check@char\first@ \ifx\dom@in\y@ %%%%%%%%%%%***** \xdef\temp@{\csname dom@num\the\loopcount\endcsname} \expandafter\get@dom@count\temp@ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@} \fi %%%%%%%%%%%***** \ifletter \ifx\dom@in\y@ \else \res@count=\csname res@count\the\loopcount\endcsname \advance\res@count by 1 \ifnum\res@count=0\relax \ifx\allow@zero\n@ \advance\res@count by 1 \fi \fi \fi \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count} \ifnum\loopcount=\exp@rt@num \xdef\sixth@{\the\res@count}\xdef\seventh@{y}\fi \ifnum\loopcount=\rule@num\relax \expandafter\ifnum\csname res@count\rule@num\endcsname>\rule@tens \innerloopcount=\rule@tens \add@to@rule@tens \fi \expandafter\ifnum\csname res@count\rule@num\endcsname=\rule@tens \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax \xdef\temp@{\rule@tens} \else \xdef\temp@{\csname alt@ruler\rule@tens\endcsname} \fi \xdef\ruler@{\ruler@ !<\temp@>} \else \xdef\ruler@{\ruler@ -} \fi \xdef\temp@{\csname res@count\rule@num\endcsname} \expandafter\ifx\csname alt@ruler\temp@\endcsname\relax \else \expandafter\xdef\csname alt@ruler\temp@\endcsname{\temp@} \fi \fi \ifx\collect@valtop\yes \ifnum\v@lseqtop=\loopcount \xdef\v@ltop{\v@ltop,\csname \ffourth@top\first@\endcsname} \fi\fi \ifx\collect@valttop\yes \ifnum\v@lseqttop=\loopcount \xdef\v@lttop{\v@lttop,\csname \ffourth@ttop\first@\endcsname} \fi\fi \ifx\collect@valtttop\yes \ifnum\v@lseqtttop=\loopcount \xdef\v@ltttop{\v@ltttop,\csname \ffourth@tttop\first@\endcsname} \fi\fi \ifx\collect@valttttop\yes \ifnum\v@lseqttttop=\loopcount \xdef\v@lttttop{\v@lttttop,\csname \ffourth@ttttop\first@\endcsname} \fi\fi \ifx\collect@valbottom\yes \ifnum\v@lseqbottom=\loopcount \xdef\v@lbottom{\v@lbottom,\csname \ffourth@bottom\first@\endcsname} \fi\fi \ifx\collect@valbbottom\yes \ifnum\v@lseqbbottom=\loopcount \xdef\v@lbbottom{\v@lbbottom,\csname \ffourth@bbottom\first@\endcsname} \fi\fi \ifx\collect@valbbbottom\yes \ifnum\v@lseqbbbottom=\loopcount \xdef\v@lbbbottom{\v@lbbbottom,\csname \ffourth@bbbottom\first@\endcsname} \fi\fi \ifx\collect@valbbbbottom\yes \ifnum\v@lseqbbbbottom=\loopcount \xdef\v@lbbbbottom{\v@lbbbbottom,\csname \ffourth@bbbbottom\first@\endcsname} \fi\fi \ifx\collect@restop\yes \ifnum\tr@nsseqtop=\loopcount \xdef\last@restop{\last@@restop} \xdef\last@@restop{\first@} \xdef\tr@nslatetop{\tr@nslatetop\first@} \innerloopcount=\triple@counttop \advance\innerloopcount by 1 \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@counttop{\the\innerloopcount} \fi\fi \ifx\collect@resttop\yes \ifnum\tr@nsseqttop=\loopcount \xdef\last@resttop{\last@@resttop} \xdef\last@@resttop{\first@} \xdef\tr@nslatettop{\tr@nslatettop\first@} \innerloopcount=\triple@countttop \advance\innerloopcount by 1 \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countttop{\the\innerloopcount} \fi\fi \ifx\collect@restttop\yes \ifnum\tr@nsseqtttop=\loopcount \xdef\last@restttop{\last@@restttop} \last@@restttop{\first@} \xdef\tr@nslatetttop{\tr@nslatetttop\first@} \innerloopcount=\triple@counttttop \advance\innerloopcount by 1 \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@counttttop{\the\innerloopcount} \fi\fi \ifx\collect@resttttop\yes \ifnum\tr@nsseqttttop=\loopcount \xdef\last@resttttop{\last@@resttttop} \xdef\last@@resttttop{\first@} \xdef\tr@nslatettttop{\tr@nslatettttop\first@} \innerloopcount=\triple@countttttop \advance\innerloopcount by 1 \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countttttop{\the\innerloopcount} \fi\fi \ifx\collect@resbottom\yes \ifnum\tr@nsseqbottom=\loopcount \xdef\last@resbottom{\last@@resbottom} \xdef\last@@resbottom{\first@} \xdef\tr@nslatebottom{\tr@nslatebottom\first@} \innerloopcount=\triple@countbottom \advance\innerloopcount by 1 \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countbottom{\the\innerloopcount} \fi\fi \ifx\collect@resbbottom\yes \ifnum\tr@nsseqbbottom=\loopcount \xdef\last@resbbottom{\last@@resbbottom} \xdef\last@@resbbottom{\first@} \xdef\tr@nslatebbottom{\tr@nslatebbottom\first@} \innerloopcount=\triple@countbbottom \advance\innerloopcount by 1 \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countbbottom{\the\innerloopcount} \fi\fi \ifx\collect@resbbbottom\yes \ifnum\tr@nsseqbbbottom=\loopcount \xdef\last@resbbbottom{\last@@resbbbottom} \xdef\last@@resbbbottom{\first@} \xdef\tr@nslatebbbottom{\tr@nslatebbbottom\first@} \innerloopcount=\triple@countbbbottom \advance\innerloopcount by 1 \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countbbbottom{\the\innerloopcount} \fi\fi \ifx\collect@resbbbbottom\yes \ifnum\tr@nsseqbbbbottom=\loopcount \xdef\last@resbbbbottom{\last@@resbbbbottom} \xdef\last@@resbbbbottom{\first@} \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom\first@} \innerloopcount=\triple@countbbbbottom \advance\innerloopcount by 1 \ifnum\innerloopcount>3 \innerloopcount=1 \fi \xdef\triple@countbbbbottom{\the\innerloopcount} \fi\fi \innerloopcount=\csname mol@weight\the\loopcount\endcsname \advance\innerloopcount by \csname \prefix@ mw\first@\endcsname \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{% \the\innerloopcount} \innerloopcount=\csname ch@rge\the\loopcount\endcsname \advance\innerloopcount by \csname pepcharge\first@\endcsname \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{% \the\innerloopcount} \else \ifnum\loopcount=\rule@num \xdef\ruler@{\ruler@ -} \fi \ifx\collect@valtop\yes \ifnum\v@lseqtop=\loopcount \xdef\v@ltop{\v@ltop,N} \fi\fi \ifx\collect@valttop\yes \ifnum\v@lseqttop=\loopcount \xdef\v@lttop{\v@lttop,N} \fi\fi \ifx\collect@valtttop\yes \ifnum\v@lseqtttop=\loopcount \xdef\v@ltttop{\v@ltttop,N} \fi\fi \ifx\collect@valttttop\yes \ifnum\v@lseqttttop=\loopcount \xdef\v@lttttop{\v@lttttop,N} \fi\fi \ifx\collect@valbottom\yes \ifnum\v@lseqbottom=\loopcount \xdef\v@lbottom{\v@lbottom,N} \fi\fi \ifx\collect@valbbottom\yes \ifnum\v@lseqbbottom=\loopcount \xdef\v@lbbottom{\v@lbbottom,N} \fi\fi \ifx\collect@valbbbottom\yes \ifnum\v@lseqbbbottom=\loopcount \xdef\v@lbbbottom{\v@lbbbottom,N} \fi\fi \ifx\collect@valbbbbottom\yes \ifnum\v@lseqbbbbottom=\loopcount \xdef\v@lbbbbottom{\v@lbbbbottom,N} \fi\fi \ifx\collect@restop\yes \ifnum\tr@nsseqtop=\loopcount \xdef\tr@nslatetop{\tr@nslatetop -} \fi\fi \ifx\collect@resttop\yes \ifnum\tr@nsseqttop=\loopcount \xdef\tr@nslatettop{\tr@nslatettop -} \fi\fi \ifx\collect@restttop\yes \ifnum\tr@nsseqtttop=\loopcount \xdef\tr@nslatetttop{\tr@nslatetttop -} \fi\fi \ifx\collect@resttttop\yes \ifnum\tr@nsseqttttop=\loopcount \xdef\tr@nslatettttop{\tr@nslatettttop -} \fi\fi \ifx\collect@resbottom\yes \ifnum\tr@nsseqbottom=\loopcount \xdef\tr@nslatebottom{\tr@nslatebottom -} \fi\fi \ifx\collect@resbbottom\yes \ifnum\tr@nsseqbbottom=\loopcount \xdef\tr@nslatebbottom{\tr@nslatebbottom -} \fi\fi \ifx\collect@resbbbottom\yes \ifnum\tr@nsseqbbbottom=\loopcount \xdef\tr@nslatebbbottom{\tr@nslatebbbottom -} \fi\fi \ifx\collect@resbbbbottom\yes \ifnum\tr@nsseqbbbbottom=\loopcount \xdef\tr@nslatebbbbottom{\tr@nslatebbbbottom -} \fi\fi \fi \ifnum\loopcount<\seq@count \repeat \ifx\collect@cons@graphtop\yes \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \xdef\v@ltop{\v@ltop,\cons@val} \fi \ifx\collect@cons@graphttop\yes \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \xdef\v@lttop{\v@lttop,\cons@val} \fi \ifx\collect@cons@graphtttop\yes \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \xdef\v@ltttop{\v@ltttop,\cons@val} \fi \ifx\collect@cons@graphttttop\yes \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \xdef\v@lttttop{\v@lttttop,\cons@val} \fi \ifx\collect@cons@graphbottom\yes \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \xdef\v@lbottom{\v@lbottom,\cons@val} \fi \ifx\collect@cons@graphbbottom\yes \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \xdef\v@lbbottom{\v@lbbottom,\cons@val} \fi \ifx\collect@cons@graphbbbottom\yes \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \xdef\v@lbbbottom{\v@lbbbottom,\cons@val} \fi \ifx\collect@cons@graphbbbbottom\yes \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \xdef\v@lbbbbottom{\v@lbbbbottom,\cons@val} \fi \ifx\collect@cons@colors\y@ \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \outerloopcount=\cons@val \advance\outerloopcount by 4 \divide\outerloopcount by 5 \multiply\outerloopcount by 5 \ifnum\outerloopcount<5\relax\outerloopcount=5\fi \xdef\c@nscol{\c@nscol\the\outerloopcount,} \fi \ifx\exp@rt\y@ \ifx\seventh@\y@ \outerloopcount=1\relax \temp@count=0\relax \sum@up@cons \outerloopcount=\cons@val \advance\outerloopcount by 4 \divide\outerloopcount by 5 \multiply\outerloopcount by 5 \ifnum\outerloopcount<5\relax\outerloopcount=5\fi \xdef\seventh@{n} \immediate\write\exp@rtfile{\string color col\the\outerloopcount, resi \sixth@} \fi \fi \xdef\g@p{n} \ifregionalshadenow \calc@regshade \fi \ifregionaltintnow \calc@regtint \fi \ifregionalemphnow \calc@regemph \fi \ifregionallowernow \calc@reglower \fi \ifframenow \calc@frame \fi \ifshadingnow\iffuncmode\else\ifT@coffee\else \calc@shading \fi\fi\fi \iftopfeaturenow \xdef\bottop@{top} \calc@feature \fi \ifttopfeaturenow \xdef\bottop@{ttop} \calc@feature \fi \iftttopfeaturenow \xdef\bottop@{tttop} \calc@feature \fi \ifttttopfeaturenow \xdef\bottop@{ttttop} \calc@feature \fi \ifbottomfeaturenow \xdef\bottop@{bottom} \calc@feature \fi \ifbbottomfeaturenow \xdef\bottop@{bbottom} \calc@feature \fi \ifbbbottomfeaturenow \xdef\bottop@{bbbottom} \calc@feature \fi \ifbbbbottomfeaturenow \xdef\bottop@{bbbbottom} \calc@feature \fi \ifnum\seq@count>1 \innerloopcount=1 \collect@similarity \fi \advance\pos@count by 1 \ifshow@logo \calc@logo \fi \ifall@fshade \all@funcshade \else \ifT@coffee \T@coffee@shade \else \ifnum\cons@num>0 \loopcount=\cons@num \else \loopcount=\seq@count \fi \xdef\match@case{0} \xdef\m@x{1} \iffuncmode \xdef\prfx{\prefix@} \xdef\prefix@{func} \xdef\c@se{3} \check@sim \xdef\prefix@{\prfx} \else \xdef\c@se{1} \check@ident \fi \ifcase\match@case \unc@nserved \or \c@nserved \or \allm@tch \else \functi@nal \fi \fi \fi \ifnum\rule@num=0 \ifx\g@p\y@ \xdef\ruler@{\ruler@ -} \else \ifnum\cons@count=\rule@tens \expandafter\ifx\csname alt@ruler\rule@tens\endcsname\relax \xdef\temp@{\rule@tens} \else \xdef\temp@{\csname alt@ruler\rule@tens\endcsname} \fi \xdef\ruler@{\ruler@ !<\temp@>} \innerloopcount=\rule@tens \advance\innerloopcount by \ruler@step\relax \ifnum\innerloopcount=0 \ifx\allow@zero\n@ \innerloopcount=\ruler@step \fi \fi \xdef\rule@tens{\the\innerloopcount} \else \xdef\ruler@{\ruler@ -} \fi \expandafter\ifx\csname alt@ruler\the\cons@count\endcsname\relax \else \expandafter\xdef\csname alt@ruler\the\cons@count\endcsname{\the\cons@count} \fi \fi \fi \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax \c@nsensus \else \global\stop@true \loopcount=\pos@count \advance\loopcount by -1 \relax \res@perline=\loopcount \iftopfeature \xdef\bottop@{top} \calc@feature \fi \ifttopfeature \xdef\bottop@{ttop} \calc@feature \fi \iftttopfeature \xdef\bottop@{tttop} \calc@feature \fi \ifttttopfeature \xdef\bottop@{ttttop} \calc@feature \fi \ifbottomfeature \xdef\bottop@{bottom} \calc@feature \fi \ifbbottomfeature \xdef\bottop@{bbottom} \calc@feature \fi \ifbbbottomfeature \xdef\bottop@{bbbottom} \calc@feature \fi \ifbbbbottomfeature \xdef\bottop@{bbbbottom} \calc@feature \fi \pos@count=0 \fi \fi} \def\prep@reexp@rtfile{ \loopcount=0 \loop \advance\loopcount by 5 \immediate\write\exp@rtfile{\string set_color col\the\loopcount, \csname\c@nsc@l\the\loopcount\endcsname} \ifnum\loopcount>95\else\repeat } \def\c@unt{% \advance\loopcount by 1 \ifT@coffee \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} \expandafter\TC@get\seq@line \fi \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\residue@get\seq@line \xdef\first@{\csname res\the\loopcount\endcsname} \expandafter\check@char\first@ \ifletter \res@count=\csname res@count\the\loopcount\endcsname \advance\res@count by 1 \ifnum\res@count=0 \ifx\allow@zero\n@ \advance\res@count by 1 \fi \fi \ifx\dom@in\y@ \xdef\temp@{\csname dom@num\the\loopcount\endcsname} \expandafter\get@dom@count\temp@ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\temp@} \fi %%%%%%%%%%%***** \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count} \ifnum\rule@num=\loopcount \temp@count=\csname res@count\the\loopcount\endcsname \advance\temp@count by \ruler@step \divide\temp@count by \ruler@step \multiply\temp@count by \ruler@step \xdef\rule@tens{\the\temp@count} \fi \fi \ifnum\loopcount<\seq@count \c@unt\fi} \def\count@first{% \advance\end@count by 1 \ifnum\end@count<\start@number \loopcount=0 \ifT@coffee \xdef\seq@line{\csname T@coffee\the\loopcount\endcsname} \expandafter\TC@get\seq@line \fi \c@unt \count@first \fi} \def\findc@nsensus{% \loopcount=0 \loop \advance\loopcount by 1 \expandafter\xdef\csname sequence\the\loopcount\endcsname{% \csname sequence\the\loopcount\endcsname @} \ifnum\loopcount<\seq@count \repeat \end@count=0 \count@first \end@count=0 \xdef\start@number{0} \topfeaturenowfalse \bottomfeaturenowfalse \ttopfeaturenowfalse \bbottomfeaturenowfalse \tttopfeaturenowfalse \bbbottomfeaturenowfalse \ttttopfeaturenowfalse \bbbbottomfeaturenowfalse \innerloopcount=\cons@count \advance\innerloopcount by \res@perline \advance\innerloopcount by 1 \loopcount=0 \ifregionalshade \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\the\loopcount\endcsname>% \innerloopcount \else \regionalshadenowtrue \fi \fi \fi \ifregionaltint \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% \innerloopcount \else \regionaltintnowtrue \fi \fi \fi \ifregionalemph \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>% \innerloopcount \else \regionalemphnowtrue \fi \fi \fi \ifregionallower \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>% \innerloopcount \else \regionallowernowtrue \fi \fi \fi \ifframe@ \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname framestart\the\loopcount\endcsname>% \innerloopcount \else \framenowtrue \fi \fi \fi \ifshading@ \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>% \innerloopcount \else \shadingnowtrue \fi \fi \fi \iftopfeature \xdef\bottop@{top} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \topfeaturenowtrue \fi \fi \fi \ifttopfeature \xdef\bottop@{ttop} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \ttopfeaturenowtrue \fi \fi \fi \iftttopfeature \xdef\bottop@{tttop} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \tttopfeaturenowtrue \fi \fi \fi \ifttttopfeature \xdef\bottop@{ttttop} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \ttttopfeaturenowtrue \fi \fi \fi \ifbottomfeature \xdef\bottop@{bottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \bottomfeaturenowtrue \fi \fi \fi \ifbbottomfeature \xdef\bottop@{bbottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \bbottomfeaturenowtrue \fi \fi \fi \ifbbbottomfeature \xdef\bottop@{bbbottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \bbbottomfeaturenowtrue \fi \fi \fi \ifbbbbottomfeature \xdef\bottop@{bbbbottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \bbbbottomfeaturenowtrue \fi \fi \fi \loop \advance\loopcount by 1 \ifnumbers@left \innerloopcount=\csname seq@len\the\loopcount\endcsname\relax \expandafter\ifnum\csname res@count\the\loopcount\endcsname=% \innerloopcount \res@count=\innerloopcount \else \res@count=\csname res@count\the\loopcount\endcsname \advance\res@count by 1 \ifnum\res@count=0 \ifx\allow@zero\n@ \advance\res@count by 1 \fi \fi \fi \ifx\dom@in\y@ \xdef\temp@{\csname dom@num\the\loopcount\endcsname} \expandafter\get@dom@count\temp@ \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\the\res@count,\temp@} \fi %%%%%%%%%%***** \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count} \ifnames@right \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname res@count\the\loopcount\endcsname)} \else \expandafter\xdef\csname seq\the\loopcount\endcsname{% <\csname newseqname\the\loopcount\endcsname> \csname res@count\the\loopcount\endcsname)} \fi \ifx\dom@in\y@ \else \expandafter\ifnum\csname res@count\the\loopcount\endcsname=% \innerloopcount \else \res@count=\csname res@count\the\loopcount\endcsname \advance\res@count by -1 \ifnum\res@count=0 \ifx\allow@zero\n@ \advance\res@count by -1 \fi \fi \expandafter\xdef\csname res@count\the\loopcount\endcsname{\the\res@count} \fi \fi \else \ifnames@right \expandafter\xdef\csname seq\the\loopcount\endcsname{} \else \expandafter\xdef\csname seq\the\loopcount\endcsname{% <\csname newseqname\the\loopcount\endcsname>} \fi \fi \ifx\dom@in\y@ \xdef\temp@{\csname dom@num@break\the\loopcount\endcsname} \expandafter\get@dom@count\temp@ \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{\temp@} \innerloopcount=\res@count \else \innerloopcount=\csname res@count\the\loopcount\endcsname \advance\innerloopcount by \res@perline \fi \advance\innerloopcount by 1 \ifregionalshade \expandafter\ifx\csname start\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\the\loopcount\endcsname>% \innerloopcount \else \regionalshadenowtrue \fi \fi \fi \ifregionaltint \expandafter\ifx\csname tintstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname tintstart\the\loopcount\endcsname>% \innerloopcount \else \regionaltintnowtrue \fi \fi \fi \ifregionalemph \expandafter\ifx\csname emphstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname emphstart\the\loopcount\endcsname>% \innerloopcount \else \regionalemphnowtrue \fi \fi \fi \ifregionallower \expandafter\ifx\csname lowerstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname lowerstart\the\loopcount\endcsname>% \innerloopcount \else \regionallowernowtrue \fi \fi \fi \ifframe@ \expandafter\ifx\csname framestart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname framestart\the\loopcount\endcsname>% \innerloopcount \else \framenowtrue \fi \fi \fi \ifshading@ \expandafter\ifx\csname shadingstart\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname shadingstart\the\loopcount\endcsname>% \innerloopcount \else \shadingnowtrue \fi \fi \fi \iftopfeature \xdef\bottop@{top} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \topfeaturenowtrue \fi \fi \fi \ifttopfeature \xdef\bottop@{ttop} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \ttopfeaturenowtrue \fi \fi \fi \iftttopfeature \xdef\bottop@{tttop} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \tttopfeaturenowtrue \fi \fi \fi \ifttttopfeature \xdef\bottop@{ttttop} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \ttttopfeaturenowtrue \fi \fi \fi \ifbottomfeature \xdef\bottop@{bottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \bottomfeaturenowtrue \fi \fi \fi \ifbbottomfeature \xdef\bottop@{bbottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \bbottomfeaturenowtrue \fi \fi \fi \ifbbbottomfeature \xdef\bottop@{bbbottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \bbbottomfeaturenowtrue \fi \fi \fi \ifbbbbottomfeature \xdef\bottop@{bbbbottom} \expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd \else \expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>% \innerloopcount \else \bbbbottomfeaturenowtrue \fi \fi \fi \ifnum\loopcount<\seq@count \repeat \c@nsensus} %%%%% Output routines \def\white@box{% \bgroup \fboxsep-0.5pt\fboxrule0.5pt \fcolorbox{Black}{White}{\box@hstrut\box@wstrut}\egroup} \def\box@rule{\vrule depth\box@depth height\box@height width\box@width} \def\box@hstrut{\vrule depth\box@depth height\box@height width 0pt} \def\box@wstrut{\vrule depth 0pt height 0pt width\box@width} \def\do@legend{% \baselineskip=1.2\baselineskip \xdef\first@{White} \fontfamily{\legend@family}% \fontseries{\legend@series}% \fontshape{\legend@shape}% \ifT@coffee \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \def\res@@style{\csname no@style\endcsname}% \def\temp@{X}\xdef\low@up{lower}% \expandafter\ifx\csname n@m@tch\the\loopcount\endcsname\low@up% \def\temp@{x}\fi% \ifhidechar\xdef\temp@{}\fi% \textcolor{TC0}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{% \ifgerm@n\kern2ex\legend@size{schlecht}% \else\ifsp@nish\kern2ex\legend@size{mala}% \else\kern2ex\legend@size{bad}\fi\fi} \newline\hbox{}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \textcolor{TC1}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{\legend@size{}} \newline\hbox{}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \textcolor{TC2}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{\legend@size{}} \newline\hbox{}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \textcolor{TC3}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{\legend@size{}} \newline\hbox{}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \textcolor{TC4}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{% \ifgerm@n\kern2ex\legend@size{Grad der}% \else\ifsp@nish\kern2ex\legend@size{conservaci\'on}% \else\kern2ex\legend@size{level of}\fi\fi} \newline\hbox{}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \textcolor{TC5}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{% \ifgerm@n\kern2ex\legend@size{Konservierung}% \else\ifsp@nish\kern2ex\legend@size{}% \else\kern2ex\legend@size{conservation}\fi\fi} \newline\hbox{}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \textcolor{TC6}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{\legend@size{}} \newline\hbox{}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \textcolor{TC7}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{\legend@size{}} \newline\hbox{}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \textcolor{TC8}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{\legend@size{}} \newline\hbox{}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \textcolor{TC9}{\box@rule}% \kern-\box@width\textcolor{Black}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{% \ifgerm@n\kern2ex\legend@size{gut}% \else\ifsp@nish\kern2ex\legend@size{buena}% \else\kern2ex\legend@size{good}\fi\fi} \newline\hbox{}% \else \iffuncmode \ifnum\fgroup@num>0 \loopcount=0 \loop \advance\loopcount by 1 \xdef\third@{\csname fg@color\the\loopcount\endcsname}% \noindent% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left\hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi% \xdef\third@{\csname fg@textcolor\the\loopcount\endcsname}% \def\res@@style{\csname func@style\the\loopcount\endcsname}% \def\temp@{X}\xdef\low@up{lower}% \expandafter\ifx\csname funcm@tch\the\loopcount\endcsname\low@up% \def\temp@{x}\fi% \ifhidechar\xdef\temp@{}\fi% \kern-\box@width\textcolor{\third@}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \kern2ex\textcolor{\legend@fg}{% \legend@size{\csname fgroup@name\the\loopcount\endcsname}} \newline\hbox{}% \ifnum\loopcount<\fgroup@num \repeat \fi \else \noindent \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi% \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi% \hbox to \hspace@legend{\hss}% \ifx\Nomatch\first@\white@box\else\textcolor{\Nomatch}{\box@rule}\fi% \def\res@@style{\csname no@style\endcsname}% \def\temp@{X}\xdef\low@up{lower}\ifx\resn@m@tch\low@up\def\temp@{x}\fi% \ifhidechar\xdef\temp@{}\fi% \kern-\box@width\textcolor{\TextNomatch}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \textcolor{\legend@fg}{% \ifgerm@n\kern2ex\legend@size{nicht konserviert}% \else\ifsp@nish\kern2ex\legend@size{no conservado}% \else\kern2ex\legend@size{non-conserved}\fi\fi} \newline\hbox{}\noindent% \ifsimmode% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi \hbox to \hspace@legend{\hss}% \ifx\Similar\first@\white@box\else\textcolor{\Similar}{\box@rule}\fi \def\res@@style{\csname sim@style\endcsname}% \def\temp@{X}\xdef\low@up{lower}\ifx\ressimm@tch\low@up\def\temp@{x}\fi% \ifhidechar\xdef\temp@{}\fi% \kern-\box@width\textcolor{\TextSimilar}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \textcolor{\legend@fg}{% \ifgerm@n\kern2ex\legend@size{\"ahnlich}% \else\ifsp@nish\kern2ex\legend@size{similar}% \else\kern2ex\legend@size{similar}\fi\fi} \newline\hbox{}\noindent% \fi% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi \hbox to \hspace@legend{\hss}% \ifx\Identical\first@\white@box\else\textcolor{\Identical}{\box@rule}\fi \def\res@@style{\csname id@style\endcsname}% \def\temp@{X}\xdef\low@up{lower}\ifx\resm@tch\low@up\def\temp@{x}\fi% \ifhidechar\xdef\temp@{}\fi% \kern-\box@width\textcolor{\TextIdentical}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \textcolor{\legend@fg}{% \ifgerm@n\kern2ex\legend@size{$\ge$\,\thresh@ld\% konserviert}% \else\ifsp@nish\kern2ex\legend@size{$\ge$\,\thresh@ld\% conservado}% \else\kern2ex\legend@size{$\ge$\,\thresh@ld\% conserved}\fi\fi} \newline\hbox{}\noindent% \ifall@shade% \ifnames@\ifnames@right\else\hbox to \name@width{\hss}\fi\fi \ifnumbers@\ifnumbers@left \hbox to \number@width{\hss}\fi\fi \hbox to \hspace@legend{\hss}% \ifx\Allmatch\first@\white@box\else\textcolor{\Allmatch}{\box@rule}\fi \def\res@@style{\csname all@style\endcsname}% \def\temp@{X}\xdef\low@up{lower}\ifx\res@llm@tch\low@up\def\temp@{x}\fi% \ifhidechar\xdef\temp@{}\fi% \kern-\box@width\textcolor{\TextAllmatch}{\hbox to \box@width{% \legend@size{\res@@style{\hss\temp@\hss}}}}% \ifnum\all@thresh@ld=100 \textcolor{\legend@fg}{% \ifgerm@n\kern2ex\legend@size{alle identisch}% \else\ifsp@nish\kern2ex\legend@size{todos id\'enticos}% \else\kern2ex\legend@size{all match}\fi\fi} \else \textcolor{\legend@fg}{% \ifgerm@n\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% konserviert}% \else\ifsp@nish\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% conservado}% \else\kern2ex\legend@size{$\ge$\,\all@thresh@ld\% conserved}\fi\fi} \fi \newline\hbox{}\noindent \fi \fi \fi } \def\put@name<#1>#2@{% \ifnames@% \expandafter\ifx\csname hide@name\the\loopcount\endcsname\yes% \xdef\temp@{}\else\xdef\temp@{#1}\fi% \expandafter\ifx\csname name@col\the\loopcount\endcsname\yes% \def\second@{\names@fg}% \else\def\second@{\csname name@col\the\loopcount\endcsname}\fi% \fontfamily{\namestext@family}% \fontseries{\namestext@series}% \fontshape{\namestext@shape}% \selectfont% \textcolor{\second@}{% \hbox to \name@width{\@kern\namestext@size{\temp@}\hss}}\fi% \xdef\first@{#2@}% } \def\put@number#1)#2@{% \ifnumbers@% \expandafter\ifx\csname hide@number\the\loopcount\endcsname\yes% \xdef\temp@{}\else\xdef\temp@{#1}\fi% \expandafter\ifx\csname number@col\the\loopcount\endcsname\yes% \def\second@{\numbering@fg}% \else\def\second@{\csname number@col\the\loopcount\endcsname}\fi% \fontfamily{\numbertext@family}% \fontseries{\numbertext@series}% \fontshape{\numbertext@shape}% \selectfont% \textcolor{\second@}{% \hbox to \number@width{\hss\numbertext@size{\temp@}\@kern}}\fi% \xdef\first@{#2@}% } \def\special@shading#1)#2#3#4@{% \xdef\second@{@\second@#1}% \xdef\third@{\second@}% \xdef\first@{#4@}% \xdef\second@{#3}% \xdef\last@{#2}% \def\res@@style{\csname relax\endcsname}% } \def\special@shade#1)#2#3#4@{% \xdef\second@{\second@#1}% \xdef\boxc@l@r{\csname bgseqregion\second@\endcsname}% \xdef\textc@l@r{\csname fgseqregion\second@\endcsname}% \xdef\first@{#4@}% \xdef\second@{#3}% \def\res@@style{\csname relax\endcsname}% } \def\get@second@#1#2@{\xdef\second@{#1}\xdef\first@{#2@}} \def\next@char#1#2#3@{% \xdef\first@{#3@}% \xdef\second@{#2}% \xdef\last@{#1}% \xdef\temp@@{}% \xdef\third@{}% \ifx\last@\p@r@gr@ph\expandafter\special@shading\first@\fi% \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% \else% \ifT@coffee% \xdef\boxc@l@r{\csname fg@color#1\endcsname}% \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% \def\res@@style{\csname func@style#1\endcsname}% \if\last@ *\def\last@{0}\fi \if\last@ /\def\last@{10}\fi \if\last@ !\def\last@{11}\fi \else% \iffuncmode% \xdef\boxc@l@r{\csname fg@color#1\endcsname}% \xdef\textc@l@r{\csname fg@textcolor#1\endcsname}% \def\res@@style{\csname func@style#1\endcsname}% \if\last@ *\def\last@{0}\fi \if\last@ /\def\last@{10}\fi \if\last@ !\def\last@{11}\fi \else% \ifcase\last@\xdef\boxc@l@r{\csname Allmatch\third@\endcsname}% \xdef\textc@l@r{\csname TextAllmatch\third@\endcsname}% \def\res@@style{\all@style}% \or\xdef\boxc@l@r{\csname Identical\third@\endcsname}% \xdef\textc@l@r{\csname TextIdentical\third@\endcsname}% \def\res@@style{\id@style}% \or\xdef\boxc@l@r{\csname Similar\third@\endcsname}% \xdef\textc@l@r{\csname TextSimilar\third@\endcsname}% \def\res@@style{\sim@style}% \or\xdef\boxc@l@r{\csname Nomatch\third@\endcsname}% \xdef\textc@l@r{\csname TextNomatch\third@\endcsname}% \def\res@@style{\no@style}% \or\xdef\boxc@l@r{\csname ConsNomatch\third@\endcsname}% \xdef\textc@l@r{\csname ConsTextNomatch\third@\endcsname}% \def\res@@style{\csname relax\endcsname}% \or\xdef\boxc@l@r{\csname ConsMatch\third@\endcsname}% \xdef\textc@l@r{\csnam ConsTextMatch\third@\endcsname}% \def\res@@style{\csname relax\endcsname}% \or\xdef\boxc@l@r{\csname ConsAllmatch\third@\endcsname}% \xdef\textc@l@r{\csname ConsTextAllmatch\third@\endcsname}% \def\res@@style{\csname relax\endcsname}% \or\xdef\boxc@l@r{\csname gap@bg\third@\endcsname}% \xdef\textc@l@r{\csname gap@fg\third@\endcsname}% \def\res@@style{\csname relax\endcsname}% \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \def\res@@style{\csname relax\endcsname}% \else\xdef\boxc@l@r{\csname domgap@bg\endcsname}% \xdef\textc@l@r{\csname domgap@fg\endcsname}% \def\res@@style{\csname relax\endcsname}% \fi\fi\fi\fi% \ifx\second@\comm@% \def\temp@{\res@style}% \expandafter\get@second@\first@% \else% \def\temp@{\csname relax\endcsname}% \fi% \ifx\second@\equ@l% \xdef\temp@@{\light@}% \expandafter\get@second@\first@% \fi% \ifx\second@\semic@n% \expandafter\get@second@\first@% \xdef\first@@{\first@}% \xdef\first@{\second@}% \make@lower% \xdef\second@{\first@}% \xdef\first@{\first@@}% \fi% \textcolor{\temp@@\boxc@l@r}{\box@rule}% \ifhidechar% \ifx\second@\o@% \def\second@{\gap@rule}% \hbox to -\box@width{\hss\textcolor{\temp@@\textc@l@r}% {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% \kern\box@width% \fi% \else% \ifx\second@\o@\def\second@{\gap@rule}\fi% \hbox to -\box@width{\hss\textcolor{\temp@@\textc@l@r}% {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% \kern\box@width\fi% } \def\put@char{% \ifnum\innerloopcount>\res@perline \else \expandafter\next@char\first@ \advance\innerloopcount by 1 \put@char% \fi} \def\next@cons#1#2#3@{% \xdef\last@{#1}% \xdef\third@{}% \ifx\last@\p@r@gr@ph\expandafter\special@shading\first@\fi% \ifx\last@\ampers@nd\def\last@{0}\expandafter\special@shade\first@% \else% \ifx\collect@cons@colors\y@% \if\last@ *% \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% \else% \if\last@ !% \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}% \else% \if\last@ /% \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \else% \expandafter\get@item\first@@@% \xdef\first@@@{\first@}% \ifx\box@scale\y@% \xdef\boxc@l@r{\c@nssc@le\fourth@}% \else% \xdef\first@{T-Coffee}% \ifx\first@\c@nssc@le% \xdef\boxc@l@r{TC\last@}% \else \xdef\boxc@l@r{\c@nssc@le}% \fi% \fi% \ifx\text@scale\y@% \xdef\textc@l@r{\c@nsc@l\fourth@}% \else% \xdef\first@{T-Coffee}% \ifx\first@\c@nsc@l% \xdef\textc@l@r{TC\last@}% \else \xdef\textc@l@r{\c@nsc@l}% \fi% \fi\fi\fi\fi% \def\res@@style{\csname relax\endcsname}% \else% \ifT@coffee% \if\last@ *% \xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@bg}% \else% \if\last@ !% \xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@bg}% \else% \if\last@ /% \xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \else% \xdef\boxc@l@r{White}\xdef\textc@l@r{TC\last@}% \def\res@@style{\csname relax\endcsname}% \fi \fi% \fi% \else% \ifcase#1\xdef\boxc@l@r{\csname Allmatch\third@\endcsname}% \xdef\textc@l@r{\csname TextAllmatch\third@\endcsname}% \def\res@@style{\all@style}% \or\xdef\boxc@l@r{\csname Identical\third@\endcsname}% \xdef\textc@l@r{\csname TextIdentical\third@\endcsname}% \def\res@@style{\id@style}% \or\xdef\boxc@l@r{\csname Similar\third@\endcsname}% \xdef\textc@l@r{\csname TextSimilar\third@\endcsname}% \def\res@@style{\sim@style}% \or\xdef\boxc@l@r{\csname Nomatch\third@\endcsname}% \xdef\textc@l@r{\csname TextNomatch\third@\endcsname}% \def\res@@style{\no@style}% \or\xdef\boxc@l@r{\ConsNomatch}\xdef\textc@l@r{\ConsTextNomatch}% \def\res@@style{\csname relax\endcsname}% \or\xdef\boxc@l@r{\ConsMatch}\xdef\textc@l@r{\ConsTextMatch}% \def\res@@style{\csname relax\endcsname}% \or\xdef\boxc@l@r{\ConsAllmatch}\xdef\textc@l@r{\ConsTextAllmatch}% \def\res@@style{\csname relax\endcsname}% \or\xdef\boxc@l@r{\gap@bg}\xdef\textc@l@r{\gap@fg}% \def\res@@style{\csname relax\endcsname}% \or\xdef\boxc@l@r{White}\xdef\textc@l@r{White}% \def\res@@style{\csname relax\endcsname}% \else\xdef\boxc@l@r{\domgap@bg}\xdef\textc@l@r{\domgap@fg}% \def\res@@style{\csname relax\endcsname}% \fi\fi\fi\fi% \xdef\first@{#3@}% \xdef\second@{#2}% \ifx\second@\comm@% \def\temp@{\res@style}% \expandafter\get@second@\first@% \else% \def\temp@{\csname relax\endcsname}% \fi% \ifx\second@\semic@n% \expandafter\get@second@\first@% \xdef\first@@{\first@}% \xdef\first@{\second@}% \make@lower% \xdef\second@{\first@}% \xdef\first@{\first@@}% \fi% \textcolor{\boxc@l@r}{\box@rule}% \ifhidechar% \ifx\second@\o@% \def\second@{\gap@rule}% \hbox to -\box@width{\hss\textcolor{\textc@l@r}% {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% \kern\box@width% \fi% \else% \ifx\second@\o@\def\second@{\gap@rule}\fi% \hbox to -\box@width{\hss\textcolor{\textc@l@r}% {\residues@size{\res@@style{\temp@{\second@}}}}\hss}% \kern\box@width\fi% } \def\put@cons{% \ifnum\innerloopcount>\res@perline \else \expandafter\next@cons\first@ \advance\innerloopcount by 1 \put@cons% \fi} \def\put@line{% \ifnames@right\else\def\@kern{\kern0em}\expandafter\put@name\first@\fi \ifnumbers@left\def\@kern{\kern1em}\expandafter\put@number\first@\fi \fontfamily{\residues@family}% \fontseries{\residues@series}% \fontshape{\residues@shape}% \selectfont% \ifx\cons@now\y@% \innerloopcount=1\relax\put@cons% \else \innerloopcount=1\relax\put@char% \fi \ifnumbers@right\def\@kern{\kern0em}\expandafter\put@number\first@\fi \ifnames@right\def\@kern{\kern1em}\expandafter\put@name\first@\fi \newline\hbox{}% } \def\set@consensus{% \ifnames@right \ifnumbers@left \ifnumbers@right \xdef\consensus{)\consensus)<\cons@name>}% \else \xdef\consensus{)\consensus<\cons@name>}% \fi \else \xdef\consensus{\consensus)<\cons@name>}% \fi \else \ifnumbers@left \ifnumbers@right \xdef\consensus{<\cons@name>)\consensus)}% \else \xdef\consensus{<\cons@name>)\consensus}% \fi \else \xdef\consensus{<\cons@name>\consensus)}% \fi \fi} \def\get@rulenum<#1>#2@{% \xdef\first@{#2@}% \xdef\fill@char{#1[,]&}% \expandafter\opt@color\fill@char% \ifx\f@color\comm@\xdef\f@color{\ruler@fg}\fi% \ifcase\rule@top \ifnum\ruler@rot=0 % \xdef\temp@{tt}% \ifx\ruler@family\temp@% \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\mathtt{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% \else \xdef\temp@{sf}% \ifx\ruler@family\temp@% \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\mathsf{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% \else \xdef\temp@{rm}% \ifx\ruler@family\temp@% \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\mathrm{\fourth@}}{\textcolor{\ruler@fg}{.}}}}% \fi\fi\fi \else \xdef\temp@{tt}% \ifx\ruler@family\temp@% \def\third@{\tt\bottomruler@size\,\,\,\,% \begin{rotopo}{90}\hbox to \ruler@width{\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}\,\fourth@\hss}\end{rotopo}}% \else \xdef\temp@{sf}% \ifx\ruler@family\temp@% \def\third@{\sf\bottomruler@size\,\,\,\,% \begin{rotopo}{90}\hbox to \ruler@width{\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}\,\fourth@\hss}\end{rotopo}}% \else \xdef\temp@{rm}% \ifx\ruler@family\temp@% \def\third@{\rm\bottomruler@size\,\,\,\,% \begin{rotopo}{90}\hbox to \ruler@width{\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}\,\fourth@\hss}\end{rotopo}}% \fi\fi\fi \fi \else \ifnum\ruler@rot=0 % \xdef\temp@{tt}% \ifx\ruler@family\temp@% \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\textcolor{\ruler@fg}{.}}{\mathtt{\fourth@}}}}% \else \xdef\temp@{sf}% \ifx\ruler@family\temp@% \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\textcolor{\ruler@fg}{.}}{\mathsf{\fourth@}}}}% \else \xdef\temp@{rm}% \ifx\ruler@family\temp@% \def\third@{\bottomruler@size\ensuremath{\,\stackrel{\textcolor{\ruler@fg}{.}}{\mathrm{\fourth@}}}}% \fi\fi\fi \else \xdef\temp@{tt}% \ifx\ruler@family\temp@% \def\third@{\tt\bottomruler@size\,\,\,\,% \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}% \else \xdef\temp@{sf}% \ifx\ruler@family\temp@% \def\third@{\sf\bottomruler@size\,\,\,\,% \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}% \else \xdef\temp@{rm}% \ifx\ruler@family\temp@% \def\third@{\rm\bottomruler@size\,\,\,\,% \begin{rotopo}{90}\hbox to \ruler@width{\hss\fourth@\,\textcolor{\ruler@fg}{\ensuremath{\cdot}}}\end{rotopo}}% \fi\fi\fi \fi \fi} \def\next@rulechar#1#2@{% \xdef\third@{#1}% \xdef\first@{#2@}% \xdef\second@{!}% \ifx\third@\second@ \expandafter\get@rulenum\first@% \else \xdef\third@{}\xdef\f@color{Black}\fi \textcolor{\f@color}{\hbox to \box@width{\hss\third@\hss}}% } \def\put@rulechar{% \ifnum\innerloopcount>\res@perline \else \expandafter\next@rulechar\first@ \advance\innerloopcount by 1 \put@rulechar% \fi} \def\put@ruler{% \ifnames@right% \ifnumbers@left% \ifnumbers@right% \xdef\ruler@{)\ruler@)<>}% \else% \xdef\ruler@{)\ruler@<>}% \fi% \else% \xdef\ruler@{\ruler@)<>}% \fi% \else% \ifnumbers@left% \ifnumbers@right% \xdef\ruler@{<>)\ruler@)}% \else% \xdef\ruler@{<>)\ruler@}% \fi% \else% \xdef\ruler@{<>\ruler@)}% \fi% \fi% \xdef\first@{\ruler@ @}% \ifnum\rule@top=1% \vspace{\ruler@sp@ce}% \vspace{-\baselineskip}% \newline\hbox{}% \fi% \ifnames@right\else\def\@kern{\kern0em}\expandafter\put@name\first@\fi% \ifnumbers@left\def\@kern{\kern1em}\expandafter\put@number\first@\fi% \vspace{-0.25\baselineskip}% \ifnum\rule@top=0% \vspace{\ruler@sp@ce}% \fi% \fontfamily{\ruler@family}% \fontseries{m}% \fontshape{n}% \selectfont% \innerloopcount=1\relax\put@rulechar% \newline\hbox{}% } \def\get@firstfill#1#2&{\xdef\second@@{#1}\xdef\fill@char{#2&}} \def\get@firstv@l#1,#2&{\xdef\second@@{#1}\xdef\fill@char{#2&}} \def\get@tripletfill#1#2#3#4&{% \multiply\temp@count by -1% \def\second@@{#1}\def\second@@@{#2}\def\second@@@@{#3}\def\fill@char{#4&}} \def\putfeature@style#1{% \residues@size% \setbox1=\hbox{\ensuremath{\overrightarrow{\hbox{}}}}% \arrow@height=\ht1% \arrow@width=\wd1% \xdef\second@@{#1}% \xdef\last@{\second@@::&}\expandafter\test@fill\last@% \xdef\last@{empty}% \ifx\second@@\last@% \hbox to \second@\box@width{\hss}% \else% \xdef\last@{translate}% \ifx\second@@\last@% \fontfamily{\featurestyles@family}% \fontseries{\featurestyles@series}% \fontshape{\featurestyles@shape}% \selectfont% \xdef\fill@char{\fill@char &}% \if\seq@type N% \loop% \expandafter\get@firstfill\fill@char% \if\second@@ -\def\second@@{\hss}\fi% \hbox to \box@width{\hss\textcolor{\f@color}{\featurestyles@size{\second@@}}\hss}% \ifx\fill@char\ampers@nd\else\repeat% \else% \temp@count=1% \loop% \expandafter\get@tripletfill\fill@char% \if\second@@ -\ifnum\tr@nsstyle>0\hbox to \box@width{\hss}\fi% \else% \ifcase\tr@nsstyle% \hbox{\trans@size\textcolor{\f@color}% {\hss\second@@\second@@@\second@@@@\,\hss}}% \or% \ifnum\temp@count=1% \vbox{\trans@size% \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% \else% \vbox{\trans@size% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}}% \fi% \or% \ifnum\temp@count=1% \vbox{\trans@size% \hbox to \box@width{\textcolor{\f@color}% {\hss\second@@\second@@@\second@@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss}}}% \else% \vbox{\trans@size% \hbox to \box@width{\textcolor{\f@color}{\hss}}% \hbox to \box@width{\textcolor{\f@color}% {\hss\second@@\second@@@\second@@@@\hss}}}% \fi% \or% \vbox{\trans@size% \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% \or% \vbox{\trans@size% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@\hss}}}% \fi% \fi% \ifx\fill@char\ampers@nd\else\repeat% \fi% \else% \xdef\last@{brace}% \ifx\second@@\last@% \xdef\last@{top}% \textcolor{\f@color}{% \ifx\bottop@\last@% \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% \else% \xdef\last@{ttop}% \ifx\bottop@\last@% \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% \else% \xdef\last@{tttop}% \ifx\bottop@\last@% \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% \else% \xdef\last@{ttttop}% \ifx\bottop@\last@% \ensuremath{\overbrace{\hbox to \second@\box@width{\hss% \rule[0.2\arrow@height]{0pt}{0pt}\hss}}}% \else% \raisebox{1.75\arrow@height}{\ensuremath{\underbrace{\hbox to % \second@\box@width{}}}}% \fi\fi\fi\fi}% \else% \xdef\last@{fill}% \ifx\second@@\last@% \fontfamily{\featurestyles@family}% \fontseries{\featurestyles@series}% \fontshape{\featurestyles@shape}% \selectfont% \xdef\last@{bottom}% \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi% \kern0.15\box@width% \loopcount=0\relax% \loop% \advance\loopcount by 1\relax% \raisebox{\last@\arrow@height}{% \hbox to \box@width{\hss{\textcolor{\f@color}{\featurestyles@size\fill@char}}\hss}}% \ifnum\loopcount<\second@ \repeat% \else% \xdef\last@{bar}% \ifx\second@@\last@% \setlength\arrow@width{\pm@shift\box@height}% \setlength\arrow@width{\b@r@stretch\arrow@width}% \ifx\fill@char\N@% \raisebox{\pm@shift\box@height}{\vrule width\box@width}% \else% \kern-0.6\box@width% \ifx\frame@color\back@color% \else% \setlength\arrow@height{\box@height}% \advance\arrow@height by -\pm@shift\box@height% \setlength\arrow@height{\b@r@stretch\arrow@height}% \raisebox{\arrow@width}{% \hbox to \box@width{\hss{\textcolor{\back@color}{\vrule depth\arrow@width% height\arrow@height width\box@width}}\hss}}% \kern-\box@width% \fi% \setlength\arrow@height{\fill@char\box@height}% \setlength\arrow@height{\b@r@stretch\arrow@height}% \divide\arrow@height by 100\relax% \ifdim\arrow@height<0pt% \arrow@height=-\arrow@height% \raisebox{\arrow@width}{% \hbox to \box@width{\hss{\textcolor{\frame@color}{\vrule depth\arrow@height width0.8\box@width}}\hss}}% \else% \raisebox{\arrow@width}{% \hbox to \box@width{\hss{\textcolor{\frame@color}{\vrule height\arrow@height width0.8\box@width}}\hss}}\fi% \kern-\box@width% \raisebox{\arrow@width}{\textcolor{Black}{\vrule height0.25pt depth0.25pt width\box@width}}% \fi% \else% \xdef\last@{color}% \ifx\second@@\last@% \setlength\arrow@height{\fill@char\box@height}% \setlength\arrow@height{\sc@le@stretch\arrow@height}% \divide\arrow@height by 100\relax% \raisebox{0.2\box@height}{% \hbox to \box@width{\hss{\textcolor{\f@color}{\vrule height\arrow@height width\box@width}}\hss}}% \else% \xdef\last@{plotcolor}% \ifx\second@@\last@% \xdef\fill@char{\fill@char,&}% \loop% \expandafter\get@firstv@l\fill@char% \ifx\second@@\N@\hbox to \box@width{\hss}% \else \loopcount=\second@@% \ifx\T@coffee@ccons\y@% \else% \advance\loopcount by -\pm@shift% \advance\loopcount by 4% \divide\loopcount by 5% \multiply\loopcount by 5% \ifnum\loopcount>100\loopcount=100\fi% \ifnum\loopcount<5\loopcount=5\fi% \fi% \setlength\arrow@height{50\box@height}% \divide\arrow@height by 100\relax% \setlength\arrow@height{\sc@le@stretch\arrow@height}% \raisebox{0.2\box@height}{% \hbox to \box@width{\hss{\textcolor{\f@color\the\loopcount}{\vrule height\arrow@height width\box@width}}\hss}}% \fi \ifx\fill@char\ampers@nd\else\repeat% \else% \xdef\last@{plotbar}% \ifx\second@@\last@% \xdef\fill@char{\fill@char,&}% \ifnum\pm@shift>0% \setlength\arrow@width{0pt}% \else \setlength\arrow@width{-\pm@shift\box@height}% \divide\arrow@width by 100% \setlength\arrow@width{\b@r@stretch\arrow@width}% \fi% \loop% \expandafter\get@firstv@l\fill@char% \ifx\second@@\N@\hbox to \box@width{\hss}% \else\relax% \ifx\frame@color\back@color% \else% \setlength\arrow@height{\b@r@stretch\box@height}% \hbox to \box@width{\hss{\textcolor{\back@color}% {\vrule height\arrow@height width\box@width}}\hss}% \kern-\box@width% \fi% \ifx\T@coffee@bcons\y@% \ifnum\second@@=99 \xdef\second@@{0}\fi% \fi \setlength\arrow@height{\second@@\box@height}% \ifx\T@coffee@bcons\y@% \setlength\arrow@height{11\arrow@height}% \fi \divide\arrow@height by 100\relax% \setlength\arrow@height{\b@r@stretch\arrow@height}% \ifdim\arrow@height<0pt% \arrow@height=-\arrow@height% \raisebox{\arrow@width}{% \hbox to \box@width{\hss{\textcolor{\frame@color}% {\vrule depth\arrow@height width0.8\box@width}}\hss}}% \else% \raisebox{\arrow@width}{% \hbox to \box@width{\hss{\textcolor{\frame@color}% {\vrule height\arrow@height width0.8\box@width}}\hss}}\fi% \kern-\box@width% \raisebox{\arrow@width}{\textcolor{Black}% {\vrule height0.25pt depth0.25pt width\box@width}}% \fi \ifx\fill@char\ampers@nd\else\repeat% \else% \xdef\last@{helix}% \ifx\second@@\last@% \fontfamily{cmr}% \fontseries{m}% \fontshape{it}% \selectfont% \ifx\bottop@\temp@\xdef\last@{0.35}\else\xdef\last@{0}\fi% \kern0.15\box@width% \setbox1=\hbox{\ensuremath{\helixhook}\kern-1.13exo\kern-1.02ex}% \arrow@width=\second@\box@width% \divide\arrow@width by \wd1% \arrow@width=2\wd1% \loop% \textcolor{\f@color}{\raisebox{-0.25ex}{\ensuremath{\helixhook}}% \kern-1.13ex\raisebox{0.3ex}{o}}\kern-1.02ex% \advance\arrow@width by \wd1\relax% \ifdim\arrow@width<\second@\box@width \repeat% \textcolor{\f@color}{\raisebox{-0.25ex}{\ensuremath{\helixhook}}}% \else% \xdef\last@{box}% \ifx\second@@\last@% \fontfamily{\featurestyles@family}% \fontseries{\featurestyles@series}% \fontshape{\featurestyles@shape}% \selectfont% \kern-\second@\box@width% \bgroup% \textcolor{\back@color}{% \vrule width\second@\box@width height\box@height depth\box@depth}% \kern-\second@\box@width% \fboxsep-\rule@@thick\fboxrule\rule@@thick% \textcolor{\frame@color}{% \fbox{\makebox[\second@\box@width]% {\vrule\@height\box@height\@depth\box@depth \@width\z@}}}% \egroup% \setbox1=\hbox{\residues@size{\fill@char}}% \temp@count=\wd1 \xdef\wd@{\the\temp@count}% \width@tmp=\second@\box@width% \temp@count=\width@tmp% \xdef\sb@{\the\temp@count}% \ifnum\wd@>\sb@ \xdef\fill@char{}\fi% \hbox to -\second@\box@width{\hss\textcolor{\f@color}% {\residues@size{\fill@char}}\hss}% \else% \expandafter\get@shape\second@@% \xdef\last@{arrow}% \ifx\second@@\last@% \kern-0.75\box@width% \ifx\bottop@\temp@ \xdef\last@{0.35}\else\xdef\last@{-0.55}\fi% \textcolor{\f@color}{% \raisebox{\last@\arrow@height}{% \if\first@@ b \xdef\first@@{,}\fi% \if\first@@ ,% \rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height% \else% \if\first@@ |% \rule{0.1\arrow@height}{2\arrow@height}\kern-0.35\arrow@height% \else% \if\first@@ `\xdef\first@@{'}\fi% \if\first@@ '% \rule[\arrow@height]% {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height% \else% \if\first@@ '% \rule[\arrow@height]% {0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height% \else% \if\first@@ -% \rule{0pt}{0pt}\kern-0.35\arrow@height% \fi% \fi% \fi% \fi% \fi% \if\third@@ v% \if\first@@ v% \ensuremath{\overleftarrow{\hbox to % \second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% \kern-\arrow@width% \ensuremath{\overrightarrow{\hbox% {\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% \else% \ensuremath{\overrightarrow{\hbox to % \second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% \fi% \else% \if\first@@ v% \ensuremath{\overleftarrow{\hbox to % \second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}% \else \kern0.35\arrow@height% \rule[0.9\arrow@height]{\second@\box@width}{0.1\arrow@height}% \kern0.35\arrow@height% \fi \if\third@@ ,% \kern-0.4\arrow@height\rule{0.1\arrow@height}{\arrow@height}% \else% \if\third@@ |% \kern-0.4\arrow@height\rule{0.1\arrow@height}{2\arrow@height}% \else% \if\third@@ `\xdef\third@@{'}\fi% \if\third@@ '% \kern-0.4\arrow@height% \rule[\arrow@height]{0.1\arrow@height}{\arrow@height}% \fi% \fi% \fi% \fi}}% \else% \xdef\last@{doublearrow}% \ifx\second@@\last@% \setbox1=\hbox{\ensuremath{\Rightarrow}}% \arrow@height=\ht1% \arrow@width=\wd1% \setbox1=\hbox to \second@\box@width{}% \width@tmp=\wd1% \kern-0.75\box@width% \xdef\temp@{top}% \ifx\bottop@\temp@ \xdef\last@{0.25}% \else% \xdef\temp@{ttop}% \ifx\bottop@\temp@ \xdef\last@{0.25}% \else% \xdef\temp@{tttop}% \ifx\bottop@\temp@ \xdef\last@{0.25}% \else% \xdef\temp@{ttttop}% \ifx\bottop@\temp@ \xdef\last@{0.25}% \else% \xdef\last@{-0.25}\fi\fi\fi\fi% \textcolor{\f@color}{% \raisebox{\last@\arrow@height}{% \if\first@@ b \xdef\first@@{,}\fi% \if\first@@ ,% \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% \kern-0.1\arrow@height% \else% \if\first@@ |% \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}% \kern-0.1\arrow@height% \else% \if\first@@ a \xdef\first@@{'}\fi% \if\first@@ ` \xdef\first@@{'}\fi% \if\first@@ '% \rule[0.4\arrow@height]% {0.1\arrow@height}{1.5\arrow@height}% \kern-0.1\arrow@height% \else% \if\first@@ <% \ensuremath{\Leftarrow}\kern-0.5\arrow@width% \advance\width@tmp by -0.5\arrow@width \else \rule{0pt}{0pt}% \fi% \fi% \fi% \fi% \if\third@@ >% \advance\width@tmp by -0.5\arrow@width% \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}% \kern-\width@tmp% \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}% \kern-0.5\arrow@width\ensuremath{\Rightarrow}% \else% \rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}% \kern-\width@tmp% \rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}% \if\first@@ b \xdef\first@@{,}\fi% \if\third@@ ,% \kern-0.05\arrow@height% \rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% \else% \if\third@@ |% \kern-0.05\arrow@height% \rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}% \else% \if\first@@ a \xdef\first@@{'}\fi% \if\third@@ ` \xdef\third@@{'}\fi% \if\third@@ '% \kern-0.05\arrow@height% \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% \else% \if\third@@ a% \kern-0.05\arrow@height% \rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}% \fi% \fi% \fi% \fi% \fi}}% \else \loopcount=0\relax% \width@tmp=\arrow@height% \temp@@length=\rule@@thick% \advance\width@tmp by -0.5\temp@@length% \if\first@@ o\xdef\first@@{O}\fi% \if\third@@ o\xdef\third@@{O}\fi% \xdef\last@{bottom}% \ifx\fe@turep@s\last@% \vspace{-20pt}\message{(((-20pt)))}% \fi% \textcolor{\f@color}{% \if\first@@ ,% \rule{\temp@@length}{\arrow@height}\kern-\temp@@length% \else% \if\first@@ b% \xdef\last@{bottom}% \ifx\fe@turep@s\last@% \rule{\temp@@length}{\arrow@height}\kern-\temp@@length% \else \xdef\shift@feature{y}% \kern-\temp@@length% \rule[-\bar@length]{\temp@@length}{\bar@length}% \kern-\temp@@length% \rule{\temp@@length}{\arrow@height}\kern-\temp@@length% \fi \else% \if\first@@ |% \rule{\temp@@length}{2\arrow@height}\kern-\temp@@length% \else% \if\first@@ O% \raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex% \rule[\width@tmp]{0.65ex}{\temp@@length}% \else% \if\first@@ S% \xdef\last@{bottom}% \ifx\fe@turep@s\last@% \advance\width@tmp by 0.5\temp@@length% \kern0.5\box@width% \kern-2\temp@@length% \rule[\width@tmp]{\temp@@length}{\arrow@height}% \advance\width@tmp by -0.5\temp@@length% \kern-\temp@@length% \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% \rule[\width@tmp]{0.5\box@width}{\temp@@length}% \else% \kern0.5\box@width% \kern-2\temp@@length% \rule{\temp@@length}{\arrow@height}% \kern-\temp@@length% \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% \rule[\width@tmp]{0.5\box@width}{\temp@@length}% \fi% \else% \if\first@@ c% \xdef\last@{bottom}% \ifx\fe@turep@s\last@% \advance\width@tmp by 0.5\temp@@length% \raisebox{\arrow@height}{\rule[\box@height]{0pt}{\bar@length}}%%%%%%%%%%%%%%%%%%%%%%% \kern0.5\box@width% \kern-2\temp@@length% \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%% \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%% \rule[\width@tmp]{\temp@@length}{\arrow@height}% \advance\width@tmp by -0.5\temp@@length% \kern-\temp@@length% \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% \rule[\width@tmp]{0.5\box@width}{\temp@@length}% \else% \xdef\shift@feature{y}% \kern0.5\box@width% \kern-2\temp@@length% \rule[-\bar@length]{\temp@@length}{\bar@length}% \kern-\temp@@length% \rule{\temp@@length}{\arrow@height}% \kern-\temp@@length% \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% \rule[\width@tmp]{0.5\box@width}{\temp@@length}% \fi% \else% \if\first@@ <% \raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex% \else \if\first@@ `\xdef\first@@{'}\fi% \if\first@@ '% \advance\width@tmp by 0.5\temp@@length% \rule[\width@tmp]{\temp@@length}{\arrow@height}\kern-\temp@@length% \advance\width@tmp by -0.5\temp@@length% \fi% \fi% \fi% \fi% \fi% \fi% \fi% \fi% \loopcount=\second@% \if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% \if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% \if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% \if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% \if\first@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% \if\third@@ S\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% \if\first@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% \if\third@@ c\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi% \xdef\second@{\the\loopcount}% \rule[\width@tmp]{\second@\box@width}{\temp@@length}% \setbox1=\hbox{\residues@size{\fill@char}}% \kern-\second@\box@width% \hbox to \second@\box@width{\textcolor{\backtext@color}{\hss\rule[\width@tmp]{1.2\wd1}{\temp@@length}\hss}}% \kern-\second@\box@width% \hbox to \second@\box@width{\textcolor{\frame@color}{\residues@size{\hss\fill@char\hss}}}% \if\third@@ ,% \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% \else% \if\third@@ b% \xdef\last@{bottom}% \ifx\fe@turep@s\last@% \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% \else \xdef\shift@feature{y}% \kern-\temp@@length% \rule[-\bar@length]{\temp@@length}{\bar@length}% \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% \fi \else% \if\third@@ |% \kern-\temp@@length\rule{\temp@@length}{2\arrow@height}% \else% \if\third@@ O% \rule[\width@tmp]{0.65ex}{\temp@@length}% \kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}% \else% \if\third@@ S% \rule[\width@tmp]{0.5\box@width}{\temp@@length}% \rule[\width@tmp]{0.5\temp@@length}{\temp@@length}% \xdef\last@{bottom}% \ifx\fe@turep@s\last@% \advance\width@tmp by 0.5\temp@@length% \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}% \else \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% \fi% \else% \if\third@@ c% \xdef\shift@feature{y}% \rule[\width@tmp]{0.5\box@width}{\temp@@length}% \xdef\last@{bottom}% \ifx\fe@turep@s\last@% \kern-\temp@@length%%%%%%%%%%%%%%%%%%%%%%%%% \rule[2\arrow@height]{\temp@@length}{\bar@length}%%%%%%%%%%%%%%%%%%%%%% \advance\width@tmp by 0.5\temp@@length% \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}% \else \kern-\temp@@length\rule[-\bar@length]{\temp@@length}{\bar@length}% \kern-\temp@@length\rule{\temp@@length}{\arrow@height}% \fi% \else% \if\third@@ >% \kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}% \else \if\third@@ `\xdef\third@@{'}\fi% \if\third@@ '% \advance\width@tmp by 0.5\temp@@length% \kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}% \fi% \fi% \fi% \fi% \fi% \fi% \fi% \fi}% \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi \fi } \def\next@featuretext#2;#3@{% \xdef\first@{#3@}% \xdef\last@{fill:#2:&}\expandafter\test@fill\last@% \ifx\f@color\comm@\xdef\f@color{Black}\fi% \fontfamily{\featuretext@family}% \fontseries{\featuretext@series}% \fontshape{\featuretext@shape}% \selectfont% \xdef\last@{translate}% \ifx\last@\second@@% \xdef\fill@char{\fill@char &}% \if\seq@type N \loop% \expandafter\get@firstfill\fill@char% \if\second@@ -\def\second@@{\hss}\fi% \hbox to \box@width{\hss\textcolor{\f@color}{% \featuretext@size{\strut\second@@}}\hss}% \ifx\fill@char\ampers@nd\else\repeat% \else \hbox to #1\box@width{\hss% \temp@count=1% \loop% \expandafter\get@tripletfill\fill@char% \if\second@@ -\ifnum\tr@nstextstyle>0\hbox to \box@width{\hss}\fi% \else% \ifcase\tr@nstextstyle% \hbox{\transtext@size\textcolor{\f@color}% {\hss\second@@\second@@@\second@@@@\,\hss}}% \or% \ifnum\temp@count=1% \vbox{\transtext@size% \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% \else% \vbox{\transtext@size% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}}% \fi% \or% \ifnum\temp@count=1% \vbox{\transtext@size% \hbox to \box@width{\textcolor{\f@color}% {\hss\second@@\second@@@\second@@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss}}}% \else% \vbox{\transtext@size% \hbox to \box@width{\textcolor{\f@color}{\hss}}% \hbox to \box@width{\textcolor{\f@color}% {\hss\second@@\second@@@\second@@@@\hss}}}% \fi% \or% \vbox{\transtext@size% \hbox to \box@width{\textcolor{\f@color}{\second@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@}}}% \or% \vbox{\transtext@size% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@\hss}}% \hbox to \box@width{\textcolor{\f@color}{\hss\second@@@@\hss}}}% \fi% \fi% \ifx\fill@char\ampers@nd\else\repeat% \hss} \fi% \else% \textcolor{\f@color}{% \hbox to #1\box@width{\hss\featuretext@size{\strut\fourth@}\hss}}% \fi% \advance\loopcount by -#1% } \def\put@featuretext{% \if\first@ @% \else \expandafter\next@featuretext\first@% \put@featuretext% \fi} \def\next@featurestyle#2;#3@{% \xdef\first@{#2}% \xdef\second@{#1}% \ifx\first@\ampers@nd \hbox to \second@\box@width{\hss}% \else% \hbox to \second@\box@width% {\hss\expandafter\putfeature@style{\first@}\hss}\fi% \xdef\first@{#3@}% \advance\loopcount by -\second@% } \def\put@featurestyle{% \if\first@ @% \else \expandafter\next@featurestyle\first@% \put@featurestyle% \fi } \def\put@feature{% \vspace{-\baselineskip}% \newline\hbox{}% \xdef\temp@{ttttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featuretext% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{tttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featuretext% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{ttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featuretext% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{top}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featuretext% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \else \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featurestyle% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \fi\fi\fi\fi% \newline\hbox{}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featurestyle% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else% \xdef\temp@{ttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featurestyle% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else \xdef\temp@{tttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featurestyle% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else \xdef\temp@{ttttop}% \ifx\temp@\bottop@% \ifnames@right\else\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname stylefeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featurestyle% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\fstyles@family}\fontseries{\fstyles@series}\fontshape{\fstyles@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname fstyles@fg@\bottop@\endcsname}{\hbox to \name@width{\fstyles@size\csname featurestylesn@me\bottop@\endcsname\hss}}\fi\fi% \else \ifnames@right\else\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \xdef\first@{\csname textfeature\bottop@\endcsname @}% \loopcount=\res@perline% \put@featuretext% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \ifnames@right\ifnames@% \fontfamily{\ftext@family}\fontseries{\ftext@series}\fontshape{\ftext@shape}% \selectfont% \kern1em\hbox to \loopcount\box@width{\hss}% \textcolor{\csname ftext@fg@\bottop@\endcsname}{\hbox to \name@width{\ftext@size\csname featuretextn@me\bottop@\endcsname\hss}}\fi\fi% \fi\fi\fi\fi% \newline\hbox{}% } \def\put@@@frame#1{% \xdef\last@{#1[,]&}\expandafter\opt@color\last@% \xdef\second@@{\fourth@}% \ifx\f@color\comm@% \xdef\third@@{0.2\box@width}% \else% \xdef\third@@{\f@color}% \fi% \setlength\arrow@width{\temp@@length}% \advance\arrow@width by -\third@@% \textcolor{\second@@}{% \rule{\second@\box@width}{\third@@}% \kern-\second@\box@width% \rule{\third@@}{\arrow@width}% \kern-\third@@% \rule[\arrow@width]{\second@\box@width}{\third@@}% \kern-\third@@% \rule{\third@@}{\arrow@width}}% } \def\next@frame#2;#3@{% \xdef\first@{#2}% \xdef\second@{#1}% \ifx\first@\ampers@nd \hbox to \second@\box@width{\hss}% \else% \expandafter\put@@@frame{\first@}% \fi% \xdef\first@{#3@}% } \def\put@@frame{% \if\first@ @% \else \expandafter\next@frame\first@% \put@@frame% \fi% } \def\put@frame{% \ifx\hide@seqs\n@% \ifshow@cons\ifnum\cons@top=1 \vspace{-\baselineskip}\fi\fi% \temp@count=\seq@count% \ifx\hide@seqs\y@ \advance\temp@count by -1 \else \loopcount=1% \xdef\first@{true}% \loop% \expandafter\ifx\csname hide@seq\the\loopcount\endcsname\first@% \advance\temp@count by -1\fi% \advance\loopcount by 1% \ifnum\loopcount>\seq@count\else\repeat% \fi \ifnum\temp@count>0% \setlength\temp@@length{\box@height}% \advance\temp@@length by \box@depth% \setlength\arrow@height{0.5\temp@@length}% \setlength\temp@@length{\temp@count\temp@@length}% \advance\temp@@length by \arrow@height% \setlength\arrow@width{\sep@space}% \setlength\arrow@width{\seq@gap@num\arrow@width}% \advance\temp@@length by \arrow@width% \vspace{\arrow@height}% \vspace{-\temp@@length}% \vspace{-\baselineskip}% \newline\hbox{}% \ifnames@right\else\ifnames@\hbox to \name@width{\hss}\fi\fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \xdef\first@{\styleframe @}% \put@@frame% \vspace{-\arrow@height}% \ifshow@cons\ifnum\cons@top=1 \vspace{\baselineskip}\fi\fi% \newline\hbox{}% \fi% \fi% } \def\decimal@A#1#2@{% \def\decimal@AB##1##2@{\xdef\temp@{##1.##2}}% \xdef\temp@@{#1}% \xdef\temp@{#2@}% \expandafter\decimal@AB\temp@% \xdef\temp@{\temp@@\temp@}% } \def\decimal@B#1#2@{\xdef\temp@{#1.#2}} \def\decimal@C#1#2@{\xdef\temp@{0.#1#2}} \def\decimal@D#1#2@{\xdef\temp@{0.0#1#2}} \def\decimal@E#1#2@{\xdef\temp@{0.00#1#2}} \def\correct@CGSO{% \setlength\temp@@length{0.12\logo@height}% \multiply\temp@@length by \third@ % \if\seq@type P % \divide\temp@@length by 4322 % \else% \divide\temp@@length by 4000 % \fi% \loopcount=\third@% \multiply\loopcount by 94 % \divide\loopcount by 100 % \xdef\third@{\the\loopcount}% } \def\correct@Q{% \setlength\temp@@length{0.063\logo@height}% \multiply\temp@@length by \third@% \if\seq@type P % \divide\temp@@length by 4322 % \else% \divide\temp@@length by 4000 % \fi% \multiply\temp@@length by 10 % \loopcount=\third@% \multiply\loopcount by 83 % \divide\loopcount by 100 % \xdef\third@{\the\loopcount}% } \def\correct@JUV{% \setlength\temp@@length{0.12\logo@height}% \multiply\temp@@length by \third@ % \if\seq@type P % \divide\temp@@length by 4322 % \else% \divide\temp@@length by 4000 % \fi% \loopcount=\third@% \multiply\loopcount by 97 % \divide\loopcount by 100 % \xdef\third@{\the\loopcount}% } \def\next@logo#1:#2,#3@{% \xdef\first@{#1}\xdef\second@{#2}\xdef\last@{#3}% \ifx\first@\ampers@nd% \ifx\clear@logo\n@% \ifx\hide@sig\n@% \expandafter\firstchar@get\sublogo@sig% \xdef\sublogo@sig{\third@}% \ifx\first@\y@% \loopcount=\temp@count% \ifnum\loopcount<0 \loopcount=0\fi% \xdef\fourth@{\the\loopcount @}% \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% \expandafter\decimal@E\fourth@% \fi\fi\fi\fi% \raisebox{\temp@\logo@height}{% \hbox to \box@width{\textcolor{\sig@color}{\hss\residues@size{\sig@char}\hss}}}% \kern-\box@width% \fi% \fi% \fi% \temp@count=0% \kern\box@width% \advance\outerloopcount by 1 % \else% \ifnum#2=1% \temp@count=0% \else% \if\seq@type N% \loopcount=\second@% \multiply\loopcount by 2% \xdef\second@{\the\loopcount}% \fi% \xdef\third@{\second@}% \if\first@ C\correct@CGSO \else% \if\first@ G\correct@CGSO \else% \if\first@ S\correct@CGSO \else% \if\first@ O\correct@CGSO \else% \if\first@ Q\correct@Q \else% \if\first@ J\correct@JUV \else% \if\first@ U\correct@JUV \else% \if\first@ V\correct@JUV \else% \setlength\temp@@length{0pt}% \fi\fi\fi\fi\fi\fi\fi\fi% \loopcount=\third@ \multiply\loopcount by \logo@stretch@IOOO% \ifnum\loopcount>0 % \divide\loopcount by 1000 \xdef\fl@g{}% \xdef\tint@{}% \else% \divide\loopcount by -1000 \xdef\fl@g{-}% \xdef\tint@{\sublogo@tint}% \fi% \ifnum\loopcount=0\relax\loopcount=1\relax\fi \xdef\third@{\the\loopcount @}% \ifnum\loopcount>9999 \expandafter\decimal@A\third@ \else% \ifnum\loopcount>999 \expandafter\decimal@B\third@ \else% \ifnum\loopcount>99 \expandafter\decimal@C\third@ \else% \ifnum\loopcount>9 \expandafter\decimal@D\third@ \else% \expandafter\decimal@E\third@% \fi\fi\fi\fi% \xdef\third@{\fl@g\temp@}% \ifnum\temp@count<0 % \ifnum\second@<0 \else\temp@count=0 \fi% \fi% \ifnum\temp@count>0 % \loopcount=\temp@count \xdef\fl@g{}% \else \loopcount=-\temp@count \xdef\fl@g{-}% \fi% \xdef\fourth@{\the\loopcount @}% \ifnum\loopcount>9999 \expandafter\decimal@A\fourth@ \else% \ifnum\loopcount>999 \expandafter\decimal@B\fourth@ \else% \ifnum\loopcount>99 \expandafter\decimal@C\fourth@ \else% \ifnum\loopcount>9 \expandafter\decimal@D\fourth@ \else% \expandafter\decimal@E\fourth@% \fi\fi\fi\fi% \xdef\fourth@{\fl@g\temp@}% \if\first@ W% \hbox to \box@width{\hss% \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch@W}[\third@]% {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{W}\hss}}}}}\hss}% \kern-\box@width% \else% \hbox to \box@width{\hss% \raisebox{\temp@@length}{\raisebox{\fourth@\logo@height}{\scalebox{\char@stretch}[\third@]% {\hbox to \box@width{\textcolor{\tint@\csname logo@col\first@\endcsname}{\hss\residues@size{\first@}\hss}}}}}\hss}% \kern-\box@width% \fi% \advance\temp@count by \second@% \fi% \fi% \xdef\temp@{\last@.}% \ifx\temp@\d@t% \else% \xdef\last@{#3@}% \ifnum\outerloopcount>\res@perline% \else \expandafter\next@logo\last@% \fi% \fi% } \def\put@logo{% \ifx\clear@logo\y@% \ifnum\logo@top=1 % \vspace{-0.5\baselineskip}% \else \vspace{-0.75\baselineskip}% \fi% \else% \ifnum\sublogo@top=1 % \vspace{-0.5\baselineskip}% \else \vspace{-0.75\baselineskip}% \fi% \fi% \newline\hbox{}% \ifnames@right% \else% \fontfamily{\namestext@family}\fontseries{\namestext@series}\fontshape{\namestext@shape}% \selectfont% \ifnames@ \textcolor{\names@fg}{% \raisebox{2\logo@height}{\hbox to \name@width{\namestext@size{\logo@name}\hss}}% \ifx\clear@logo\n@ \ifx\hide@negatives\n@% \kern-\name@width\raisebox{-3\logo@height}{\hbox to \name@width{\namestext@size{\sublogo@name@neg}\hss}}% \fi% \fi}% \fi% \fi% \ifnumbers@left\ifnumbers@\hbox to \number@width{\hss}\fi\fi% \fontfamily{cmss}\fontseries{m}\fontshape{n}\selectfont% \ifx\show@logoscale\n@% \if\seq@type P% \ifnum\corr@max>600\relax% \rule[5.4\logo@height]{0pt}{0pt}% \else% \rule[4.4\logo@height]{0pt}{0pt}% \fi% \else% \rule[4.0688\logo@height]{0pt}{0pt}% \fi% \else% \xdef\first@{right}% \ifx\show@logoscale\first@% \else% \textcolor{\logo@scalecol}{% \kern-0.7\box@width% \rule[-0.05\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[2\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[4\logo@height]{0.4\box@width}{0.1\box@width}% \if\seq@type P% \kern-0.4\box@width% \rule[1\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[3\logo@height]{0.4\box@width}{0.1\box@width}% \ifnum\corr@max>600\relax% \kern-0.4\box@width\rule[5\logo@height]{0.4\box@width}{0.1\box@width}\fi% \setbox1=\hbox{\bottomruler@size 2}% \kern-1.2\box@width% \ifdim\logo@height>1.25\ht1 \relax% \raisebox{-0.5\ht1}{\raisebox{1\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 1}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{3\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 3}}}% \kern-0.6\box@width% \ifnum\corr@max>600\relax% \raisebox{-0.5\ht1}{\raisebox{5\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 5}}}% \kern-0.6\box@width% \fi \fi \raisebox{-0.5\ht1}{\raisebox{2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 2}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 4}}}% \kern0.6\box@width% \ifnum\corr@max>600\relax% \rule[5.4\logo@height]{0pt}{0pt}% \else \rule[4.4\logo@height]{0pt}{0pt}% \fi \else% \setbox1=\hbox{\bottomruler@size 2}% \kern-1.2\box@width% \raisebox{-0.5\ht1}{\raisebox{2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 1}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss 2}}}% \kern0.6\box@width% \rule[4.0688\logo@height]{0pt}{0pt}% \fi% \kern-0.1\box@width% \ifnum\corr@max>600\relax% \rule{0.1\box@width}{5\logo@height}% \else% \rule{0.1\box@width}{4\logo@height}% \fi% \ifx\clear@logo\n@% \ifx\hide@negatives\n@% \kern-0.4\box@width% \rule[-2\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[-4\logo@height]{0.4\box@width}{0.1\box@width}% \if\seq@type P% \kern-0.4\box@width% \rule[-\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[-3\logo@height]{0.4\box@width}{0.1\box@width}% \ifnum\corr@max>600\relax% \kern-0.4\box@width\rule[-5\logo@height]{0.4\box@width}{0.1\box@width}\fi% \setbox1=\hbox{\bottomruler@size 2}% \kern-1.2\box@width% \ifdim\logo@height>1.25\ht1 \relax% \raisebox{-0.5\ht1}{\raisebox{-\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -1}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{-3\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -3}}}% \kern-0.6\box@width% \ifnum\corr@max>600\relax% \raisebox{-0.5\ht1}{\raisebox{-5\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -5}}}% \kern-0.6\box@width% \fi \fi \raisebox{-0.5\ht1}{\raisebox{-2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -2}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{-4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -4}}}% \kern0.6\box@width% \ifnum\corr@max>600\relax% \rule[-5.4\logo@height]{0pt}{0pt}% \else \rule[-4.4\logo@height]{0pt}{0pt}% \fi \else% \setbox1=\hbox{\bottomruler@size 2}% \kern-1.2\box@width% \raisebox{-0.5\ht1}{\raisebox{-2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -1}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{-4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size\hss -2}}}% \kern0.6\box@width% \rule[-4.0688\logo@height]{0pt}{0pt}% \fi% \kern-0.1\box@width% \ifnum\corr@max>600\relax% \rule[-5\logo@height]{0.1\box@width}{5\logo@height}% \else% \rule[-4\logo@height]{0.1\box@width}{4\logo@height}% \fi% \fi% \fi \kern0.3\box@width}% \fi% \fi% \temp@count=0% \outerloopcount=1 \expandafter\next@logo\last@% \ifx\clear@logo\n@% \ifx\hide@negatives\n@% \textcolor{\logo@scalecol}{% \kern-\res@perline\box@width\rule[-0.03\box@width]{\res@perline\box@width}{0.06\box@width}}% \fi% \fi% \def\@kern{\kern1em}% \ifx\show@logoscale\n@% \else% \xdef\first@{left}% \ifx\show@logoscale\first@% \kern0.1\box@width% \else% \def\@kern{\kern2em}% \textcolor{\logo@scalecol}{% \kern0.3\box@width% \rule[-0.05\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[2\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[4\logo@height]{0.4\box@width}{0.1\box@width}% \if\seq@type P% \kern-0.4\box@width% \rule[1\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[3\logo@height]{0.4\box@width}{0.1\box@width}% \ifnum\corr@max>600\relax% \kern-0.4\box@width\rule[5\logo@height]{0.4\box@width}{0.1\box@width}\fi% \setbox1=\hbox{\bottomruler@size 2}% \kern0.2\box@width% \ifdim\logo@height>1.25\ht1 \relax% \raisebox{-0.5\ht1}{\raisebox{1\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 1 \hss}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{3\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 3 \hss}}}% \kern-0.6\box@width% \ifnum\corr@max>600\relax% \raisebox{-0.5\ht1}{\raisebox{5\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 5 \hss}}}% \kern-0.6\box@width% \fi \fi \raisebox{-0.5\ht1}{\raisebox{2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 2 \hss}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 4 \hss}}}% \kern-0.8\box@width% \ifnum\corr@max>600\relax% \rule[5.4\logo@height]{0pt}{0pt}% \else \rule[4.4\logo@height]{0pt}{0pt}% \fi \else% \setbox1=\hbox{\bottomruler@size 2}% \kern0.2\box@width% \raisebox{-0.5\ht1}{\raisebox{2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 1 \hss}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size 2 \hss}}}% \kern-0.8\box@width% \rule[4.0688\logo@height]{0pt}{0pt}% \fi% \kern-0.4\box@width% \ifnum\corr@max>600\relax% \rule{0.1\box@width}{5\logo@height}% \else% \rule{0.1\box@width}{4\logo@height}% \fi% \ifx\clear@logo\n@% \ifx\hide@negatives\n@% \kern-0.1\box@width% \rule[-2\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[-4\logo@height]{0.4\box@width}{0.1\box@width}% \if\seq@type P% \kern-0.4\box@width% \rule[-\logo@height]{0.4\box@width}{0.1\box@width}\kern-0.4\box@width% \rule[-3\logo@height]{0.4\box@width}{0.1\box@width}% \ifnum\corr@max>600\relax% \kern-0.4\box@width\rule[-5\logo@height]{0.4\box@width}{0.1\box@width}\fi% \setbox1=\hbox{\bottomruler@size 2}% \kern0.2\box@width% \ifdim\logo@height>1.25\ht1 \relax% \raisebox{-0.5\ht1}{\raisebox{-\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -1 \hss}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{-3\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -3 \hss}}}% \kern-0.6\box@width% \ifnum\corr@max>600\relax% \raisebox{-0.5\ht1}{\raisebox{-5\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -5 \hss}}}% \kern-0.6\box@width% \fi \fi \raisebox{-0.5\ht1}{\raisebox{-2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -2 \hss}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{-4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -4 \hss}}}% \kern-0.8\box@width% \ifnum\corr@max>600\relax% \rule[-5.4\logo@height]{0pt}{0pt}% \else \rule[-4.4\logo@height]{0pt}{0pt}% \fi \else% \setbox1=\hbox{\bottomruler@size 2}% \kern0.2\box@width% \raisebox{-0.5\ht1}{\raisebox{-2\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -1 \hss}}}% \kern-0.6\box@width% \raisebox{-0.5\ht1}{\raisebox{-4\logo@height}{\hbox to 0.6\box@width{\bottomruler@size -2 \hss}}}% \kern-0.8\box@width% \rule[-4.0688\logo@height]{0pt}{0pt}% \fi% \kern-0.4\box@width% \ifnum\corr@max>600\relax% \rule[-5\logo@height]{0.1\box@width}{5\logo@height}% \else% \rule[-4\logo@height]{0.1\box@width}{4\logo@height}% \fi% \fi% \fi% \kern-0.3\box@width}% \fi% \fi% \ifnumbers@right\ifnumbers@\hbox to \number@width{\hss}\def\@kern{\kern1em}\fi\fi% \ifnames@right% \fontfamily{\namestext@family}\fontseries{\namestext@series}\fontshape{\namestext@shape}% \selectfont% \ifnames@ \textcolor{\names@fg}{% \raisebox{2\logo@height}{\hbox to \name@width{\namestext@size{\@kern\logo@name}\hss}}% \ifx\clear@logo\n@ \ifx\hide@negatives\n@% \kern-\name@width\raisebox{-3\logo@height}{\hbox to \name@width{\namestext@size{\@kern\sublogo@name@neg}\hss}}% \fi% \fi}% \fi% \fi% \ifx\clear@logo\y@\xdef\stack@sequencelogo{}% \else% \ifx\hide@negatives\n@ \newline\hbox{}\fi% \fi% \newline\hbox{}% } \def\set@lines{% \pos@count=1 \xdef\frame@pos{1}\xdef\bar@pos{0}% \xdef\featurepostop{1} \xdef\featureposbottom{1}% \xdef\featureposttop{1} \xdef\featureposbbottom{1}% \xdef\featurepostttop{1} \xdef\featureposbbbottom{1}% \xdef\featureposttttop{1} \xdef\featureposbbbbottom{1}% \findc@nsensus% \noindent% \setlength{\bar@length}{0pt}% \xdef\fe@turep@s{top}% \ifnum\feature@ttttop=1 \advance\bar@length by \feature@tttop\baselineskip% \advance\bar@length by \feature@ttop\baselineskip% \advance\bar@length by \feature@top\baselineskip% \multiply\bar@length by 2% \advance\bar@length by \tttt@sp@ce% \advance\bar@length by \ttt@sp@ce% \advance\bar@length by \tt@sp@ce% \ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi \xdef\bottop@{ttttop}% \xdef\shift@feature{n}% \put@feature% \advance\bar@length by -\baselineskip% \ifx\shift@feature\y@ \vspace{-\bar@length}\fi% \setlength{\bar@length}{0pt}% \vspace{\tttt@sp@ce}% \vspace{-\baselineskip}% \newline\hbox{}% \else \iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi \fi \ifnum\feature@tttop=1 \advance\bar@length by \feature@ttop\baselineskip% \advance\bar@length by \feature@top\baselineskip% \multiply\bar@length by 2% \advance\bar@length by \ttt@sp@ce% \advance\bar@length by \tt@sp@ce% \ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi \xdef\bottop@{tttop}% \xdef\shift@feature{n}% \put@feature% \advance\bar@length by -\baselineskip% \ifx\shift@feature\y@ \vspace{-\bar@length}\fi% \setlength{\bar@length}{0pt}% \vspace{\ttt@sp@ce}% \vspace{-\baselineskip}% \newline\hbox{}% \else \iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi \fi \ifnum\feature@ttop=1 \advance\bar@length by \feature@top\baselineskip% \multiply\bar@length by 2% \advance\bar@length by \tt@sp@ce\message{tt\the\bar@length tt}% \ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi \xdef\bottop@{ttop}% \xdef\shift@feature{n}% \put@feature% \advance\bar@length by -\baselineskip% \ifx\shift@feature\y@ \vspace{-\bar@length}\fi% \setlength{\bar@length}{0pt}% \vspace{\tt@sp@ce}% \vspace{-\baselineskip}% \newline\hbox{}% \else \iffix@\ifttopfeature \vspace{\tt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi \fi \ifnum\feature@top=1 \ifnum\featureontop=0 \xdef\feature@top{0} \fi \xdef\bottop@{top}% \put@feature% \vspace{\t@sp@ce}% \vspace{-\baselineskip}% \newline\hbox{}% \else \iffix@\iftopfeature \vspace{\t@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi \fi \ifnum\rule@num<0 \else \ifnum\rule@top=0 \loopcount=0 \put@ruler \fi\fi \ifshow@logo\ifnum\logo@top=0 \xdef\last@{\stack@sequencelogo @}% \ifx\logo@name@user\ampers@nd\xdef\logo@name{logo}\else\xdef\logo@name{\logo@name@user}\fi \xdef\clear@logo{y}% \put@logo% \xdef\clear@logo{n}% \fi\fi \ifshow@sublogo\ifnum\sublogo@top=0 \read@sublogo% \xdef\last@{\stack@sublogo @}% \ifx\sublogo@name@user\ampers@nd\xdef\logo@name{subfamily}\else\xdef\logo@name{\sublogo@name@user}\fi \put@logo% \fi\fi \set@consensus \ifshow@cons\ifnum\cons@top=0 \xdef\cons@now{y}% \xdef\first@{\consensus @}% \xdef\first@@@{\c@nscol @}% \loopcount=0\relax% \put@line% \xdef\c@nscol{}% \xdef\cons@now{no}% \fi\fi \ifx\hide@seqs\n@% \loopcount=0 % \loop \advance\loopcount by 1 % \xdef\second@{\csname hide@seq\the\loopcount\endcsname}% \xdef\first@{noshade}\nosh@defalse% \ifx\second@\first@ \nosh@detrue \xdef\second@{false}\fi \xdef\first@{false}% \ifx\second@\first@ \ifnames@right \ifnumbers@right \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% \csname res@count\the\loopcount\endcsname)% <\csname newseqname\the\loopcount\endcsname>}% \else \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% <\csname newseqname\the\loopcount\endcsname>}% \fi \else \ifnumbers@right \expandafter\xdef\csname seq\the\loopcount\endcsname{% \csname seq\the\loopcount\endcsname% \csname res@count\the\loopcount\endcsname)}% \fi \fi \xdef\first@{\csname seq\the\loopcount\endcsname @}% \expandafter\ifx\csname seq@gap\the\loopcount\endcsname\yes% \ifnum\finger@linenum=0\seq@skip% \else% \ifnum\loopcount<\seq@count\seq@skip\fi% \fi% \fi% \put@line% \fi% \ifnum\loopcount<\seq@count\repeat% \fi% \ifshow@cons\ifnum\cons@top=1 % \xdef\cons@now{y}% \xdef\first@{\consensus @}% \xdef\first@@@{\c@nscol @}% \loopcount=0\relax% \put@line% \xdef\c@nscol{}% \xdef\cons@now{no}% \fi\fi% \ifnum\frame@=1 % \ifnum\frame@on=0 \xdef\frame@{0}\fi% \put@frame% \fi% \ifshow@logo\ifnum\logo@top=1 % \xdef\last@{\stack@sequencelogo @}% \ifx\logo@name@user\ampers@nd\xdef\logo@name{logo}\else\xdef\logo@name{\logo@name@user}\fi \xdef\clear@logo{y}% \put@logo% \xdef\clear@logo{n}% \fi\fi% \ifshow@sublogo\ifnum\sublogo@top=1 \read@sublogo% \xdef\last@{\stack@sublogo @} \ifx\sublogo@name@user\ampers@nd\xdef\logo@name{subfamily}\else\xdef\logo@name{\sublogo@name@user}\fi \put@logo% \fi\fi% \ifnum\rule@num<0 % \else% \ifnum\rule@top=1 % \loopcount=0\relax% \ifnum\ruler@rot=0 % \else \vspace{\ruler@width}\vspace{-1.75\baselineskip}\newline\hbox{}% \fi \put@ruler% \ifnum\ruler@rot=0 \vspace{0.25\baselineskip}\fi% \fi% \fi% \xdef\fe@turep@s{bottom}% \setlength{\bar@length}{0pt}% \xdef\b@feature@count{0} \ifnum\feature@bottom=1 % \ifnum\featureonbottom=0 \xdef\feature@bottom{0}\fi% \xdef\bottop@{bottom}% \vspace{\b@sp@ce}% \if\bottom@stretch y% \vspace{-\box@height}% \vspace{\b@r@stretch\box@height}% \fi% \put@feature% \temp@@count=\b@feature@count% \advance\temp@@count by 1% \xdef\b@feature@count{\the\temp@@count}% \else \iffix@ \if\bottom@stretch y% \vspace{-\box@height}% \vspace{\b@r@stretch\box@height}% \fi% \ifbottomfeature% \vspace{\b@sp@ce}\newline\hbox{}\newline\hbox{}% \fi% \fi% \fi% \ifnum\feature@bbottom=1 % \advance\bar@length by \b@feature@count \baselineskip% \multiply\bar@length by \b@r@stretch% \multiply\bar@length by 2% \advance\bar@length by \bb@sp@ce\message{bb\the\bar@length bb}% \ifnum\featureonbbottom=0 \xdef\feature@bbottom{0}\fi% \xdef\bottop@{bbottom}% \vspace{\bb@sp@ce}% \if\bbottom@stretch y% \advance\bar@length by -\box@height% \advance\bar@length by \b@r@stretch\box@height% \vspace{-\box@height}% \vspace{\b@r@stretch\box@height}% \fi% \setlength{\bar@length}{0pt}%%%%%%%%%%%%%%%%%%%%%%% \put@feature% \temp@@count=\b@feature@count% \advance\temp@@count by 1% \xdef\b@feature@count{\the\temp@@count}% \else \iffix@ \if\bbottom@stretch y% \vspace{-\box@height}% \vspace{\b@r@stretch\box@height}% \fi% \ifbbottomfeature \vspace{\bb@sp@ce}\newline\hbox{}\newline\hbox{}% \fi \fi \fi \ifnum\feature@bbbottom=1 % \advance\bar@length by \b@feature@count\baselineskip% \multiply\bar@length by \b@r@stretch% \multiply\bar@length by 2% \advance\bar@length by \bbb@sp@ce\message{bbb\the\bar@length bbb}% \ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi% \xdef\bottop@{bbbottom}% \vspace{\bbb@sp@ce}% \if\bbbottom@stretch y% \vspace{-\box@height}% \vspace{\b@r@stretch\box@height}% \fi% \put@feature% \temp@@count=\b@feature@count% \advance\temp@@count by 1% \xdef\b@feature@count{\the\temp@@count}% \else \iffix@ \if\bbbottom@stretch y% \vspace{-\box@height}% \vspace{\b@r@stretch\box@height}% \fi% \ifbbbottomfeature \vspace{\bbb@sp@ce}\newline\hbox{}\newline\hbox{}% \fi \fi \fi \ifnum\feature@bbbbottom=1 % \advance\bar@length by \b@feature@count\baselineskip% \multiply\bar@length by \b@r@stretch% \multiply\bar@length by 2% \advance\bar@length by \bbbb@sp@ce\message{bbbb\the\bar@length bbbb}% \ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi% \xdef\bottop@{bbbbottom}% \vspace{\bbbb@sp@ce}% \if\bbbbottom@stretch y% \vspace{-\box@height}% \vspace{\b@r@stretch\box@height}% \fi% \put@feature% \else \iffix@ \if\bbbbottom@stretch y% \vspace{-\box@height}% \vspace{\b@r@stretch\box@height}% \fi% \ifbbbbottomfeature \vspace{\bbbb@sp@ce}\newline\hbox{}\newline\hbox{}% \fi \fi \fi \xdef\consensus{} \xdef\ruler@{} \xdef\styleframe{} \xdef\textfeaturetop{} \xdef\textfeaturebottom{} \xdef\textfeaturettop{} \xdef\textfeaturebbottom{} \xdef\textfeaturetttop{} \xdef\textfeaturebbbottom{} \xdef\textfeaturettttop{} \xdef\textfeaturebbbbottom{} \xdef\stylefeaturetop{} \xdef\stylefeaturebottom{} \xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{} \xdef\stylefeaturetttop{} \xdef\stylefeaturebbbottom{} \xdef\stylefeaturettttop{} \xdef\stylefeaturebbbbottom{} \loopcount=0 \loop \advance\loopcount by 1 \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\remove@fromseq\seq@line \ifnum\loopcount<\seq@count \repeat} \def\block@output{% \expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax \message{.} \ifx\out@put\y@ \vbox{\set@lines}\par \block@skip \else \pos@count=1 \findc@nsensus \loopcount=0 \loop \advance\loopcount by 1\relax \xdef\seq@line{\csname sequence\the\loopcount\endcsname} \expandafter\remove@fromseq\seq@line \ifT@coffee \xdef\TC@cons{\csname TC0\endcsname} \expandafter\remove@fromTC\TC@cons \fi \ifnum\loopcount<\seq@count \repeat \fi \ifstop@ \else \advance\seq@pointer by -\res@perline \ifnum\seq@pointer>\res@perline \block@output \fi \fi \fi} %%%%% Basic input routines \def\savedseqlength#1#2#3{% \expandafter\xdef\csname savelength#1seq#2\endcsname{#3}} \def\set@savedseqlength{% \loopcount=0 \loop \advance\loopcount by 1 \expandafter\ifx% \csname savelength\@lign@count seq\the\loopcount\endcsname\relax \else \expandafter\xdef\csname seq@len\the\loopcount\endcsname{% \csname savelength\@lign@count seq\the\loopcount\endcsname} \fi \ifnum\loopcount<\seq@count\repeat } \def\save@lengths{% \loopcount=0 \loop \advance\loopcount by 1\relax \immediate\write\@auxout{% \string\savedseqlength{\@lign@count}{\the\loopcount}% {\csname res@count\the\loopcount\endcsname}} \ifnum\loopcount<\seq@count \repeat } \def\do@cleanup{% \expandafter\firstchar@get\third@ \expandafter\check@char\first@ \ifletter \xdef\second@{\second@\first@} \else \ifnumber \ifx\first@\gre@ter \xdef\second@{\second@{$>$}} \else \ifx\first@\sm@ller \xdef\second@{\second@{$<$}} \else \xdef\second@{\second@\first@} \fi\fi \else \ifnum\code@num=6 \xdef\second@{\second@\#} \else \ifnum\code@num=14 \xdef\second@{\second@\%} \else \xdef\second@{\second@\noexpand\string\first@} \fi\fi \fi \fi \ifx\third@\@t \else \do@cleanup \fi } \def\cleanup@name{% \xdef\third@{\csname seqname\the\loopcount\endcsname @} \xdef\second@{} \do@cleanup \expandafter\xdef\csname newseqname\the\loopcount\endcsname{\second@} } \def\clear@seq{% \loopcount=0 \loop \advance\loopcount by 1 \expandafter\def\csname sequence\the\loopcount\endcsname{} \ifnum\loopcount<\seq@count \repeat \xdef\consensus{} \xdef\constopo{} \xdef\frame@on{0} \xdef\textfeaturetop{} \xdef\featureontop{0} \xdef\textfeaturettop{} \xdef\featureonttop{0} \xdef\textfeaturetttop{} \xdef\featureontttop{0} \xdef\textfeaturettttop{} \xdef\featureonttttop{0} \xdef\textfeaturebottom{} \xdef\featureonbottom{0} \xdef\textfeaturebbottom{} \xdef\featureonbbottom{0} \xdef\textfeaturebbbottom{} \xdef\featureonbbbottom{0} \xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0} \xdef\styleframe{} \xdef\stylefeaturetop{} \xdef\stylefeaturettop{} \xdef\stylefeaturetttop{} \xdef\stylefeaturettttop{} \xdef\stylefeaturebottom{} \xdef\stylefeaturebbottom{} \xdef\stylefeaturebbbottom{} \xdef\stylefeaturebbbbottom{}} \def\guess@protein{\seqtype{P}\message{}} \def\guess@DNA{\seqtype{N}\message{}} \def\allmatch@out{% \xdef\leave@in{n} \loopcount=1 \xdef\seq@line{\csname seq\the\loopcount\endcsname} \expandafter\res@get\seq@line \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line} \ifnum\loopcount=\start@seq\relax \expandafter\check@char\first@ \ifletter \advance\temp@@count by 1 \ifnum\temp@@count=\end@num\relax \advance\temp@count by 1 \xdef\second@{\the\temp@count} \advance\temp@count by -1 \fi \fi \fi \ifx\first@\ampers@nd \ifx\domain@active\y@ \xdef\stack@dom{\stack@dom\the\temp@count;} \fi \xdef\stack@dom{\stack@dom &;&;@} \else \xdef\first@@{\first@} \advance\temp@count by 1 \loop \advance\loopcount by 1 \xdef\seq@line{\csname seq\the\loopcount\endcsname} \expandafter\res@get\seq@line \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line} \ifx\first@@\first@\else\xdef\leave@in{y}\fi \ifnum\loopcount=\start@seq\relax \expandafter\check@char\first@ \ifletter \advance\temp@@count by 1 \ifnum\temp@@count=\end@num\relax \xdef\second@{\the\temp@count}\fi \fi \fi \ifnum\loopcount<\seq@count\repeat \ifx\leave@in\y@ \ifx\domain@active\n@ \ifnum\start@seq=0 \xdef\domain@active{y} \xdef\stack@dom{\stack@dom\the\temp@count;} \else \ifnum\temp@@count<\start@num\relax \else \ifnum\temp@@count>\end@num\relax \else \xdef\domain@active{y} \xdef\stack@dom{\stack@dom\the\temp@count;} \fi \fi \fi \else \ifnum\start@seq>0 \ifnum\temp@@count<\end@num\relax \else \xdef\domain@active{n} \xdef\stack@dom{\stack@dom\second@;} \fi \fi \fi \else \ifx\domain@active\y@ \xdef\domain@active{n} \advance\temp@count by -1 \xdef\stack@dom{\stack@dom\the\temp@count;} \advance\temp@count by 1 \fi \fi \allmatch@out \fi } \def\domain@count{% \xdef\@ddg@p{n} \loopcount=0 \ifT@coffee \xdef\seq@line{\csname T@cof\the\loopcount\endcsname} \expandafter\res@get\seq@line \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@} \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line} \fi \loop \advance\loopcount by 1 \xdef\seq@line{\csname seq\the\loopcount\endcsname} \expandafter\res@get\seq@line \expandafter\xdef\csname res\the\loopcount\endcsname{\first@} \expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line} \ifT@coffee \xdef\seq@line{\csname T@cof\the\loopcount\endcsname} \expandafter\res@get\seq@line \expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@} \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line} \fi \ifnum\loopcount<\seq@count\repeat \ifx\first@\ampers@nd \else \ifnum\next@domain@num>-99999\relax \ifnum\domain@seq=0 \temp@count=\csname dom@count0\endcsname \advance\temp@count by 1 \expandafter\xdef\csname dom@count0\endcsname{\the\temp@count} \fi \loopcount=0 \loop \advance\loopcount by 1 \xdef\first@{\csname res\the\loopcount\endcsname} \expandafter\check@char\first@ \ifletter \temp@count=\csname dom@count\the\loopcount\endcsname \advance\temp@count by 1 \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\the\temp@count} \if\seq@type A \relax \temp@count=\char@num \ifnum\temp@count>96 \advance\temp@count by -32 \fi \ifnum\temp@count=69 \guess@protein \else \ifnum\temp@count=70 \guess@protein \else \ifnum\temp@count=73 \guess@protein \else \ifnum\temp@count=76 \guess@protein \else \ifnum\temp@count=80 \guess@protein \else \ifnum\temp@count=81 \guess@protein \fi\fi\fi\fi\fi\fi \fi \else \ifx\d@m@in\y@ \ifnum\loopcount=\domain@seq \xdef\@ddg@p{y} \fi \fi \fi \ifnum\loopcount<\seq@count\repeat \ifx\@ddg@p\y@ \ifx\g@p\n@ \loopcount=0 \loop \advance\loopcount by 1 \ifT@coffee \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} \fi \expandafter\xdef\csname sequence\the\loopcount\endcsname{% \csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname} \expandafter\xdef\csname dom@num\the\loopcount\endcsname{% \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} \ifnum\loopcount<\seq@count\repeat \advance\total@count by 1 \advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi \fi \fi \expandafter\ifnum\csname dom@count\domain@seq\endcsname=\next@domain@num \xdef\d@m@in{y} \advance\total@count by 1 \advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi \loopcount=0 \ifx\g@p\y@ \ifT@coffee \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} \fi \fi \ifT@coffee \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} \fi \loop \advance\loopcount by 1 \ifx\g@p\y@ \ifT@coffee \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} \fi \expandafter\xdef\csname sequence\the\loopcount\endcsname{% \csname sequence\the\loopcount\endcsname\equ@l} \expandafter\xdef\csname dom@num\the\loopcount\endcsname{% \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} \ifnum\outerloopcount=0 \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} \fi \fi \ifT@coffee \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{% \csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname} \fi \expandafter\xdef\csname sequence\the\loopcount\endcsname{% \csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname} \expandafter\xdef\csname dom@num\the\loopcount\endcsname{% \csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} \ifnum\outerloopcount=0 \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} \fi \ifnum\loopcount<\seq@count\repeat \ifx\@ddg@p\n@ \expandafter\get@item\domain@num@list \xdef\domain@num@list{\first@} \fi \ifx\fourth@\ampers@nd \xdef\next@domain@num{-99999} \else \loopcount=\next@domain@num \advance\loopcount by 1 \ifnum\loopcount=\fourth@ \xdef\g@p{n} \else \xdef\g@p{y} \advance\total@count by 1 \advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \loopcount=0 \loop \advance\loopcount by 1 \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,} \ifnum\loopcount<\seq@count\repeat \fi \fi \xdef\next@domain@num{\fourth@} \xdef\end@num{\fourth@} \fi \fi \domain@count \fi \fi } \def\residue@count{% \expandafter\res@get\seq@line \if\first@\ampers@nd \else \advance\total@count by 1 \advance\innerloopcount by 1 \ifstart@ \advance\res@count by 1 \fi \ifnum\start@seq=0 \advance\end@count by 1 %%%%%%%%%% \ifnum\end@count=\start@num\relax \xdef\start@number{\the\innerloopcount} \start@true \res@count=1 \fi %%%%%%%%%% \else \expandafter\check@char\first@ \ifletter \advance\end@count by 1 \if\seq@type A \relax \temp@count=\char@num \ifnum\temp@count>96 \advance\temp@count by -32 \fi \ifnum\temp@count=69 \guess@protein \else \ifnum\temp@count=70 \guess@protein \else \ifnum\temp@count=73 \guess@protein \else \ifnum\temp@count=76 \guess@protein \else \ifnum\temp@count=80 \guess@protein \else \ifnum\temp@count=81 \guess@protein \fi\fi\fi\fi\fi\fi \fi \fi \ifnum\end@count=\start@num\relax \xdef\start@number{\the\innerloopcount} \start@true \res@count=1 \fi \fi \residue@count \fi} \def\clean@seq{% \expandafter\res@get\seq@line \if\first@\ampers@nd \xdef\seq@line{\seq@@line} \else \expandafter\check@char\first@ \ifnum\char@num>64 \ifnum\char@num>96 \make@upper \fi \xdef\seq@@line{\seq@@line\first@} \else \ifnum\char@num=46 \xdef\seq@@line{\seq@@line\d@t} \else \ifnum\char@num=45 \xdef\seq@@line{\seq@@line\d@t} \else \ifnum\char@num=42 \xdef\seq@@line{\seq@@line\questi@n} \fi \fi \fi \fi \clean@seq \fi} \def\read@loop{% \read\alignfile to \inline \xdef\last@{\expandafter\string\inline} \ifx\last@\par@ \else \xdef\inline{\inline @} \expandafter\seq@get\inline \ifstop@ \else \innerloopcount=\csname @rd\the\loopcount\endcsname\relax \expandafter\ifx\csname seq@name\the\loopcount\endcsname\first@ \xdef\seq@@line{} \xdef\seq@line{\seq@line &@} \clean@seq \expandafter\xdef\csname sequence\the\innerloopcount\endcsname{% \csname sequence\the\innerloopcount\endcsname\seq@line} \advance\loopcount by 1 \ifnum\loopcount>\seq@count \loopcount=1 \fi \fi \fi \fi \ifeof\alignfile \ifx\all@out\y@ \xdef\domain@seq{0} \loopcount=0 \loop \advance\loopcount by 1 \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} \ifnum\loopcount<\seq@count\repeat \xdef\domain@active{n} \xdef\stack@dom{} \temp@count=0 \temp@@count=0 \allmatch@out \xdef\dom@in{y} \fi \ifx\dom@in\y@ \loopcount=0 \ifT@coffee \xdef\temp@{\csname T@coffee\the\loopcount\endcsname} \expandafter\get@temp\temp@ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@} \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} \fi \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0} \loop \advance\loopcount by 1 \ifT@coffee \xdef\temp@{\csname T@coffee\the\loopcount\endcsname} \expandafter\get@temp\temp@ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@} \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} \fi \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} \expandafter\xdef\csname sequence\the\loopcount\endcsname{} \expandafter\xdef\csname dom@num\the\loopcount\endcsname{} \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{} \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname} \ifnum\loopcount<\seq@count\repeat \xdef\domain@num@list{} \xdef\last@{\stack@dom} \get@domain \xdef\domain@num@list{\domain@num@list &,@} \expandafter\get@item\domain@num@list \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@} \xdef\d@m@in{n} \domain@count \loopcount=0 \ifT@coffee \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} \fi \loop \advance\loopcount by 1 \ifT@coffee \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} \fi \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @} \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@} \ifnum\loopcount<\seq@count\repeat \if\seq@type A \guess@DNA \fi \advance\seq@pointer by \total@count\relax \xdef\total@pos{\the\total@count} \else \ifnum\start@seq=0 \xdef\seq@line{\csname sequence1\endcsname &@} \else \xdef\seq@line{\csname sequence\start@seq\endcsname &@} \fi \res@count=0 \innerloopcount=0 \residue@count \if\seq@type A \guess@DNA \fi \advance\seq@pointer by \res@count\relax \xdef\total@pos{\the\total@count} \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi \total@count=\end@count\relax \xdef\first@{\csname res@count\start@seq\endcsname} \advance\total@count by \first@\relax \xdef\first@{\the\total@count} \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi \fi \ifshow@sublogo \prep@sublogo \fi \ifshow@logo \prep@logo \fi \ifx\label@motif\y@ \prep@motif \fi \ifnum\seq@pointer>\res@perline \block@output \fi \else \read@loop \fi} \def\read@fasta{% \read\alignfile to \inline \xdef\last@{\expandafter\string\inline} \ifx\last@\par@ \else \xdef\seq@line{\inline} \xdef\inline{\inline @} \expandafter\firstchar@get\inline \ifstop@ \else \ifx\first@\gre@ter \advance\loopcount by 1\relax \expandafter\seq@get\third@ \xdef\seq@name{\first@} \xdef\second@{\first@ &} \ifx\second@\ampers@nd \xdef\seq@name{seq\the\loopcount}\fi \innerloopcount=\csname @rd\the\loopcount\endcsname\relax \else \expandafter\ifx\csname seq@name\the\loopcount\endcsname\seq@name \xdef\seq@@line{} \xdef\seq@line{\seq@line &@} \clean@seq \expandafter\xdef\csname sequence\the\innerloopcount\endcsname{% \csname sequence\the\innerloopcount\endcsname\seq@line} \fi \fi \fi \fi \ifeof\alignfile \ifx\all@out\y@ \xdef\domain@seq{0} \loopcount=0 \loop \advance\loopcount by 1 \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} \ifnum\loopcount<\seq@count\repeat \xdef\domain@active{n} \xdef\stack@dom{} \temp@count=0 \temp@@count=0 \allmatch@out \xdef\dom@in{y} \fi \ifx\dom@in\y@ \loopcount=0 \ifT@coffee \xdef\temp@{\csname T@coffee\the\loopcount\endcsname} \expandafter\get@temp\temp@ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@} \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} \fi \expandafter\xdef\csname dom@count\the\loopcount\endcsname{0} \loop \advance\loopcount by 1 \ifT@coffee \xdef\temp@{\csname T@coffee\the\loopcount\endcsname} \expandafter\get@temp\temp@ \expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@} \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{} \fi \expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@} \expandafter\xdef\csname sequence\the\loopcount\endcsname{} \expandafter\xdef\csname dom@num\the\loopcount\endcsname{} \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{} \expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname} \ifnum\loopcount<\seq@count\repeat \xdef\domain@num@list{} \xdef\last@{\stack@dom} \get@domain \xdef\domain@num@list{\domain@num@list &,@} \expandafter\get@item\domain@num@list \xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@} \xdef\d@m@in{n} \domain@count \loopcount=0 \ifT@coffee \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} \fi \loop \advance\loopcount by 1 \ifT@coffee \expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @} \fi \expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @} \expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{% \csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@} \ifnum\loopcount<\seq@count\repeat \if\seq@type A \guess@DNA \fi \advance\seq@pointer by \total@count\relax \xdef\total@pos{\the\total@count} \else \ifnum\start@seq=0 \xdef\seq@line{\csname sequence1\endcsname &@} \else \xdef\seq@line{\csname sequence\start@seq\endcsname &@} \fi \res@count=0 \innerloopcount=0 \residue@count \if\seq@type A \guess@DNA \fi \advance\seq@pointer by \res@count \xdef\total@pos{\the\total@count} \ifx\end@num\n@\xdef\end@num{\the\end@count}\fi \total@count=\end@count\relax \xdef\first@{\csname res@count\start@seq\endcsname} \advance\total@count by \first@\relax \xdef\first@{\the\total@count} \ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi \fi \ifshow@sublogo \prep@sublogo \fi \ifshow@logo \prep@logo \fi \ifx\label@motif\y@ \prep@motif \fi \ifnum\seq@pointer>\res@perline \block@output \fi \else \read@fasta \fi} \def\read@lines{% \openin\alignfile = \alignfilename \clear@seq \ifnum\start@seq>0 \xdef\start@seq{\csname @rd\start@seq\endcsname} \fi \loopcount=\start@num \advance\loopcount by -\csname res@count\start@seq\endcsname\relax \expandafter\ifnum\csname res@count\start@seq\endcsname<\start@num\relax \xdef\start@num{\the\loopcount} \else \start@true \fi \res@count=0 \seq@pointer=0 \end@count=0 \total@count=0 \xdef\start@number{0} \ifx\exp@rt\y@ \prep@reexp@rtfile \fi \ifx\f@st@\y@ \loopcount=0 \read@fasta \else \loopcount=1 \read@loop \fi \ifnum\seq@pointer>0 \ifstop@ \else \res@count=\res@perline \res@perline=\seq@pointer \block@output \fi \fi \ifshow@sublogo \closein\sublogofile \fi \ifx\exp@rt\y@ \closeout\exp@rtfile \fi \closein\alignfile \message{)} } %%%%% Read alignment, decide whether MSF or ALN, interpret \def\readalignfile#1{% \def\alignfilename{#1} \xdef\first@{byhand} \ifx\alignfilename\first@ \else \openin\alignfile = #1 \ifeof\alignfile \PackageError{TeXshade} {File `#1' not found} {\MessageBreak The alignment file you specified is missing or you have \MessageBreak misspelled it. \MessageBreak\MessageBreak Stop here, otherwise you're likely getting in trouble. \MessageBreak Type X to quit. \MessageBreak } \else \message{(\alignfilename :} \xdef\seq@type{A} \xdef\he@der{no} \xdef\f@st@{no} \xdef\first@line{y} \seq@count=0 \loopcount=0 \innerloopcount=0 \temp@count=0 \loop \read\alignfile to \inline \xdef\test@{\expandafter\string\inline} \ifx\test@\par@ \innerloopcount=0 \else \xdef\msfline{\inline & & & & @} \expandafter\inf@@get\msfline \ifx\first@\@msf \expandafter\type@get\msfline \fi \ifx\second@\@msf \expandafter\type@get\msfline \fi \ifx\third@\@msf \expandafter\type@get\msfline \fi \ifx\first@\n@me \advance\loopcount by 1\relax \expandafter\xdef\csname seqname\the\loopcount\endcsname{\second@} \expandafter\xdef\csname seq@len\the\loopcount\endcsname{\fourth@} \fi \ifx\first@\he@derend \ifnum\loopcount>0 \xdef\he@der{yes} \fi \fi \xdef\alnline{\inline @} \expandafter\check@letter\alnline \ifletter \expandafter\seq@get\alnline \advance\innerloopcount by 1\relax \seq@count=\innerloopcount \expandafter\xdef\csname newseqname\the\seq@count\endcsname{\first@} \else \expandafter\firstchar@get\alnline \ifx\first@\gre@ter \ifx\first@line\y@ \xdef\f@st@{y}\fi \expandafter\seq@get\third@ \advance\temp@count by 1\relax \xdef\second@{\first@ &} \ifx\second@\ampers@nd \xdef\first@{seq\the\temp@count}\fi \expandafter\xdef\csname seq@name\the\temp@count\endcsname{\first@} \fi \fi \fi \xdef\first@line{n} \ifeof\alignfile \else\repeat \closein\alignfile \xdef\first@{no} \ifx\he@der\first@ \loopcount=0 \ifx\f@st@\y@ \seq@count=\temp@count \loopcount=0 \loop \advance\loopcount by 1 \expandafter\xdef\csname seqname\the\loopcount\endcsname{% \csname seq@name\the\loopcount\endcsname} \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% \csname seq@name\the\loopcount\endcsname} \expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999} \ifnum\loopcount<\seq@count \repeat \else \loop \advance\loopcount by 1 \expandafter\xdef\csname seqname\the\loopcount\endcsname{% \csname newseqname\the\loopcount\endcsname} \expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999} \ifnum\loopcount<\seq@count \repeat \fi \else \seq@count=\loopcount \loopcount=0 \box@width=0pt \loop \advance\loopcount by 1 \expandafter\xdef\csname newseqname\the\loopcount\endcsname{% \csname seqname\the\loopcount\endcsname} \ifnum\loopcount<\seq@count \repeat \fi \set@savedseqlength \loopcount=0 \xdef\seq@order{} \expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes} \loop \advance\loopcount by 1 \expandafter\xdef\csname @rd\the\loopcount\endcsname{\the\loopcount} \expandafter\xdef\csname res@count\the\loopcount\endcsname{0} \cleanup@name \expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n} \expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n} \expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n} \expandafter\xdef\csname hide@seq\the\loopcount\endcsname{false} \expandafter\xdef\csname hide@@@seq\the\loopcount\endcsname{false} \expandafter\xdef\csname hide@name\the\loopcount\endcsname{no} \expandafter\xdef\csname name@col\the\loopcount\endcsname{yes} \expandafter\xdef\csname hide@number\the\loopcount\endcsname{no} \expandafter\xdef\csname number@col\the\loopcount\endcsname{yes} \expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{&;&;&;@} \expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@} \expandafter\xdef\csname seq@gap\the\loopcount\endcsname{no} \expandafter\xdef\csname seq@start\the\loopcount\endcsname{1} \expandafter\xdef\csname mol@weight\the\loopcount\endcsname{0} \expandafter\xdef\csname ch@rge\the\loopcount\endcsname{0} \ifnum\loopcount=1 \xdef\seq@order{\the\loopcount} \else \xdef\seq@order{\seq@order,\the\loopcount}\fi \ifnum\loopcount<\seq@count \repeat \xdef\seq@order{\seq@order,@} \killseq@count=\seq@count \fi \fi } %%%%% TeXshade \def\calc@widths{% \fontfamily{cmss}\fontseries{m}\fontshape{n} \selectfont \setbox1=\hbox{\residues@size{A}}\logo@height=\ht1 \setlength\logo@height{\logo@stretch\logo@height} \fontfamily{\residues@family} \fontseries{\residues@series} \fontshape{\residues@shape} \selectfont \setbox1=\hbox{\residues@size{W}}\box@width=1.15\wd1 \global\setlength\box@width{\char@stretch\box@width} \box@height=1.2\ht1 \setbox1=\hbox{\residues@size{g}}\box@depth=1.1\dp1 \global\setlength\box@height{\line@stretch\box@height} \global\setlength\box@depth{\line@stretch\box@depth} \baselineskip=\box@height \advance\baselineskip by \box@depth \lineskip=0pt \ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi \loopcount=0 \expandafter\getregion@fromstack{\the\loopcount} \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromlowerstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} \expandafter\getregion@fromshadingstack{\the\loopcount} \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \fontfamily{\namestext@family} \fontseries{\namestext@series} \fontshape{\namestext@shape} \selectfont \ifshow@logo \ifx\logo@name@user\ampers@nd \setbox1=\hbox{\namestext@size logo\kern1em} \else \setbox1=\hbox{\namestext@size\logo@name@user\kern1em} \fi \ifnum\wd1>\name@width \name@width=\wd1 \fi \fi \ifshow@sublogo \ifx\sublogo@name@user\ampers@nd \setbox1=\hbox{\namestext@size family\kern1em} \else \setbox1=\hbox{\namestext@size\sublogo@name@user\kern1em} \fi \ifnum\wd1>\name@width \name@width=\wd1 \fi \ifx\hide@negatives\n@ \setbox1=\hbox{\namestext@size\sublogo@name@neg\kern1em} \fi \ifnum\wd1>\name@width \name@width=\wd1 \fi \fi \loopcount=1 \loop \setbox1=\hbox{\namestext@size\csname newseqname\the\loopcount\endcsname} \ifnum\wd1>\name@width \name@width=\wd1 \fi \ifnum\ht1>\box@height \box@height=1.1\ht1 \global\setlength\box@height{\line@stretch\box@height} \baselineskip=\box@height \advance\baselineskip by \box@depth \fi \ifnum\dp1>\box@depth \box@depth=1.1\dp1 \global\setlength\box@depth{\line@stretch\box@depth} \baselineskip=\box@height \advance\baselineskip by \box@depth \fi \expandafter\getregion@fromstack{\the\loopcount} \expandafter\getregion@fromtintstack{\the\loopcount} \expandafter\getregion@fromemphstack{\the\loopcount} \expandafter\getregion@fromlowerstack{\the\loopcount} \expandafter\getregion@fromframestack{\the\loopcount} \expandafter\getregion@fromshadingstack{\the\loopcount} \xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount} \innerloopcount = \csname seq@len\the\loopcount\endcsname \advance\innerloopcount by \csname seq@start\the\loopcount\endcsname \advance\innerloopcount by -1 \expandafter\xdef\csname seq@len\the\loopcount\endcsname{\the\innerloopcount} \advance\loopcount by 1 \ifnum\loopcount>\seq@count \else \repeat \advance\name@width by -2em \global\xdef\name@@width{\the\name@width} \advance\name@width by 3em \fontfamily{\numbertext@family} \fontseries{\numbertext@series} \fontshape{\numbertext@shape} \selectfont \setbox1=\hbox{\bottomruler@size\num@width\,-} \xdef\ruler@width{\the\wd1} \setbox1=\hbox{\numbertext@size\num@width} \number@width=\wd1 \advance\number@width by 1em \loopcount=\linewidth \ifnames@ \advance\loopcount by -\name@width \fi \width@tmp=1.6\box@width \ifnumbers@ \ifnumbers@left \advance\loopcount by -\number@width \else \xdef\first@{left} \ifx\show@logoscale\first@ \advance\loopcount by -\width@tmp \fi \fi \ifnumbers@right \advance\loopcount by -\number@width \else \xdef\first@{right} \ifx\show@logoscale\first@ \advance\loopcount by -\width@tmp \fi \fi \else \xdef\first@{left} \ifx\show@logoscale\first@ \advance\loopcount by -\width@tmp \fi \xdef\first@{right} \ifx\show@logoscale\first@ \advance\loopcount by -\width@tmp \fi \xdef\first@{leftright} \ifx\show@logoscale\first@ \advance\loopcount by -\width@tmp \advance\loopcount by -\width@tmp \fi \fi \divide\loopcount by \box@width \divide\loopcount by 5 \multiply\loopcount by 5 \ifrpl@fix\else \ifnum\res@perline>\loopcount \res@perline=\loopcount\fi\fi \ifnum\finger@linenum>0 \width@tmp=\linewidth \ifnames@ \advance\width@tmp by -\name@width \fi \ifnumbers@ \advance\width@tmp by -\number@width \fi \divide\width@tmp by \finger@linenum \global\setlength\box@width{\width@tmp} \fi \center@fill=\linewidth \ifnames@ \advance\center@fill by -\name@width \fi \ifnumbers@ \advance\center@fill by -\number@width \fi \width@tmp=\box@width \multiply\width@tmp by \res@perline \advance\center@fill by -\width@tmp \ifx\out@put\y@\leftskip\c@factor\center@fill\fi \ifx\logo@colors@set\n@ \if\seq@type N \clearlogocolors[Yellow] \logocolor{G}{Black} \logocolor{A}{Green} \logocolor{TU}{Red} \logocolor{C}{Blue} \else \clearlogocolors \logocolor{DE}{Red} \logocolor{CM}{Yellow} \logocolor{KR}{Blue} \logocolor{ST}{Orange} \logocolor{FY}{MidnightBlue} \logocolor{NQ}{Cyan} \logocolor{G}{LightGray} \logocolor{LVI}{Green} \logocolor{A}{DarkGray} \logocolor{W}{CarnationPink} \logocolor{H}{CornflowerBlue} \logocolor{P}{Apricot} \logocolor{BZ}{LightMagenta} \fi \fi } \def\multiple@dssp{% \advance\loopcount by 1 \include@DSSP \ifnum\loopcount<\dssp@num\multiple@dssp\fi} \def\multiple@stride{% \advance\loopcount by 1 \include@stride \ifnum\loopcount<\stride@num\multiple@stride\fi} \def\multiple@PHD{% \advance\loopcount by 1 \include@PHD \ifnum\loopcount<\PHD@num\multiple@PHD\fi} \def\multiple@HMMTOP{% \advance\loopcount by 1 \include@HMMTOP \ifnum\loopcount<\HMMTOP@num\multiple@HMMTOP\fi} \newenvironment{texshade}[2][&]% {\standarddefinitions \c@d@ns \xdef\first@{#1}\ifx\first@\ampers@nd\else\input{#1}\fi \readalignfile{#2} }% {\ifnum\seq@count>0 \loopcount=0 \ifnum\loopcount<\dssp@num \multiple@dssp\fi \loopcount=0 \ifnum\loopcount<\stride@num \multiple@stride\fi \loopcount=0 \ifnum\loopcount<\PHD@num \multiple@PHD\fi \loopcount=0 \ifnum\loopcount<\HMMTOP@num \multiple@HMMTOP\fi \loopcount=1 \kill@seqnow \reorder@seqs\seq@order \seq@count=\killseq@count \global\xdef\seq@num{\the\seq@count} \clear@sim@count \ifnum\csname res@count\start@seq\endcsname<0 \ifnum\start@num>0 \loopcount=\start@num \advance\loopcount by -1 \xdef\start@num{\the\loopcount} \fi \fi \ifnum\rule@num>0 \loopcount=\csname res@count\rule@num\endcsname \divide\loopcount by \ruler@step \multiply\loopcount by \ruler@step \ifnum\loopcount<0 \ifnum\ruler@step<3 \advance\loopcount by \ruler@step \fi \else \advance\loopcount by \ruler@step \fi \xdef\rule@tens{\the\loopcount} \else \loopcount=\cons@count \divide\loopcount by \ruler@step \multiply\loopcount by \ruler@step \ifnum\loopcount<0 \ifnum\ruler@step<3 \advance\loopcount by \ruler@step \fi \else \advance\loopcount by \ruler@step \fi \xdef\rule@tens{\the\loopcount} \fi \xdef\first@{top} \ifx\cap@pos\first@ \xdef\@captype{figure} \ifx\c@pshort\n@ \caption{\c@p} \else \caption[\c@pshort]{\c@p} \fi \fi \loopcount = \thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100 \xdef\thresh@ld@{\the\loopcount} \loopcount = \all@thresh@ld \multiply\loopcount by \seq@count \divide\loopcount by 100 \xdef\all@thresh@ld@{\the\loopcount} \bgroup \ifx\out@put\y@\bigskip\fi \iffuncmode \show@consfalse \fi \ifall@fshade \iffuncmode \else \all@fshadefalse \fi\fi \ifnum\finger@linenum>0 \show@consfalse \hidechartrue \message{} \fi \calc@widths \read@lines \save@lengths \iflegend@ \vspace{\vspace@legend} \setbox1=\vbox{\do@legend} \vbox{\do@legend}\par \ifnum\ht1<-\vspace@legend \vspace{-\ht1}\vspace{-\vspace@legend} \fi \fi \egroup \xdef\first@{bottom} \ifx\cap@pos\first@ \vspace{-\baselineskip} \xdef\@captype{figure} \ifx\c@pshort\n@ \caption{\c@p} \else \caption[\c@pshort]{\c@p} \fi \fi \fi} \def\standarddefinitions{% \xdef\prfx{pep}\clear@groups\clear@sims \xdef\prfx{DNA}\clear@groups\clear@sims \clearfuncgroups \clear@simpairs \shadingcolors{blues} \shadingcolors{reds} \shadingcolors{greens} \shadingcolors{grays} \shadingcolors{black} \loopcount=\@lign@count \advance\loopcount by 1\relax \xdef\@lign@count{\the\loopcount} \start@true \xdef\start@num{1} \xdef\start@seq{0} \stop@false \xdef\end@num{n} \xdef\seq@regions{0} \cons@count=0 \expandafter\xdef\csname res@count0\endcsname{0} \xdef\allow@zero{n} \xdef\c@ns@shift{0} \regionalshadefalse\regionalemphfalse\regionallowerfalse\regionaltintfalse \frame@false\shading@false \xdef\ruler@rot{0} \topfeaturefalse \bottomfeaturefalse \ttopfeaturefalse \bbottomfeaturefalse \tttopfeaturefalse \bbbottomfeaturefalse \ttttopfeaturefalse \bbbbottomfeaturefalse \all@fshadefalse\hidecharfalse \xdef\finger@linenum{0} \xdef\hide@seqs{n} \xdef\dssp@num{0} \xdef\stride@num{0} \xdef\PHD@num{0} \xdef\HMMTOP@num{0} \xdef\bottop@{top} \expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\bottop@{ttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\bottop@{tttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\bottop@{ttttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\bottop@{bottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\bottop@{bbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\bottop@{bbbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\bottop@{bbbbottom}\expandafter\xdef\csname feature@\bottop@\endcsname{0} \xdef\frame@{0} \xdef\show@Hdssp{no} \xdef\show@Gdssp{no} \xdef\show@Idssp{no} \xdef\show@Edssp{no} \xdef\show@Bdssp{no} \xdef\show@Tdssp{no} \xdef\show@Sdssp{no} \xdef\show@Hstride{no} \xdef\show@Gstride{no} \xdef\show@Istride{no} \xdef\show@Estride{no} \xdef\show@Bstride{no} \xdef\show@Tstride{no} \xdef\show@itop{no} \xdef\show@etop{no} \xdef\show@TMtop{no} \xdef\show@i@HMMTOP{no} \xdef\show@e@HMMTOP{no} \xdef\show@TM@HMMTOP{no} \xdef\show@Hsec{no} \xdef\show@Esec{no} \xdef\collect@restop{no} \xdef\collect@resttop{no} \xdef\collect@restttop{no} \xdef\collect@resttttop{no} \xdef\collect@resbottom{no} \xdef\collect@resbbottom{no} \xdef\collect@resbbbottom{no}\xdef\collect@resbbbbottom{no} \xdef\tr@nslatetop{} \xdef\tr@nslatettop{} \xdef\tr@nslatetttop{} \xdef\tr@nslatettttop{} \xdef\tr@nslatebottom{} \xdef\tr@nslatebbottom{} \xdef\tr@nslatebbbottom{} \xdef\tr@nslatebbbbottom{} \xdef\tr@nsseqtop{0} \xdef\tr@nsseqttop{0} \xdef\tr@nsseqtttop{0} \xdef\tr@nsseqttttop{0} \xdef\tr@nsseqbottom{0} \xdef\tr@nsseqbbottom{0} \xdef\tr@nsseqbbbottom{0} \xdef\tr@nsseqbbbbottom{0} \xdef\triple@counttop{0} \xdef\triple@countttop{0} \xdef\triple@counttttop{0} \xdef\triple@countttttop{0} \xdef\triple@countbottom{0} \xdef\triple@countbbottom{0} \xdef\triple@countbbbottom{0}\xdef\triple@countbbbbottom{0} \xdef\last@@restop{} \xdef\last@@resttop{} \xdef\last@@restttop{} \xdef\last@@resttttop{} \xdef\last@@resbottom{} \xdef\last@@resbbottom{} \xdef\last@@resbbbottom{} \xdef\last@@resbbbbottom{} \xdef\out@put{y} \xdef\m@p{no} \xdef\t@sp@ce{0mm} \xdef\tt@sp@ce{0mm} \xdef\ttt@sp@ce{0mm} \xdef\tttt@sp@ce{0mm} \xdef\b@sp@ce{0mm} \xdef\bb@sp@ce{0mm} \xdef\bbb@sp@ce{0mm} \xdef\bbbb@sp@ce{0mm} \xdef\ruler@sp@ce{0mm} \xdef\seq@gap@num{0} \xdef\h@ndalign{no} \xdef\sep@space{0pt} \xdef\c@pshort{n} \xdef\bottom@stretch{n} \xdef\bbottom@stretch{n} \xdef\bbbottom@stretch{n} \xdef\bbbbottom@stretch{n} \xdef\c@nscol{} \xdef\c@nssc@le{ColdHot} \xdef\collect@cons@colors{no} \xdef\cons@now{no} \xdef\res@numA{0} \xdef\res@numB{0} \xdef\res@numC{0} \xdef\res@numD{0} \xdef\res@numE{0} \xdef\res@numF{0} \xdef\res@numG{0} \xdef\res@numH{0} \xdef\res@numI{0} \xdef\res@numJ{0} \xdef\res@numK{0} \xdef\res@numL{0} \xdef\res@numM{0} \xdef\res@numN{0} \xdef\res@numO{0} \xdef\res@numP{0} \xdef\res@numQ{0} \xdef\res@numR{0} \xdef\res@numS{0} \xdef\res@numT{0} \xdef\res@numU{0} \xdef\res@numV{0} \xdef\res@numW{0} \xdef\res@numX{0} \xdef\res@numY{0} \xdef\res@numZ{0} \expandafter\xdef\csname res@num\questi@n\endcsname{0} \expandafter\xdef\csname res@num\d@t\endcsname{0} \expandafter\xdef\csname res@num\equ@l\endcsname{0} \xdef\res@corrA{0} \xdef\res@corrB{0} \xdef\res@corrC{0} \xdef\res@corrD{0} \xdef\res@corrE{0} \xdef\res@corrF{0} \xdef\res@corrG{0} \xdef\res@corrH{0} \xdef\res@corrI{0} \xdef\res@corrJ{0} \xdef\res@corrK{0} \xdef\res@corrL{0} \xdef\res@corrM{0} \xdef\res@corrN{0} \xdef\res@corrO{0} \xdef\res@corrP{0} \xdef\res@corrQ{0} \xdef\res@corrR{0} \xdef\res@corrS{0} \xdef\res@corrT{0} \xdef\res@corrU{0} \xdef\res@corrV{0} \xdef\res@corrW{0} \xdef\res@corrX{0} \xdef\res@corrY{0} \xdef\res@corrZ{0} \expandafter\xdef\csname res@corr\questi@n\endcsname{0} \expandafter\xdef\csname res@corr\d@t\endcsname{0} \expandafter\xdef\csname res@corr\equ@l\endcsname{0} \xdef\corr@max{0} \xdef\do@freq@correction{n} \xdef\res@total{0} \xdef\stack@sequencelogo{} \xdef\bit@total{0} \clearlogocolors \xdef\logo@colors@set{n} \show@sublogofalse \xdef\stack@sublogo{} \xdef\clear@logo{n} \xdef\subfamily@threshold{50} \xdef\subfamily@seq{1} \xdef\sig@max{100000} \xdef\sublogo@num{} \xdef\sublogo@sig{} \xdef\subfamily@count{0} \xdef\sublogo@name@neg{} \xdef\logo@name@user{&} \xdef\sublogo@name@user{&} \expandafter\xdef\csname group@num1\endcsname{0} \expandafter\xdef\csname group@num2\endcsname{0} \xdef\exp@rt@num{0} \xdef\exp@rt{n} \xdef\divref@{0} \xdef\all@thresh@ld{100} \all@shadefalse \hidefeaturenames \hidefeaturestylenames \xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n} \xdef\dom@in{no} \xdef\label@motif{no} \xdef\motif@num{0} \xdef\all@out{n} \hfuzz9999pt %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% %%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%% %%%%% %%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%% %%%%% %%%%% Under any circumstances: %%%%% %%%%% %%%%% %%%%% DO NOT CHANGE ANY SETTINGS HERE !!! %%%%% %%%%% %%%%% %%%%% Please define your personal parameter file! Store your new file %%%%% %%%%% together with this style-file in the same directory and load the %%%%% %%%%% file by naming it as an optional parameter in the `texshade' en- %%%%% %%%%% vironment. The file `texshade.def' can be used as a template for %%%%% %%%%% the new creation. See the manual for further help. %%%%% %%%%% %%%%% %%%%% THANK YOU !!! %%%%% %%%%% %%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \shadingmode{identical} % Shade identical residues only \shadingcolors{blues} % Select the blue color scheme for shading \constoallseqs % Calculate consensus considering all seqs \threshold{50} % Consensus threshold percentage is 50 \residuesperline{999} % As many residues as possible per line \numberingwidth{9999} % Assign space for 4 digit numbering \charstretch{1} % Do not stretch character width \linestretch{1} % Do not stretch lines vertically \gapchar{.} % . is printed in sequence gaps \gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt \gapcolors{Black}{White} % Gap symbols appear `Black on White' \domaingaprule{1pt} % If a rule is set between domains use 1 pt \domaingapcolors{Red}{White} % Domain separation line appears `Red on White' \numberingcolor{Black} % Numbering color is `Black' \shownumbering{right} % Show sequence numbering on the left \namescolor{Black} % Names' color is `Black' \featurenamescolor{Black} % Feature names' color is `Black' \featurestylenamescolor{Black} % Feature names' color is `Black' \shownames{left} % Show sequence names on the right \consensuscolors{Black}{White} % All consensus symbols/letters {Black}{White} % appear `Black on White' {Black}{White} % \showconsensus{bottom} % Show consensus line at bottom with \hidesequencelogo % Do not show a sequence logo as consensus \showlogoscale{leftright} % Show vertical scale bar if logo is on \logostretch{1} % Do not stretch sequence logo vertically \hidesubfamilylogo % Do not show a subfamily logo \subfamilythreshold{50} % Set subfamily threshold to 50% \shownegatives % Show negative values in subfamily logo \showrelevance[Black]{*} % Label relevant subfamily deviations \defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match \showleadinggaps % Show gap symbols before sequence start \rulercolor{Black} % Ruler's color is `Black' \hideruler % Do not show the ruler \rulersteps{10} % Ruler ticks every 10 residues \legendcolor{Black} % Legend text color is `Black' \hidelegend % Do not show the legend \alignment{center} % Center alignment on page \medsepline % Medium height if separation line is on \medblockskip % Medium skip between sequence blocks \flexblockspace % Use optimized space between blocks \featurerule{0.5ex} % Set feature rule thickness to 1/2 ex \bargraphstretch{1} % Do not stretch bars in feature graphs \colorscalestretch{1} % Do not stretch color scales in features \backtranstext{horizontal} % Horizontal triplets in feature texts \backtranslabel{alternating} % Alternating triplets in feature styles \setfamily{residues}{tt} % Use typewriter family for residues \setseries{residues}{md} % Use normal series for residues \setshape {residues}{up} % Use upright shape for residues \setsize {residues}{normalsize} % Use normal size for residues \setfamily{numbering}{tt} % Use typewriter family for numbering \setseries{numbering}{md} % Use normal series for numbering \setshape {numbering}{up} % Use upright shape for numbering \setsize {numbering}{normalsize} % Use normal size for numbering \setfamily{names}{tt} % Use typewriter family for names \setseries{names}{md} % Use normal series for names \setshape {names}{up} % Use upright shape for names \setsize {names}{normalsize} % Use normal size for names \setfamily{featurenames}{tt} % Use typewriter family for feature names \setseries{featurenames}{md} % Use normal series for feature names \setshape {featurenames}{up} % Use upright shape for feature names \setsize {featurenames}{normalsize}% Use normal size for feature names \setfamily{featurestylenames}{tt} % Use typewriter family for feature style names \setseries{featurestylenames}{md} % Use normal series for feature style names \setshape {featurestylenames}{up} % Use upright shape for feature style names \setsize {featurestylenames}{normalsize}% Use normal size for feature style names \setfamily{features}{rm} % Use roman family for feature texts \setseries{features}{md} % Use normal series for feature texts \setshape {features}{it} % Use italics shape for feature texts \setsize {features}{normalsize} % Use normal size for feature texts \setfamily{featurestyles}{tt} % Use typewriter family for feature styles \setseries{featurestyles}{md} % Use normal series for feature styles \setshape {featurestyles}{up} % Use upright shape for feature styles \setsize {featurestyles}{normalsize}% Use normal size for feature styles \setfamily{legend}{tt} % Use typewriter family for legend texts \setseries{legend}{md} % Use normal series for legend texts \setshape {legend}{up} % Use upright shape for legend texts \setsize {legend}{normalsize} % Use normal size for legend texts \setfamily{ruler}{sf} % Use sans serif font for ruler numbers \tintdefault{medium} % Use medium tint intensity \emphdefault{it} % Use italics to emphasize regions \showonPHDsec{alpha,beta} % Show helices and strands (PHD input) \showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input) \showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input) \showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input) \showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input) \secondcolumnDSSP % Use numbering from 2. column in DSSP \appearance{PHDtopo}{internal} % \ {bottom}{'-'} % \ {int.\ \Alphacount} % | \appearance{PHDtopo}{external} % | {top}{,-,} % | {ext.\ \Alphacount} % | \appearance{PHDtopo}{TM}{top} % | {box[LightGray]:TM\numcount}{} % | \appearance{HMMTOP}{internal} % | {bottom}{'-'} % | {int.\ \Alphacount} % | \appearance{HMMTOP}{external} % | {top}{,-,} % | {ext.\ \Alphacount} % | \appearance{HMMTOP}{TM}{top} % | {helix}{TM\numcount} % | \appearance{PHDsec}{alpha}{top} % | {box:$\alpha$\numcount}{} % | \appearance{PHDsec}{beta}{top} % | {-->}{$\beta$\numcount} % | \appearance{STRIDE}{alpha}{top} % | {box:$\alpha$\numcount}{} % | Definitions for the appearance of \appearance{STRIDE}{3-10}{top} % \ {fill:$\circ$}{3$_{10}$} % > secondary structures included from| \appearance{STRIDE}{pi} % / {top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files. \appearance{STRIDE}{beta}{top} % | {-->}{$\beta$\numcount} % | \appearance{STRIDE}{bridge} % | {top}{fill:$\uparrow$}{} % | \appearance{STRIDE}{turn} % | {top}{,-,}{turn} % | \appearance{DSSP}{alpha}{top} % | {box:$\alpha$\numcount}{} % | \appearance{DSSP}{3-10}{top} % | {fill:$\circ$}{3$_{10}$} % | \appearance{DSSP}{pi} % | {top}{---}{$\pi$} % | \appearance{DSSP}{beta}{top} % | {-->}{$\beta$\numcount} % | \appearance{DSSP}{bridge} % | {top}{fill:$\uparrow$}{} % | \appearance{DSSP}{turn} % | {top}{,-,}{turn} % | \appearance{DSSP}{bend}{top} % / {fill:$\diamond$}{} % / \pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity \pepsims{F}{YW} % Y and W are similar to F \pepsims{Y}{WF} % W and F are similar to Y \pepsims{W}{YF} % Y and F are similar to W \pepsims{I}{LVM} % L, V and M are similar to I \pepsims{L}{VMI} % V, M and I are similar to L \pepsims{V}{MIL} % M, I and L are similar to V \pepsims{R}{KH} % K and H are similar to R \pepsims{K}{HR} % H and R are similar to K \pepsims{H}{RK} % R and K are similar to H \pepsims{A}{GS} % G and S are similar to A \pepsims{G}{A} % A (but not S) is similar to G \pepsims{S}{TA} % T and A are similar to S \pepsims{T}{S} % S (but not A) is similar to T \pepsims{D}{EN} % E and N (but not Q) are similar to D \pepsims{E}{DQ} % D and Q (but not N) are similar to E \pepsims{N}{QD} % Q and D (but not E) are similar to N \pepsims{Q}{NE} % N and E (but not D) are similar to Q \DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity \DNAsims{A}{GR} % G and R are similar to A \DNAsims{G}{AR} % A and R are similar to G \DNAsims{R}{AG} % A and G are similar to R \DNAsims{C}{TY} % T and Y are similar to C \DNAsims{T}{CY} % C and Y are similar to T \DNAsims{Y}{CT} % C and T are similar to Y } \catcode`\@=12 \endinput %% %% End of file `texshade.sty'.