| dafeef0b |
%%
%% 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}[2011/05/13 LaTeX TeXshade (v1.24)]
\message{Package `texshade', Version 1.24 of 2011/12/01.}
\PassOptionsToPackage{dvips}{color}
\PassOptionsToPackage{dvips}{graphicx}
\DeclareOption*{%
\PassOptionsToPackage{\CurrentOption}{color}%
\PassOptionsToPackage{\CurrentOption}{graphicx}%
}
\ProcessOptions
\RequirePackage{color,graphics}
\expandafter\ifx\csname TeXshade\endcsname\relax \else \endinput \fi
\expandafter\ifx\csname TeXtopo\endcsname\relax \else
\PackageError{TeXtopo}
{TeXtopo loaded before TeXshade}
{\MessageBreak
For the proper function of the TeXtopo/TeXshade combo the \MessageBreak
TeXshade package must be loaded before the TeXtopo package.\MessageBreak
Please change the order of the \noexpand\usepackage commands in your
\MessageBreak
document header section or use the `biotex.sty'.\MessageBreak\MessageBreak
Quit here by typing \space X <return>. \MessageBreak
}
\fi
\catcode`\@11
\def\rotopo#1{%
\Grot@setangle{#1}%
\setbox\z@\hbox\bgroup\ignorespaces}
\def\endrotopo{%
\unskip\egroup
\Grot@x\z@
\Grot@y\z@
\wd0\z@\dp0\z@\ht0\z@
\Grot@box
}
\newread\structurefile \newwrite\featurefile
\newread\alignfile \newread\sublogofile
\newwrite\exp@rtfile
\expandafter\ifx\csname blacktriangleright\endcsname\relax
\openin\structurefile = amssymb.sty
\ifeof\structurefile
\message{<AMS symbol style `amssymb.sty' not installed - using round heads>}
\def\blacktriangleright{%
\rule[\width@tmp]{0.65ex}{\temp@@length}\kern-0.55ex\ensuremath{\bullet}%
}
\def\blacktriangleleft{%
\ensuremath{\bullet}\kern-0.55ex\rule[\width@tmp]{0.65ex}{\temp@@length}%
}
\else \RequirePackage[]{amssymb} \fi
\closein\structurefile
\fi
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\DeclareMathSymbol{\helixhook}{\mathrel}{alphahelix}{"5E}
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\newcount\seq@percent \newcount\res@count
\newcount\seq@pointer \newcount\pos@count
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\newcount\temp@count \newcount\triple@count
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\newlength\hspace@legend
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\newif\ifsimmode
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\newif\iftopfeaturenow
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\newif\ifframenow
\newif\ifshadingnow
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\else \germ@ntrue \sp@nishfalse \def\cons@name{Konsensus} \fi
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\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{�}
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\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}
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\expandafter\xdef\csname \prfx simE\endcsname{(1)E}
\expandafter\xdef\csname \prfx simF\endcsname{(1)F}
\expandafter\xdef\csname \prfx simG\endcsname{(1)G}
\expandafter\xdef\csname \prfx simH\endcsname{(1)H}
\expandafter\xdef\csname \prfx simI\endcsname{(1)I}
\expandafter\xdef\csname \prfx simJ\endcsname{(1)J}
\expandafter\xdef\csname \prfx simK\endcsname{(1)K}
\expandafter\xdef\csname \prfx simL\endcsname{(1)L}
\expandafter\xdef\csname \prfx simM\endcsname{(1)M}
\expandafter\xdef\csname \prfx simN\endcsname{(1)N}
\expandafter\xdef\csname \prfx simO\endcsname{(1)O}
\expandafter\xdef\csname \prfx simP\endcsname{(1)P}
\expandafter\xdef\csname \prfx simQ\endcsname{(1)Q}
\expandafter\xdef\csname \prfx simR\endcsname{(1)R}
\expandafter\xdef\csname \prfx simS\endcsname{(1)S}
\expandafter\xdef\csname \prfx simT\endcsname{(1)T}
\expandafter\xdef\csname \prfx simU\endcsname{(1)U}
\expandafter\xdef\csname \prfx simV\endcsname{(1)V}
\expandafter\xdef\csname \prfx simW\endcsname{(1)W}
\expandafter\xdef\csname \prfx simX\endcsname{(1)X}
\expandafter\xdef\csname \prfx simY\endcsname{(1)Y}
\expandafter\xdef\csname \prfx simZ\endcsname{(1)Z}
}
\def\clear@simpairs{%
\xdef\simpairCC{1} \xdef\simpairCS{0} \xdef\simpairCT{0} \xdef\simpairCP{0} \xdef\simpairCA{0}
\xdef\simpairCG{0} \xdef\simpairCN{0} \xdef\simpairCD{0} \xdef\simpairCE{0} \xdef\simpairCQ{0}
\xdef\simpairCH{0} \xdef\simpairCR{0} \xdef\simpairCK{0} \xdef\simpairCM{0} \xdef\simpairCI{0}
\xdef\simpairCL{0} \xdef\simpairCV{0} \xdef\simpairCF{0} \xdef\simpairCY{0} \xdef\simpairCW{0}
\xdef\simpairCB{0} \xdef\simpairCJ{0} \xdef\simpairCO{0} \xdef\simpairCU{0} \xdef\simpairCX{0} \xdef\simpairCZ{0}
\xdef\simpairSC{0} \xdef\simpairSS{1} \xdef\simpairST{0} \xdef\simpairSP{0} \xdef\simpairSA{0}
\xdef\simpairSG{0} \xdef\simpairSN{0} \xdef\simpairSD{0} \xdef\simpairSE{0} \xdef\simpairSQ{0}
\xdef\simpairSH{0} \xdef\simpairSR{0} \xdef\simpairSK{0} \xdef\simpairSM{0} \xdef\simpairSI{0}
\xdef\simpairSL{0} \xdef\simpairSV{0} \xdef\simpairSF{0} \xdef\simpairSY{0} \xdef\simpairSW{0}
\xdef\simpairSB{0} \xdef\simpairSJ{0} \xdef\simpairSO{0} \xdef\simpairSU{0} \xdef\simpairSX{0} \xdef\simpairSZ{0}
\xdef\simpairTC{0} \xdef\simpairTS{0} \xdef\simpairTT{1} \xdef\simpairTP{0} \xdef\simpairTA{0}
\xdef\simpairTG{0} \xdef\simpairTN{0} \xdef\simpairTD{0} \xdef\simpairTE{0} \xdef\simpairTQ{0}
\xdef\simpairTH{0} \xdef\simpairTR{0} \xdef\simpairTK{0} \xdef\simpairTM{0} \xdef\simpairTI{0}
\xdef\simpairTL{0} \xdef\simpairTV{0} \xdef\simpairTF{0} \xdef\simpairTY{0} \xdef\simpairTW{0}
\xdef\simpairTB{0} \xdef\simpairTJ{0} \xdef\simpairTO{0} \xdef\simpairTU{0} \xdef\simpairTX{0} \xdef\simpairTZ{0}
\xdef\simpairPC{0} \xdef\simpairPS{0} \xdef\simpairPT{0} \xdef\simpairPP{1} \xdef\simpairPA{0}
\xdef\simpairPG{0} \xdef\simpairPN{0} \xdef\simpairPD{0} \xdef\simpairPE{0} \xdef\simpairPQ{0}
\xdef\simpairPH{0} \xdef\simpairPR{0} \xdef\simpairPK{0} \xdef\simpairPM{0} \xdef\simpairPI{0}
\xdef\simpairPL{0} \xdef\simpairPV{0} \xdef\simpairPF{0} \xdef\simpairPY{0} \xdef\simpairPW{0}
\xdef\simpairPB{0} \xdef\simpairPJ{0} \xdef\simpairPO{0} \xdef\simpairPU{0} \xdef\simpairPX{0} \xdef\simpairPZ{0}
\xdef\simpairAC{0} \xdef\simpairAS{0} \xdef\simpairAT{0} \xdef\simpairAP{0} \xdef\simpairAA{1}
\xdef\simpairAG{0} \xdef\simpairAN{0} \xdef\simpairAD{0} \xdef\simpairAE{0} \xdef\simpairAQ{0}
\xdef\simpairAH{0} \xdef\simpairAR{0} \xdef\simpairAK{0} \xdef\simpairAM{0} \xdef\simpairAI{0}
\xdef\simpairAL{0} \xdef\simpairAV{0} \xdef\simpairAF{0} \xdef\simpairAY{0} \xdef\simpairAW{0}
\xdef\simpairAB{0} \xdef\simpairAJ{0} \xdef\simpairAO{0} \xdef\simpairAU{0} \xdef\simpairAX{0} \xdef\simpairAZ{0}
\xdef\simpairGC{0} \xdef\simpairGS{0} \xdef\simpairGT{0} \xdef\simpairGP{0} \xdef\simpairGA{0}
\xdef\simpairGG{1} \xdef\simpairGN{0} \xdef\simpairGD{0} \xdef\simpairGE{0} \xdef\simpairGQ{0}
\xdef\simpairGH{0} \xdef\simpairGR{0} \xdef\simpairGK{0} \xdef\simpairGM{0} \xdef\simpairGI{0}
\xdef\simpairGL{0} \xdef\simpairGV{0} \xdef\simpairGF{0} \xdef\simpairGY{0} \xdef\simpairGW{0}
\xdef\simpairGB{0} \xdef\simpairGJ{0} \xdef\simpairGO{0} \xdef\simpairGU{0} \xdef\simpairGX{0} \xdef\simpairGZ{0}
\xdef\simpairNC{0} \xdef\simpairNS{0} \xdef\simpairNT{0} \xdef\simpairNP{0} \xdef\simpairNA{0}
\xdef\simpairNG{0} \xdef\simpairNN{1} \xdef\simpairND{0} \xdef\simpairNE{0} \xdef\simpairNQ{0}
\xdef\simpairNH{0} \xdef\simpairNR{0} \xdef\simpairNK{0} \xdef\simpairNM{0} \xdef\simpairNI{0}
\xdef\simpairNL{0} \xdef\simpairNV{0} \xdef\simpairNF{0} \xdef\simpairNY{0} \xdef\simpairNW{0}
\xdef\simpairNB{0} \xdef\simpairNJ{0} \xdef\simpairNO{0} \xdef\simpairNU{0} \xdef\simpairNX{0} \xdef\simpairNZ{0}
\xdef\simpairDC{0} \xdef\simpairDS{0} \xdef\simpairDT{0} \xdef\simpairDP{0} \xdef\simpairDA{0}
\xdef\simpairDG{0} \xdef\simpairDN{0} \xdef\simpairDD{1} \xdef\simpairDE{0} \xdef\simpairDQ{0}
\xdef\simpairDH{0} \xdef\simpairDR{0} \xdef\simpairDK{0} \xdef\simpairDM{0} \xdef\simpairDI{0}
\xdef\simpairDL{0} \xdef\simpairDV{0} \xdef\simpairDF{0} \xdef\simpairDY{0} \xdef\simpairDW{0}
\xdef\simpairDB{0} \xdef\simpairDJ{0} \xdef\simpairDO{0} \xdef\simpairDU{0} \xdef\simpairDX{0} \xdef\simpairDZ{0}
\xdef\simpairEC{0} \xdef\simpairES{0} \xdef\simpairET{0} \xdef\simpairEP{0} \xdef\simpairEA{0}
\xdef\simpairEG{0} \xdef\simpairEN{0} \xdef\simpairED{0} \xdef\simpairEE{1} \xdef\simpairEQ{0}
\xdef\simpairEH{0} \xdef\simpairER{0} \xdef\simpairEK{0} \xdef\simpairEM{0} \xdef\simpairEI{0}
\xdef\simpairEL{0} \xdef\simpairEV{0} \xdef\simpairEF{0} \xdef\simpairEY{0} \xdef\simpairEW{0}
\xdef\simpairEB{0} \xdef\simpairEJ{0} \xdef\simpairEO{0} \xdef\simpairEU{0} \xdef\simpairEX{0} \xdef\simpairEZ{0}
\xdef\simpairQC{0} \xdef\simpairQS{0} \xdef\simpairQT{0} \xdef\simpairQP{0} \xdef\simpairQA{0}
\xdef\simpairQG{0} \xdef\simpairQN{0} \xdef\simpairQD{0} \xdef\simpairQE{0} \xdef\simpairQQ{1}
\xdef\simpairQH{0} \xdef\simpairQR{0} \xdef\simpairQK{0} \xdef\simpairQM{0} \xdef\simpairQI{0}
\xdef\simpairQL{0} \xdef\simpairQV{0} \xdef\simpairQF{0} \xdef\simpairQY{0} \xdef\simpairQW{0}
\xdef\simpairQB{0} \xdef\simpairQJ{0} \xdef\simpairQO{0} \xdef\simpairQU{0} \xdef\simpairQX{0} \xdef\simpairQZ{0}
\xdef\simpairHC{0} \xdef\simpairHS{0} \xdef\simpairHT{0} \xdef\simpairHP{0} \xdef\simpairHA{0}
\xdef\simpairHG{0} \xdef\simpairHN{0} \xdef\simpairHD{0} \xdef\simpairHE{0} \xdef\simpairHQ{0}
\xdef\simpairHH{1} \xdef\simpairHR{0} \xdef\simpairHK{0} \xdef\simpairHM{0} \xdef\simpairHI{0}
\xdef\simpairHL{0} \xdef\simpairHV{0} \xdef\simpairHF{0} \xdef\simpairHY{0} \xdef\simpairHW{0}
\xdef\simpairHB{0} \xdef\simpairHJ{0} \xdef\simpairHO{0} \xdef\simpairHU{0} \xdef\simpairHX{0} \xdef\simpairHZ{0}
\xdef\simpairRC{0} \xdef\simpairRS{0} \xdef\simpairRT{0} \xdef\simpairRP{0} \xdef\simpairRA{0}
\xdef\simpairRG{0} \xdef\simpairRN{0} \xdef\simpairRD{0} \xdef\simpairRE{0} \xdef\simpairRQ{0}
\xdef\simpairRH{0} \xdef\simpairRR{1} \xdef\simpairRK{0} \xdef\simpairRM{0} \xdef\simpairRI{0}
\xdef\simpairRL{0} \xdef\simpairRV{0} \xdef\simpairRF{0} \xdef\simpairRY{0} \xdef\simpairRW{0}
\xdef\simpairRB{0} \xdef\simpairRJ{0} \xdef\simpairRO{0} \xdef\simpairRU{0} \xdef\simpairRX{0} \xdef\simpairRZ{0}
\xdef\simpairKC{0} \xdef\simpairKS{0} \xdef\simpairKT{0} \xdef\simpairKP{0} \xdef\simpairKA{0}
\xdef\simpairKG{0} \xdef\simpairKN{0} \xdef\simpairKD{0} \xdef\simpairKE{0} \xdef\simpairKQ{0}
\xdef\simpairKH{0} \xdef\simpairKR{0} \xdef\simpairKK{1} \xdef\simpairKM{0} \xdef\simpairKI{0}
\xdef\simpairKL{0} \xdef\simpairKV{0} \xdef\simpairKF{0} \xdef\simpairKY{0} \xdef\simpairKW{0}
\xdef\simpairKB{0} \xdef\simpairKJ{0} \xdef\simpairKO{0} \xdef\simpairKU{0} \xdef\simpairKX{0} \xdef\simpairKZ{0}
\xdef\simpairMC{0} \xdef\simpairMS{0} \xdef\simpairMT{0} \xdef\simpairMP{0} \xdef\simpairMA{0}
\xdef\simpairMG{0} \xdef\simpairMN{0} \xdef\simpairMD{0} \xdef\simpairME{0} \xdef\simpairMQ{0}
\xdef\simpairMH{0} \xdef\simpairMR{0} \xdef\simpairMK{0} \xdef\simpairMM{1} \xdef\simpairMI{0}
\xdef\simpairML{0} \xdef\simpairMV{0} \xdef\simpairMF{0} \xdef\simpairMY{0} \xdef\simpairMW{0}
\xdef\simpairMB{0} \xdef\simpairMJ{0} \xdef\simpairMO{0} \xdef\simpairMU{0} \xdef\simpairMX{0} \xdef\simpairMZ{0}
\xdef\simpairIC{0} \xdef\simpairIS{0} \xdef\simpairIT{0} \xdef\simpairIP{0} \xdef\simpairIA{0}
\xdef\simpairIG{0} \xdef\simpairIN{0} \xdef\simpairID{0} \xdef\simpairIE{0} \xdef\simpairIQ{0}
\xdef\simpairIH{0} \xdef\simpairIR{0} \xdef\simpairIK{0} \xdef\simpairIM{0} \xdef\simpairII{1}
\xdef\simpairIL{0} \xdef\simpairIV{0} \xdef\simpairIF{0} \xdef\simpairIY{0} \xdef\simpairIW{0}
\xdef\simpairIB{0} \xdef\simpairIJ{0} \xdef\simpairIO{0} \xdef\simpairIU{0} \xdef\simpairIX{0} \xdef\simpairIZ{0}
\xdef\simpairLC{0} \xdef\simpairLS{0} \xdef\simpairLT{0} \xdef\simpairLP{0} \xdef\simpairLA{0}
\xdef\simpairLG{0} \xdef\simpairLN{0} \xdef\simpairLD{0} \xdef\simpairLE{0} \xdef\simpairLQ{0}
\xdef\simpairLH{0} \xdef\simpairLR{0} \xdef\simpairLK{0} \xdef\simpairLM{0} \xdef\simpairLI{0}
\xdef\simpairLL{1} \xdef\simpairLV{0} \xdef\simpairLF{0} \xdef\simpairLY{0} \xdef\simpairLW{0}
\xdef\simpairLB{0} \xdef\simpairLJ{0} \xdef\simpairLO{0} \xdef\simpairLU{0} \xdef\simpairLX{0} \xdef\simpairLZ{0}
\xdef\simpairVC{0} \xdef\simpairVS{0} \xdef\simpairVT{0} \xdef\simpairVP{0} \xdef\simpairVA{0}
\xdef\simpairVG{0} \xdef\simpairVN{0} \xdef\simpairVD{0} \xdef\simpairVE{0} \xdef\simpairVQ{0}
\xdef\simpairVH{0} \xdef\simpairVR{0} \xdef\simpairVK{0} \xdef\simpairVM{0} \xdef\simpairVI{0}
\xdef\simpairVL{0} \xdef\simpairVV{1} \xdef\simpairVF{0} \xdef\simpairVY{0} \xdef\simpairVW{0}
\xdef\simpairVB{0} \xdef\simpairVJ{0} \xdef\simpairVO{0} \xdef\simpairVU{0} \xdef\simpairVX{0} \xdef\simpairVZ{0}
\xdef\simpairFC{0} \xdef\simpairFS{0} \xdef\simpairFT{0} \xdef\simpairFP{0} \xdef\simpairFA{0}
\xdef\simpairFG{0} \xdef\simpairFN{0} \xdef\simpairFD{0} \xdef\simpairFE{0} \xdef\simpairFQ{0}
\xdef\simpairFH{0} \xdef\simpairFR{0} \xdef\simpairFK{0} \xdef\simpairFM{0} \xdef\simpairFI{0}
\xdef\simpairFL{0} \xdef\simpairFV{0} \xdef\simpairFF{1} \xdef\simpairFY{0} \xdef\simpairFW{0}
\xdef\simpairFB{0} \xdef\simpairFJ{0} \xdef\simpairFO{0} \xdef\simpairFU{0} \xdef\simpairFX{0} \xdef\simpairFZ{0}
\xdef\simpairYC{0} \xdef\simpairYS{0} \xdef\simpairYT{0} \xdef\simpairYP{0} \xdef\simpairYA{0}
\xdef\simpairYG{0} \xdef\simpairYN{0} \xdef\simpairYD{0} \xdef\simpairYE{0} \xdef\simpairYQ{0}
\xdef\simpairYH{0} \xdef\simpairYR{0} \xdef\simpairYK{0} \xdef\simpairYM{0} \xdef\simpairYI{0}
\xdef\simpairYL{0} \xdef\simpairYV{0} \xdef\simpairYF{0} \xdef\simpairYY{1} \xdef\simpairYW{0}
\xdef\simpairYB{0} \xdef\simpairYJ{0} \xdef\simpairYO{0} \xdef\simpairYU{0} \xdef\simpairYX{0} \xdef\simpairYZ{0}
\xdef\simpairWC{0} \xdef\simpairWS{0} \xdef\simpairWT{0} \xdef\simpairWP{0} \xdef\simpairWA{0}
\xdef\simpairWG{0} \xdef\simpairWN{0} \xdef\simpairWD{0} \xdef\simpairWE{0} \xdef\simpairWQ{0}
\xdef\simpairWH{0} \xdef\simpairWR{0} \xdef\simpairWK{0} \xdef\simpairWM{0} \xdef\simpairWI{0}
\xdef\simpairWL{0} \xdef\simpairWV{0} \xdef\simpairWF{0} \xdef\simpairWY{0} \xdef\simpairWW{1}
\xdef\simpairWB{0} \xdef\simpairWJ{0} \xdef\simpairWO{0} \xdef\simpairWU{0} \xdef\simpairWX{0} \xdef\simpairWZ{0}
\xdef\simpairBC{0} \xdef\simpairBS{0} \xdef\simpairBT{0} \xdef\simpairBP{0} \xdef\simpairBA{0}
\xdef\simpairBG{0} \xdef\simpairBN{0} \xdef\simpairBD{0} \xdef\simpairBE{0} \xdef\simpairBQ{0}
\xdef\simpairBH{0} \xdef\simpairBR{0} \xdef\simpairBK{0} \xdef\simpairBM{0} \xdef\simpairBI{0}
\xdef\simpairBL{0} \xdef\simpairBV{0} \xdef\simpairBF{0} \xdef\simpairBY{0} \xdef\simpairBW{0}
\xdef\simpairBB{1} \xdef\simpairBJ{0} \xdef\simpairBO{0} \xdef\simpairBU{0} \xdef\simpairBX{0} \xdef\simpairBZ{0}
\xdef\simpairJC{0} \xdef\simpairJS{0} \xdef\simpairJT{0} \xdef\simpairJP{0} \xdef\simpairJA{0}
\xdef\simpairJG{0} \xdef\simpairJN{0} \xdef\simpairJD{0} \xdef\simpairJE{0} \xdef\simpairJQ{0}
\xdef\simpairJH{0} \xdef\simpairJR{0} \xdef\simpairJK{0} \xdef\simpairJM{0} \xdef\simpairJI{0}
\xdef\simpairJL{0} \xdef\simpairJV{0} \xdef\simpairJF{0} \xdef\simpairJY{0} \xdef\simpairJW{0}
\xdef\simpairJB{0} \xdef\simpairJJ{1} \xdef\simpairJO{0} \xdef\simpairJU{0} \xdef\simpairJX{0} \xdef\simpairJZ{0}
\xdef\simpairOC{0} \xdef\simpairOS{0} \xdef\simpairOT{0} \xdef\simpairOP{0} \xdef\simpairOA{0}
\xdef\simpairOG{0} \xdef\simpairON{0} \xdef\simpairOD{0} \xdef\simpairOE{0} \xdef\simpairOQ{0}
\xdef\simpairOH{0} \xdef\simpairOR{0} \xdef\simpairOK{0} \xdef\simpairOM{0} \xdef\simpairOI{0}
\xdef\simpairOL{0} \xdef\simpairOV{0} \xdef\simpairOF{0} \xdef\simpairOY{0} \xdef\simpairOW{0}
\xdef\simpairOB{0} \xdef\simpairOJ{0} \xdef\simpairOO{1} \xdef\simpairOU{0} \xdef\simpairOX{0} \xdef\simpairOZ{0}
\xdef\simpairUC{0} \xdef\simpairUS{0} \xdef\simpairUT{0} \xdef\simpairUP{0} \xdef\simpairUA{0}
\xdef\simpairUG{0} \xdef\simpairUN{0} \xdef\simpairUD{0} \xdef\simpairUE{0} \xdef\simpairUQ{0}
\xdef\simpairUH{0} \xdef\simpairUR{0} \xdef\simpairUK{0} \xdef\simpairUM{0} \xdef\simpairUI{0}
\xdef\simpairUL{0} \xdef\simpairUV{0} \xdef\simpairUF{0} \xdef\simpairUY{0} \xdef\simpairUW{0}
\xdef\simpairUB{0} \xdef\simpairUJ{0} \xdef\simpairUO{0} \xdef\simpairUU{1} \xdef\simpairUX{0} \xdef\simpairUZ{0}
\xdef\simpairXC{0} \xdef\simpairXS{0} \xdef\simpairXT{0} \xdef\simpairXP{0} \xdef\simpairXA{0}
\xdef\simpairXG{0} \xdef\simpairXN{0} \xdef\simpairXD{0} \xdef\simpairXE{0} \xdef\simpairXQ{0}
\xdef\simpairXH{0} \xdef\simpairXR{0} \xdef\simpairXK{0} \xdef\simpairXM{0} \xdef\simpairXI{0}
\xdef\simpairXL{0} \xdef\simpairXV{0} \xdef\simpairXF{0} \xdef\simpairXY{0} \xdef\simpairXW{0}
\xdef\simpairXB{0} \xdef\simpairXJ{0} \xdef\simpairXO{0} \xdef\simpairXU{0} \xdef\simpairXX{1} \xdef\simpairXZ{0}
\xdef\simpairZC{0} \xdef\simpairZS{0} \xdef\simpairZT{0} \xdef\simpairZP{0} \xdef\simpairZA{0}
\xdef\simpairZG{0} \xdef\simpairZN{0} \xdef\simpairZD{0} \xdef\simpairZE{0} \xdef\simpairZQ{0}
\xdef\simpairZH{0} \xdef\simpairZR{0} \xdef\simpairZK{0} \xdef\simpairZM{0} \xdef\simpairZI{0}
\xdef\simpairZL{0} \xdef\simpairZV{0} \xdef\simpairZF{0} \xdef\simpairZY{0} \xdef\simpairZW{0}
\xdef\simpairZB{0} \xdef\simpairZJ{0} \xdef\simpairZO{0} \xdef\simpairZU{0} \xdef\simpairZX{0} \xdef\simpairZZ{1}
}
\def\clear@sim@count{
\def\clear@sim@nums{%
\advance\innerloopcount by 1
\ifnum\innerloopcount>\seq@count
\else
\expandafter\xdef\csname poscount\the\outerloopcount @\the\innerloopcount\endcsname{0}
\expandafter\xdef\csname identcount\the\outerloopcount @\the\innerloopcount\endcsname{0}
\expandafter\xdef\csname simcount\the\outerloopcount @\the\innerloopcount\endcsname{0}
\clear@sim@nums
\fi
}
\outerloopcount=1
\loop
\innerloopcount=\outerloopcount
\clear@sim@nums
\advance\outerloopcount by 1
\ifnum\outerloopcount<\seq@count \repeat
}
\xdef\pepmwA{711} \xdef\pepmwB{1146} \xdef\pepmwC{1032}
\xdef\pepmwD{1151} \xdef\pepmwE{1291} \xdef\pepmwF{1472}
\xdef\pepmwG{571} \xdef\pepmwH{1372} \xdef\pepmwI{1132}
\xdef\pepmwJ{0} \xdef\pepmwK{1282} \xdef\pepmwL{1132}
\xdef\pepmwM{1312} \xdef\pepmwN{1141} \xdef\pepmwO{0}
\xdef\pepmwP{971} \xdef\pepmwQ{1281} \xdef\pepmwR{1562}
\xdef\pepmwS{871} \xdef\pepmwT{1011} \xdef\pepmwU{0}
\xdef\pepmwV{991} \xdef\pepmwW{1862} \xdef\pepmwX{1282}
\xdef\pepmwY{1632} \xdef\pepmwZ{1286}
\xdef\DNAmwA{3462} \xdef\DNAmwB{0} \xdef\DNAmwC{3222}
\xdef\DNAmwD{0} \xdef\DNAmwE{0} \xdef\DNAmwF{0}
\xdef\DNAmwG{3622} \xdef\DNAmwH{0} \xdef\DNAmwI{0}
\xdef\DNAmwJ{0} \xdef\DNAmwK{0} \xdef\DNAmwL{0}
\xdef\DNAmwM{0} \xdef\DNAmwN{0} \xdef\DNAmwO{0}
\xdef\DNAmwP{0} \xdef\DNAmwQ{0} \xdef\DNAmwR{0}
\xdef\DNAmwS{0} \xdef\DNAmwT{3372} \xdef\DNAmwU{3232}
\xdef\DNAmwV{0} \xdef\DNAmwW{0} \xdef\DNAmwX{0}
\xdef\DNAmwY{0} \xdef\DNAmwZ{0}
\xdef\pepchargeA{0} \xdef\pepchargeB{0} \xdef\pepchargeC{-30}
\xdef\pepchargeD{-1000} \xdef\pepchargeE{-1000} \xdef\pepchargeF{0}
\xdef\pepchargeG{0} \xdef\pepchargeH{165} \xdef\pepchargeI{0}
\xdef\pepchargeJ{0} \xdef\pepchargeK{1000} \xdef\pepchargeL{0}
\xdef\pepchargeM{0} \xdef\pepchargeN{0} \xdef\pepchargeO{0}
\xdef\pepchargeP{0} \xdef\pepchargeQ{0} \xdef\pepchargeR{1000}
\xdef\pepchargeS{0} \xdef\pepchargeT{0} \xdef\pepchargeU{0}
\xdef\pepchargeV{0} \xdef\pepchargeW{0} \xdef\pepchargeX{0}
\xdef\pepchargeY{0} \xdef\pepchargeZ{0}
\xdef\chargeNterm{910} \xdef\chargeCterm{-1000}
\xdef\chargeA{0} \xdef\chargeB{0} \xdef\chargeC{0}
\xdef\chargeD{-50} \xdef\chargeE{-50} \xdef\chargeF{0}
\xdef\chargeG{0} \xdef\chargeH{30} \xdef\chargeI{0}
\xdef\chargeJ{0} \xdef\chargeK{50} \xdef\chargeL{0}
\xdef\chargeM{0} \xdef\chargeN{0} \xdef\chargeO{0}
\xdef\chargeP{0} \xdef\chargeQ{0} \xdef\chargeR{50}
\xdef\chargeS{0} \xdef\chargeT{0} \xdef\chargeU{0}
\xdef\chargeV{0} \xdef\chargeW{0} \xdef\chargeX{0}
\xdef\chargeY{0} \xdef\chargeZ{0}
\xdef\molwA{11} \xdef\molwB{45} \xdef\molwC{36}
\xdef\molwD{45} \xdef\molwE{66} \xdef\molwF{70}
\xdef\molwG{1} \xdef\molwH{62} \xdef\molwI{44}
\xdef\molwJ{N} \xdef\molwK{55} \xdef\molwL{44}
\xdef\molwM{58} \xdef\molwN{44} \xdef\molwO{N}
\xdef\molwP{31} \xdef\molwQ{55} \xdef\molwR{77}
\xdef\molwS{19} \xdef\molwT{34} \xdef\molwU{N}
\xdef\molwV{33} \xdef\molwW{100} \xdef\molwX{55}
\xdef\molwY{82} \xdef\molwZ{66}
\xdef\HydroA{21} \xdef\HydroB{N} \xdef\HydroC{10}
\xdef\HydroD{-31} \xdef\HydroE{-25} \xdef\HydroF{41}
\xdef\HydroG{16} \xdef\HydroH{-14} \xdef\HydroI{47}
\xdef\HydroJ{N} \xdef\HydroK{-52} \xdef\HydroL{36}
\xdef\HydroM{22} \xdef\HydroN{-27} \xdef\HydroO{N}
\xdef\HydroP{4} \xdef\HydroQ{-29} \xdef\HydroR{-53}
\xdef\HydroS{-6} \xdef\HydroT{-2} \xdef\HydroU{N}
\xdef\HydroV{37} \xdef\HydroW{28} \xdef\HydroX{N}
\xdef\HydroY{9} \xdef\HydroZ{N}
\xdef\consCB{0} \xdef\consCJ{0} \xdef\consCO{0} \xdef\consCU{0} \xdef\consCX{0} \xdef\consCZ{0}
\expandafter\xdef\csname consC?\endcsname{0}
\xdef\consSB{0} \xdef\consSJ{0} \xdef\consSO{0} \xdef\consSU{0} \xdef\consSX{0} \xdef\consSZ{0}
\expandafter\xdef\csname consS?\endcsname{0}
\xdef\consTB{0} \xdef\consTJ{0} \xdef\consTO{0} \xdef\consTU{0} \xdef\consTX{0} \xdef\consTZ{0}
\expandafter\xdef\csname consT?\endcsname{0}
\xdef\consPB{0} \xdef\consPJ{0} \xdef\consPO{0} \xdef\consPU{0} \xdef\consPX{0} \xdef\consPZ{0}
\expandafter\xdef\csname consP?\endcsname{0}
\xdef\consAB{0} \xdef\consAJ{0} \xdef\consAO{0} \xdef\consAU{0} \xdef\consAX{0} \xdef\consAZ{0}
\expandafter\xdef\csname consA?\endcsname{0}
\xdef\consGB{0} \xdef\consGJ{0} \xdef\consGO{0} \xdef\consGU{0} \xdef\consGX{0} \xdef\consGZ{0}
\expandafter\xdef\csname consG?\endcsname{0}
\xdef\consNB{0} \xdef\consNJ{0} \xdef\consNO{0} \xdef\consNU{0} \xdef\consNX{0} \xdef\consNZ{0}
\expandafter\xdef\csname consN?\endcsname{0}
\xdef\consDB{0} \xdef\consDJ{0} \xdef\consDO{0} \xdef\consDU{0} \xdef\consDX{0} \xdef\consDZ{0}
\expandafter\xdef\csname consD?\endcsname{0}
\xdef\consEB{0} \xdef\consEJ{0} \xdef\consEO{0} \xdef\consEU{0} \xdef\consEX{0} \xdef\consEZ{0}
\expandafter\xdef\csname consE?\endcsname{0}
\xdef\consQB{0} \xdef\consQJ{0} \xdef\consQO{0} \xdef\consQU{0} \xdef\consQX{0} \xdef\consQZ{0}
\expandafter\xdef\csname consQ?\endcsname{0}
\xdef\consHB{0} \xdef\consHJ{0} \xdef\consHO{0} \xdef\consHU{0} \xdef\consHX{0} \xdef\consHZ{0}
\expandafter\xdef\csname consH?\endcsname{0}
\xdef\consRB{0} \xdef\consRJ{0} \xdef\consRO{0} \xdef\consRU{0} \xdef\consRX{0} \xdef\consRZ{0}
\expandafter\xdef\csname consR?\endcsname{0}
\xdef\consKB{0} \xdef\consKJ{0} \xdef\consKO{0} \xdef\consKU{0} \xdef\consKX{0} \xdef\consKZ{0}
\expandafter\xdef\csname consK?\endcsname{0}
\xdef\consMB{0} \xdef\consMJ{0} \xdef\consMO{0} \xdef\consMU{0} \xdef\consMX{0} \xdef\consMZ{0}
\expandafter\xdef\csname consM?\endcsname{0}
\xdef\consIB{0} \xdef\consIJ{0} \xdef\consIO{0} \xdef\consIU{0} \xdef\consIX{0} \xdef\consIZ{0}
\expandafter\xdef\csname consI?\endcsname{0}
\xdef\consLB{0} \xdef\consLJ{0} \xdef\consLO{0} \xdef\consLU{0} \xdef\consLX{0} \xdef\consLZ{0}
\expandafter\xdef\csname consL?\endcsname{0}
\xdef\consVB{0} \xdef\consVJ{0} \xdef\consVO{0} \xdef\consVU{0} \xdef\consVX{0} \xdef\consVZ{0}
\expandafter\xdef\csname consV?\endcsname{0}
\xdef\consFB{0} \xdef\consFJ{0} \xdef\consFO{0} \xdef\consFU{0} \xdef\consFX{0} \xdef\consFZ{0}
\expandafter\xdef\csname consF?\endcsname{0}
\xdef\consYB{0} \xdef\consYJ{0} \xdef\consYO{0} \xdef\consYU{0} \xdef\consYX{0} \xdef\consYZ{0}
\expandafter\xdef\csname consY?\endcsname{0}
\xdef\consWB{0} \xdef\consWJ{0} \xdef\consWO{0} \xdef\consWU{0} \xdef\consWX{0} \xdef\consWZ{0}
\expandafter\xdef\csname consW?\endcsname{0}
\xdef\consBC{0} \xdef\consBS{0} \xdef\consBT{0} \xdef\consBP{0} \xdef\consBA{0}
\xdef\consBG{0} \xdef\consBN{0} \xdef\consBD{0} \xdef\consBE{0} \xdef\consBQ{0}
\xdef\consBH{0} \xdef\consBR{0} \xdef\consBK{0} \xdef\consBM{0} \xdef\consBI{0}
\xdef\consBL{0} \xdef\consBV{0} \xdef\consBF{0} \xdef\consBY{0} \xdef\consBW{0}
\xdef\consBB{10} \xdef\consBJ{0} \xdef\consBO{0} \xdef\consBU{0} \xdef\consBX{0} \xdef\consBZ{0}
\expandafter\xdef\csname consB.\endcsname{0}
\expandafter\xdef\csname consB?\endcsname{0}
\xdef\consJC{0} \xdef\consJS{0} \xdef\consJT{0} \xdef\consJP{0} \xdef\consJA{0}
\xdef\consJG{0} \xdef\consJN{0} \xdef\consJD{0} \xdef\consJE{0} \xdef\consJQ{0}
\xdef\consJH{0} \xdef\consJR{0} \xdef\consJK{0} \xdef\consJM{0} \xdef\consJI{0}
\xdef\consJL{0} \xdef\consJV{0} \xdef\consJF{0} \xdef\consJY{0} \xdef\consJW{0}
\xdef\consJB{0} \xdef\consJJ{10} \xdef\consJO{0} \xdef\consJU{0} \xdef\consJX{0} \xdef\consJZ{0}
\expandafter\xdef\csname consJ.\endcsname{0}
\expandafter\xdef\csname consJ?\endcsname{0}
\xdef\consOC{0} \xdef\consOS{0} \xdef\consOT{0} \xdef\consOP{0} \xdef\consOA{0}
\xdef\consOG{0} \xdef\consON{0} \xdef\consOD{0} \xdef\consOE{0} \xdef\consOQ{0}
\xdef\consOH{0} \xdef\consOR{0} \xdef\consOK{0} \xdef\consOM{0} \xdef\consOI{0}
\xdef\consOL{0} \xdef\consOV{0} \xdef\consOF{0} \xdef\consOY{0} \xdef\consOW{0}
\xdef\consOB{0} \xdef\consOJ{0} \xdef\consOO{10} \xdef\consOU{0} \xdef\consOX{0} \xdef\consOZ{0}
\expandafter\xdef\csname consO.\endcsname{0}
\expandafter\xdef\csname consO?\endcsname{0}
\xdef\consUC{0} \xdef\consUS{0} \xdef\consUT{0} \xdef\consUP{0} \xdef\consUA{0}
\xdef\consUG{0} \xdef\consUN{0} \xdef\consUD{0} \xdef\consUE{0} \xdef\consUQ{0}
\xdef\consUH{0} \xdef\consUR{0} \xdef\consUK{0} \xdef\consUM{0} \xdef\consUI{0}
\xdef\consUL{0} \xdef\consUV{0} \xdef\consUF{0} \xdef\consUY{0} \xdef\consUW{0}
\xdef\consUB{0} \xdef\consUJ{0} \xdef\consUO{0} \xdef\consUU{10} \xdef\consUX{0} \xdef\consUZ{0}
\expandafter\xdef\csname consU.\endcsname{0}
\expandafter\xdef\csname consU?\endcsname{0}
\xdef\consXC{0} \xdef\consXS{0} \xdef\consXT{0} \xdef\consXP{0} \xdef\consXA{0}
\xdef\consXG{0} \xdef\consXN{0} \xdef\consXD{0} \xdef\consXE{0} \xdef\consXQ{0}
\xdef\consXH{0} \xdef\consXR{0} \xdef\consXK{0} \xdef\consXM{0} \xdef\consXI{0}
\xdef\consXL{0} \xdef\consXV{0} \xdef\consXF{0} \xdef\consXY{0} \xdef\consXW{0}
\xdef\consXB{0} \xdef\consXJ{0} \xdef\consXO{0} \xdef\consXU{0} \xdef\consXX{10} \xdef\consXZ{0}
\expandafter\xdef\csname consX.\endcsname{0}
\expandafter\xdef\csname consX?\endcsname{0}
\xdef\consZC{0} \xdef\consZS{0} \xdef\consZT{0} \xdef\consZP{0} \xdef\consZA{0}
\xdef\consZG{0} \xdef\consZN{0} \xdef\consZD{0} \xdef\consZE{0} \xdef\consZQ{0}
\xdef\consZH{0} \xdef\consZR{0} \xdef\consZK{0} \xdef\consZM{0} \xdef\consZI{0}
\xdef\consZL{0} \xdef\consZV{0} \xdef\consZF{0} \xdef\consZY{0} \xdef\consZW{0}
\xdef\consZB{0} \xdef\consZJ{0} \xdef\consZO{0} \xdef\consZU{0} \xdef\consZX{0} \xdef\consZZ{10}
\expandafter\xdef\csname consZ.\endcsname{0}
\expandafter\xdef\csname consZ?\endcsname{0}
\expandafter\xdef\csname cons..\endcsname{0}
\expandafter\xdef\csname cons.?\endcsname{0}
\expandafter\xdef\csname cons?C\endcsname{0}
\expandafter\xdef\csname cons?S\endcsname{0}
\expandafter\xdef\csname cons?T\endcsname{0}
\expandafter\xdef\csname cons?P\endcsname{0}
\expandafter\xdef\csname cons?A\endcsname{0}
\expandafter\xdef\csname cons?G\endcsname{0}
\expandafter\xdef\csname cons?N\endcsname{0}
\expandafter\xdef\csname cons?D\endcsname{0}
\expandafter\xdef\csname cons?E\endcsname{0}
\expandafter\xdef\csname cons?Q\endcsname{0}
\expandafter\xdef\csname cons?H\endcsname{0}
\expandafter\xdef\csname cons?R\endcsname{0}
\expandafter\xdef\csname cons?K\endcsname{0}
\expandafter\xdef\csname cons?M\endcsname{0}
\expandafter\xdef\csname cons?I\endcsname{0}
\expandafter\xdef\csname cons?L\endcsname{0}
\expandafter\xdef\csname cons?V\endcsname{0}
\expandafter\xdef\csname cons?F\endcsname{0}
\expandafter\xdef\csname cons?Y\endcsname{0}
\expandafter\xdef\csname cons?W\endcsname{0}
\expandafter\xdef\csname cons?B\endcsname{0}
\expandafter\xdef\csname cons?J\endcsname{0}
\expandafter\xdef\csname cons?O\endcsname{0}
\expandafter\xdef\csname cons?U\endcsname{0}
\expandafter\xdef\csname cons?X\endcsname{0}
\expandafter\xdef\csname cons?Z\endcsname{0}
\expandafter\xdef\csname cons?.\endcsname{0}
\expandafter\xdef\csname cons??\endcsname{0}
\expandafter\xdef\csname cons==\endcsname{0}
\def\gappenalty#1{%
\expandafter\xdef\csname cons.C\endcsname{#1} \expandafter\xdef\csname consC.\endcsname{#1}
\expandafter\xdef\csname cons.S\endcsname{#1} \expandafter\xdef\csname consS.\endcsname{#1}
\expandafter\xdef\csname cons.T\endcsname{#1} \expandafter\xdef\csname consT.\endcsname{#1}
\expandafter\xdef\csname cons.P\endcsname{#1} \expandafter\xdef\csname consP.\endcsname{#1}
\expandafter\xdef\csname cons.A\endcsname{#1} \expandafter\xdef\csname consA.\endcsname{#1}
\expandafter\xdef\csname cons.G\endcsname{#1} \expandafter\xdef\csname consG.\endcsname{#1}
\expandafter\xdef\csname cons.N\endcsname{#1} \expandafter\xdef\csname consN.\endcsname{#1}
\expandafter\xdef\csname cons.D\endcsname{#1} \expandafter\xdef\csname consD.\endcsname{#1}
\expandafter\xdef\csname cons.E\endcsname{#1} \expandafter\xdef\csname consE.\endcsname{#1}
\expandafter\xdef\csname cons.Q\endcsname{#1} \expandafter\xdef\csname consQ.\endcsname{#1}
\expandafter\xdef\csname cons.H\endcsname{#1} \expandafter\xdef\csname consH.\endcsname{#1}
\expandafter\xdef\csname cons.R\endcsname{#1} \expandafter\xdef\csname consR.\endcsname{#1}
\expandafter\xdef\csname cons.K\endcsname{#1} \expandafter\xdef\csname consK.\endcsname{#1}
\expandafter\xdef\csname cons.M\endcsname{#1} \expandafter\xdef\csname consM.\endcsname{#1}
\expandafter\xdef\csname cons.I\endcsname{#1} \expandafter\xdef\csname consI.\endcsname{#1}
\expandafter\xdef\csname cons.L\endcsname{#1} \expandafter\xdef\csname consL.\endcsname{#1}
\expandafter\xdef\csname cons.V\endcsname{#1} \expandafter\xdef\csname consV.\endcsname{#1}
\expandafter\xdef\csname cons.F\endcsname{#1} \expandafter\xdef\csname consF.\endcsname{#1}
\expandafter\xdef\csname cons.Y\endcsname{#1} \expandafter\xdef\csname consY.\endcsname{#1}
\expandafter\xdef\csname cons.W\endcsname{#1} \expandafter\xdef\csname consW.\endcsname{#1}
\expandafter\xdef\csname cons.B\endcsname{#1} \expandafter\xdef\csname consB.\endcsname{#1}
\expandafter\xdef\csname cons.J\endcsname{#1} \expandafter\xdef\csname consJ.\endcsname{#1}
\expandafter\xdef\csname cons.O\endcsname{#1} \expandafter\xdef\csname consO.\endcsname{#1}
\expandafter\xdef\csname cons.U\endcsname{#1} \expandafter\xdef\csname consU.\endcsname{#1}
\expandafter\xdef\csname cons.X\endcsname{#1} \expandafter\xdef\csname consX.\endcsname{#1}
\expandafter\xdef\csname cons.Z\endcsname{#1} \expandafter\xdef\csname consZ.\endcsname{#1}
}
\def\weighttable#1{%
\xdef\first@{#1}
\xdef\temp@{identity}
\ifx\first@\temp@
%%%% identity matrix
\xdef\consCC{10} \xdef\consCS{0} \xdef\consCT{0} \xdef\consCP{0} \xdef\consCA{0}
\xdef\consCG{0} \xdef\consCN{0} \xdef\consCD{0} \xdef\consCE{0} \xdef\consCQ{0}
\xdef\consCH{0} \xdef\consCR{0} \xdef\consCK{0} \xdef\consCM{0} \xdef\consCI{0}
\xdef\consCL{0} \xdef\consCV{0} \xdef\consCF{0} \xdef\consCY{0} \xdef\consCW{0}
\xdef\consSC{0} \xdef\consSS{10} \xdef\consST{0} \xdef\consSP{0} \xdef\consSA{0}
\xdef\consSG{0} \xdef\consSN{0} \xdef\consSD{0} \xdef\consSE{0} \xdef\consSQ{0}
\xdef\consSH{0} \xdef\consSR{0} \xdef\consSK{0} \xdef\consSM{0} \xdef\consSI{0}
\xdef\consSL{0} \xdef\consSV{0} \xdef\consSF{0} \xdef\consSY{0} \xdef\consSW{0}
\xdef\consTC{0} \xdef\consTS{0} \xdef\consTT{10} \xdef\consTP{0} \xdef\consTA{0}
\xdef\consTG{0} \xdef\consTN{0} \xdef\consTD{0} \xdef\consTE{0} \xdef\consTQ{0}
\xdef\consTH{0} \xdef\consTR{0} \xdef\consTK{0} \xdef\consTM{0} \xdef\consTI{0}
\xdef\consTL{0} \xdef\consTV{0} \xdef\consTF{0} \xdef\consTY{0} \xdef\consTW{0}
\xdef\consPC{0} \xdef\consPS{0} \xdef\consPT{0} \xdef\consPP{10} \xdef\consPA{0}
\xdef\consPG{0} \xdef\consPN{0} \xdef\consPD{0} \xdef\consPE{0} \xdef\consPQ{0}
\xdef\consPH{0} \xdef\consPR{0} \xdef\consPK{0} \xdef\consPM{0} \xdef\consPI{0}
\xdef\consPL{0} \xdef\consPV{0} \xdef\consPF{0} \xdef\consPY{0} \xdef\consPW{0}
\xdef\consAC{0} \xdef\consAS{0} \xdef\consAT{0} \xdef\consAP{0} \xdef\consAA{10}
\xdef\consAG{0} \xdef\consAN{0} \xdef\consAD{0} \xdef\consAE{0} \xdef\consAQ{0}
\xdef\consAH{0} \xdef\consAR{0} \xdef\consAK{0} \xdef\consAM{0} \xdef\consAI{0}
\xdef\consAL{0} \xdef\consAV{0} \xdef\consAF{0} \xdef\consAY{0} \xdef\consAW{0}
\xdef\consGC{0} \xdef\consGS{0} \xdef\consGT{0} \xdef\consGP{0} \xdef\consGA{0}
\xdef\consGG{10} \xdef\consGN{0} \xdef\consGD{0} \xdef\consGE{0} \xdef\consGQ{0}
\xdef\consGH{0} \xdef\consGR{0} \xdef\consGK{0} \xdef\consGM{0} \xdef\consGI{0}
\xdef\consGL{0} \xdef\consGV{0} \xdef\consGF{0} \xdef\consGY{0} \xdef\consGW{0}
\xdef\consNC{0} \xdef\consNS{0} \xdef\consNT{0} \xdef\consNP{0} \xdef\consNA{0}
\xdef\consNG{0} \xdef\consNN{10} \xdef\consND{0} \xdef\consNE{0} \xdef\consNQ{0}
\xdef\consNH{0} \xdef\consNR{0} \xdef\consNK{0} \xdef\consNM{0} \xdef\consNI{0}
\xdef\consNL{0} \xdef\consNV{0} \xdef\consNF{0} \xdef\consNY{0} \xdef\consNW{0}
\xdef\consDC{0} \xdef\consDS{0} \xdef\consDT{0} \xdef\consDP{0} \xdef\consDA{0}
\xdef\consDG{0} \xdef\consDN{0} \xdef\consDD{10} \xdef\consDE{0} \xdef\consDQ{0}
\xdef\consDH{0} \xdef\consDR{0} \xdef\consDK{0} \xdef\consDM{0} \xdef\consDI{0}
\xdef\consDL{0} \xdef\consDV{0} \xdef\consDF{0} \xdef\consDY{0} \xdef\consDW{0}
\xdef\consEC{0} \xdef\consES{0} \xdef\consET{0} \xdef\consEP{0} \xdef\consEA{0}
\xdef\consEG{0} \xdef\consEN{0} \xdef\consED{0} \xdef\consEE{10} \xdef\consEQ{0}
\xdef\consEH{0} \xdef\consER{0} \xdef\consEK{0} \xdef\consEM{0} \xdef\consEI{0}
\xdef\consEL{0} \xdef\consEV{0} \xdef\consEF{0} \xdef\consEY{0} \xdef\consEW{0}
\xdef\consQC{0} \xdef\consQS{0} \xdef\consQT{0} \xdef\consQP{0} \xdef\consQA{0}
\xdef\consQG{0} \xdef\consQN{0} \xdef\consQD{0} \xdef\consQE{0} \xdef\consQQ{10}
\xdef\consQH{0} \xdef\consQR{0} \xdef\consQK{0} \xdef\consQM{0} \xdef\consQI{0}
\xdef\consQL{0} \xdef\consQV{0} \xdef\consQF{0} \xdef\consQY{0} \xdef\consQW{0}
\xdef\consHC{0} \xdef\consHS{0} \xdef\consHT{0} \xdef\consHP{0} \xdef\consHA{0}
\xdef\consHG{0} \xdef\consHN{0} \xdef\consHD{0} \xdef\consHE{0} \xdef\consHQ{0}
\xdef\consHH{10} \xdef\consHR{0} \xdef\consHK{0} \xdef\consHM{0} \xdef\consHI{0}
\xdef\consHL{0} \xdef\consHV{0} \xdef\consHF{0} \xdef\consHY{0} \xdef\consHW{0}
\xdef\consRC{0} \xdef\consRS{0} \xdef\consRT{0} \xdef\consRP{0} \xdef\consRA{0}
\xdef\consRG{0} \xdef\consRN{0} \xdef\consRD{0} \xdef\consRE{0} \xdef\consRQ{0}
\xdef\consRH{0} \xdef\consRR{10} \xdef\consRK{0} \xdef\consRM{0} \xdef\consRI{0}
\xdef\consRL{0} \xdef\consRV{0} \xdef\consRF{0} \xdef\consRY{0} \xdef\consRW{0}
\xdef\consKC{0} \xdef\consKS{0} \xdef\consKT{0} \xdef\consKP{0} \xdef\consKA{0}
\xdef\consKG{0} \xdef\consKN{0} \xdef\consKD{0} \xdef\consKE{0} \xdef\consKQ{0}
\xdef\consKH{0} \xdef\consKR{0} \xdef\consKK{10} \xdef\consKM{0} \xdef\consKI{0}
\xdef\consKL{0} \xdef\consKV{0} \xdef\consKF{0} \xdef\consKY{0} \xdef\consKW{0}
\xdef\consMC{0} \xdef\consMS{0} \xdef\consMT{0} \xdef\consMP{0} \xdef\consMA{0}
\xdef\consMG{0} \xdef\consMN{0} \xdef\consMD{0} \xdef\consME{0} \xdef\consMQ{0}
\xdef\consMH{0} \xdef\consMR{0} \xdef\consMK{0} \xdef\consMM{10} \xdef\consMI{0}
\xdef\consML{0} \xdef\consMV{0} \xdef\consMF{0} \xdef\consMY{0} \xdef\consMW{0}
\xdef\consIC{0} \xdef\consIS{0} \xdef\consIT{0} \xdef\consIP{0} \xdef\consIA{0}
\xdef\consIG{0} \xdef\consIN{0} \xdef\consID{0} \xdef\consIE{0} \xdef\consIQ{0}
\xdef\consIH{0} \xdef\consIR{0} \xdef\consIK{0} \xdef\consIM{0} \xdef\consII{10}
\xdef\consIL{0} \xdef\consIV{0} \xdef\consIF{0} \xdef\consIY{0} \xdef\consIW{0}
\xdef\consLC{0} \xdef\consLS{0} \xdef\consLT{0} \xdef\consLP{0} \xdef\consLA{0}
\xdef\consLG{0} \xdef\consLN{0} \xdef\consLD{0} \xdef\consLE{0} \xdef\consLQ{0}
\xdef\consLH{0} \xdef\consLR{0} \xdef\consLK{0} \xdef\consLM{0} \xdef\consLI{0}
\xdef\consLL{10} \xdef\consLV{0} \xdef\consLF{0} \xdef\consLY{0} \xdef\consLW{0}
\xdef\consVC{0} \xdef\consVS{0} \xdef\consVT{0} \xdef\consVP{0} \xdef\consVA{0}
\xdef\consVG{0} \xdef\consVN{0} \xdef\consVD{0} \xdef\consVE{0} \xdef\consVQ{0}
\xdef\consVH{0} \xdef\consVR{0} \xdef\consVK{0} \xdef\consVM{0} \xdef\consVI{0}
\xdef\consVL{0} \xdef\consVV{10} \xdef\consVF{0} \xdef\consVY{0} \xdef\consVW{0}
\xdef\consFC{0} \xdef\consFS{0} \xdef\consFT{0} \xdef\consFP{0} \xdef\consFA{0}
\xdef\consFG{0} \xdef\consFN{0} \xdef\consFD{0} \xdef\consFE{0} \xdef\consFQ{0}
\xdef\consFH{0} \xdef\consFR{0} \xdef\consFK{0} \xdef\consFM{0} \xdef\consFI{0}
\xdef\consFL{0} \xdef\consFV{0} \xdef\consFF{10} \xdef\consFY{0} \xdef\consFW{0}
\xdef\consYC{0} \xdef\consYS{0} \xdef\consYT{0} \xdef\consYP{0} \xdef\consYA{0}
\xdef\consYG{0} \xdef\consYN{0} \xdef\consYD{0} \xdef\consYE{0} \xdef\consYQ{0}
\xdef\consYH{0} \xdef\consYR{0} \xdef\consYK{0} \xdef\consYM{0} \xdef\consYI{0}
\xdef\consYL{0} \xdef\consYV{0} \xdef\consYF{0} \xdef\consYY{10} \xdef\consYW{0}
\xdef\consWC{0} \xdef\consWS{0} \xdef\consWT{0} \xdef\consWP{0} \xdef\consWA{0}
\xdef\consWG{0} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{0} \xdef\consWQ{0}
\xdef\consWH{0} \xdef\consWR{0} \xdef\consWK{0} \xdef\consWM{0} \xdef\consWI{0}
\xdef\consWL{0} \xdef\consWV{0} \xdef\consWF{0} \xdef\consWY{0} \xdef\consWW{10}
\gappenalty{0} \xdef\m@trixf@ctor{10}
\else
\xdef\temp@{structural}
\ifx\first@\temp@
%%%% structural
\xdef\consCC{10} \xdef\consCS{6} \xdef\consCT{3} \xdef\consCP{3} \xdef\consCA{3}
\xdef\consCG{5} \xdef\consCN{3} \xdef\consCD{1} \xdef\consCE{0} \xdef\consCQ{1}
\xdef\consCH{3} \xdef\consCR{3} \xdef\consCK{0} \xdef\consCM{3} \xdef\consCI{3}
\xdef\consCL{3} \xdef\consCV{3} \xdef\consCF{5} \xdef\consCY{5} \xdef\consCW{5}
\xdef\consSC{6} \xdef\consSS{10} \xdef\consST{8} \xdef\consSP{6} \xdef\consSA{8}
\xdef\consSG{8} \xdef\consSN{8} \xdef\consSD{6} \xdef\consSE{5} \xdef\consSQ{5}
\xdef\consSH{5} \xdef\consSR{5} \xdef\consSK{5} \xdef\consSM{3} \xdef\consSI{3}
\xdef\consSL{3} \xdef\consSV{6} \xdef\consSF{5} \xdef\consSY{5} \xdef\consSW{3}
\xdef\consTC{3} \xdef\consTS{8} \xdef\consTT{10} \xdef\consTP{6} \xdef\consTA{8}
\xdef\consTG{6} \xdef\consTN{6} \xdef\consTD{5} \xdef\consTE{5} \xdef\consTQ{5}
\xdef\consTH{3} \xdef\consTR{5} \xdef\consTK{6} \xdef\consTM{5} \xdef\consTI{5}
\xdef\consTL{3} \xdef\consTV{6} \xdef\consTF{3} \xdef\consTY{3} \xdef\consTW{1}
\xdef\consPC{3} \xdef\consPS{6} \xdef\consPT{6} \xdef\consPP{10} \xdef\consPA{8}
\xdef\consPG{6} \xdef\consPN{3} \xdef\consPD{5} \xdef\consPE{5} \xdef\consPQ{5}
\xdef\consPH{5} \xdef\consPR{5} \xdef\consPK{3} \xdef\consPM{3} \xdef\consPI{3}
\xdef\consPL{5} \xdef\consPV{6} \xdef\consPF{5} \xdef\consPY{3} \xdef\consPW{3}
\xdef\consAC{3} \xdef\consAS{8} \xdef\consAT{8} \xdef\consAP{8} \xdef\consAA{10}
\xdef\consAG{8} \xdef\consAN{5} \xdef\consAD{6} \xdef\consAE{6} \xdef\consAQ{5}
\xdef\consAH{3} \xdef\consAR{3} \xdef\consAK{5} \xdef\consAM{5} \xdef\consAI{3}
\xdef\consAL{3} \xdef\consAV{8} \xdef\consAF{5} \xdef\consAY{3} \xdef\consAW{3}
\xdef\consGC{5} \xdef\consGS{8} \xdef\consGT{6} \xdef\consGP{6} \xdef\consGA{8}
\xdef\consGG{10} \xdef\consGN{5} \xdef\consGD{6} \xdef\consGE{6} \xdef\consGQ{3}
\xdef\consGH{1} \xdef\consGR{5} \xdef\consGK{3} \xdef\consGM{1} \xdef\consGI{3}
\xdef\consGL{3} \xdef\consGV{6} \xdef\consGF{3} \xdef\consGY{3} \xdef\consGW{5}
\xdef\consNC{3} \xdef\consNS{8} \xdef\consNT{6} \xdef\consNP{3} \xdef\consNA{5}
\xdef\consNG{5} \xdef\consNN{10} \xdef\consND{8} \xdef\consNE{6} \xdef\consNQ{5}
\xdef\consNH{6} \xdef\consNR{5} \xdef\consNK{6} \xdef\consNM{1} \xdef\consNI{3}
\xdef\consNL{1} \xdef\consNV{3} \xdef\consNF{3} \xdef\consNY{5} \xdef\consNW{0}
\xdef\consDC{1} \xdef\consDS{6} \xdef\consDT{5} \xdef\consDP{5} \xdef\consDA{6}
\xdef\consDG{6} \xdef\consDN{8} \xdef\consDD{10} \xdef\consDE{8} \xdef\consDQ{6}
\xdef\consDH{5} \xdef\consDR{3} \xdef\consDK{5} \xdef\consDM{3} \xdef\consDI{1}
\xdef\consDL{1} \xdef\consDV{5} \xdef\consDF{1} \xdef\consDY{3} \xdef\consDW{0}
\xdef\consEC{0} \xdef\consES{5} \xdef\consET{5} \xdef\consEP{5} \xdef\consEA{6}
\xdef\consEG{6} \xdef\consEN{6} \xdef\consED{8} \xdef\consEE{10} \xdef\consEQ{6}
\xdef\consEH{3} \xdef\consER{5} \xdef\consEK{6} \xdef\consEM{3} \xdef\consEI{1}
\xdef\consEL{1} \xdef\consEV{6} \xdef\consEF{3} \xdef\consEY{1} \xdef\consEW{1}
\xdef\consQC{1} \xdef\consQS{5} \xdef\consQT{5} \xdef\consQP{5} \xdef\consQA{5}
\xdef\consQG{3} \xdef\consQN{5} \xdef\consQD{6} \xdef\consQE{6} \xdef\consQQ{10}
\xdef\consQH{6} \xdef\consQR{5} \xdef\consQK{6} \xdef\consQM{3} \xdef\consQI{1}
\xdef\consQL{3} \xdef\consQV{3} \xdef\consQF{1} \xdef\consQY{3} \xdef\consQW{1}
\xdef\consHC{3} \xdef\consHS{5} \xdef\consHT{3} \xdef\consHP{5} \xdef\consHA{3}
\xdef\consHG{1} \xdef\consHN{6} \xdef\consHD{5} \xdef\consHE{3} \xdef\consHQ{6}
\xdef\consHH{10} \xdef\consHR{6} \xdef\consHK{5} \xdef\consHM{3} \xdef\consHI{3}
\xdef\consHL{5} \xdef\consHV{1} \xdef\consHF{3} \xdef\consHY{5} \xdef\consHW{1}
\xdef\consRC{3} \xdef\consRS{5} \xdef\consRT{5} \xdef\consRP{5} \xdef\consRA{3}
\xdef\consRG{5} \xdef\consRN{5} \xdef\consRD{3} \xdef\consRE{5} \xdef\consRQ{5}
\xdef\consRH{6} \xdef\consRR{10} \xdef\consRK{8} \xdef\consRM{3} \xdef\consRI{3}
\xdef\consRL{3} \xdef\consRV{3} \xdef\consRF{1} \xdef\consRY{1} \xdef\consRW{3}
\xdef\consKC{0} \xdef\consKS{5} \xdef\consKT{6} \xdef\consKP{3} \xdef\consKA{5}
\xdef\consKG{3} \xdef\consKN{6} \xdef\consKD{5} \xdef\consKE{6} \xdef\consKQ{6}
\xdef\consKH{5} \xdef\consKR{8} \xdef\consKK{10} \xdef\consKM{3} \xdef\consKI{3}
\xdef\consKL{3} \xdef\consKV{5} \xdef\consKF{1} \xdef\consKY{1} \xdef\consKW{1}
\xdef\consMC{3} \xdef\consMS{5} \xdef\consMT{5} \xdef\consMP{3} \xdef\consMA{5}
\xdef\consMG{1} \xdef\consMN{1} \xdef\consMD{3} \xdef\consME{3} \xdef\consMQ{3}
\xdef\consMH{3} \xdef\consMR{3} \xdef\consMK{3} \xdef\consMM{10} \xdef\consMI{6}
\xdef\consML{8} \xdef\consMV{6} \xdef\consMF{5} \xdef\consMY{3} \xdef\consMW{5}
\xdef\consIC{3} \xdef\consIS{3} \xdef\consIT{5} \xdef\consIP{3} \xdef\consIA{3}
\xdef\consIG{3} \xdef\consIN{3} \xdef\consID{1} \xdef\consIE{1} \xdef\consIQ{1}
\xdef\consIH{3} \xdef\consIR{3} \xdef\consIK{3} \xdef\consIM{6} \xdef\consII{10}
\xdef\consIL{8} \xdef\consIV{3} \xdef\consIF{6} \xdef\consIY{5} \xdef\consIW{5}
\xdef\consLC{3} \xdef\consLS{3} \xdef\consLT{3} \xdef\consLP{5} \xdef\consLA{3}
\xdef\consLG{3} \xdef\consLN{1} \xdef\consLD{1} \xdef\consLE{1} \xdef\consLQ{3}
\xdef\consLH{5} \xdef\consLR{3} \xdef\consLK{3} \xdef\consLM{8} \xdef\consLI{8}
\xdef\consLL{10} \xdef\consLV{3} \xdef\consLF{6} \xdef\consLY{5} \xdef\consLW{6}
\xdef\consVC{3} \xdef\consVS{6} \xdef\consVT{6} \xdef\consVP{6} \xdef\consVA{8}
\xdef\consVG{6} \xdef\consVN{3} \xdef\consVD{5} \xdef\consVE{6} \xdef\consVQ{3}
\xdef\consVH{1} \xdef\consVR{3} \xdef\consVK{5} \xdef\consVM{6} \xdef\consVI{3}
\xdef\consVL{3} \xdef\consVV{10} \xdef\consVF{6} \xdef\consVY{5} \xdef\consVW{5}
\xdef\consFC{5} \xdef\consFS{5} \xdef\consFT{3} \xdef\consFP{5} \xdef\consFA{5}
\xdef\consFG{3} \xdef\consFN{3} \xdef\consFD{1} \xdef\consFE{3} \xdef\consFQ{1}
\xdef\consFH{3} \xdef\consFR{1} \xdef\consFK{1} \xdef\consFM{5} \xdef\consFI{6}
\xdef\consFL{6} \xdef\consFV{6} \xdef\consFF{10} \xdef\consFY{8} \xdef\consFW{5}
\xdef\consYC{5} \xdef\consYS{5} \xdef\consYT{3} \xdef\consYP{3} \xdef\consYA{3}
\xdef\consYG{3} \xdef\consYN{5} \xdef\consYD{3} \xdef\consYE{1} \xdef\consYQ{3}
\xdef\consYH{5} \xdef\consYR{1} \xdef\consYK{1} \xdef\consYM{3} \xdef\consYI{5}
\xdef\consYL{5} \xdef\consYV{5} \xdef\consYF{8} \xdef\consYY{10} \xdef\consYW{5}
\xdef\consWC{5} \xdef\consWS{3} \xdef\consWT{1} \xdef\consWP{3} \xdef\consWA{3}
\xdef\consWG{5} \xdef\consWN{0} \xdef\consWD{0} \xdef\consWE{1} \xdef\consWQ{1}
\xdef\consWH{1} \xdef\consWR{3} \xdef\consWK{1} \xdef\consWM{5} \xdef\consWI{5}
\xdef\consWL{6} \xdef\consWV{5} \xdef\consWF{5} \xdef\consWY{5} \xdef\consWW{10}
\gappenalty{0} \xdef\m@trixf@ctor{10}
\else
\xdef\temp@{PAM250}
\ifx\first@\temp@
%%%% PAM250
\xdef\consCC{4} \xdef\consCS{0} \xdef\consCT{-2} \xdef\consCP{-3} \xdef\consCA{-2}
\xdef\consCG{-3} \xdef\consCN{-4} \xdef\consCD{2} \xdef\consCE{-5} \xdef\consCQ{-5}
\xdef\consCH{-3} \xdef\consCR{-4} \xdef\consCK{-5} \xdef\consCM{-5} \xdef\consCI{-2}
\xdef\consCL{-6} \xdef\consCV{-2} \xdef\consCF{-4} \xdef\consCY{0} \xdef\consCW{-8}
\xdef\consCB{-4} \xdef\consCZ{-5} \xdef\consCX{-3}
\xdef\consSC{0} \xdef\consSS{3} \xdef\consST{1} \xdef\consSP{1} \xdef\consSA{1}
\xdef\consSG{1} \xdef\consSN{1} \xdef\consSD{0} \xdef\consSE{0} \xdef\consSQ{-1}
\xdef\consSH{-1} \xdef\consSR{0} \xdef\consSK{0} \xdef\consSM{-2} \xdef\consSI{-1}
\xdef\consSL{-3} \xdef\consSV{-1} \xdef\consSF{-3} \xdef\consSY{-3} \xdef\consSW{-2}
\xdef\consSB{0} \xdef\consSZ{0} \xdef\consSX{0}
\xdef\consTC{-2} \xdef\consTS{1} \xdef\consTT{3} \xdef\consTP{0} \xdef\consTA{1}
\xdef\consTG{0} \xdef\consTN{0} \xdef\consTD{0} \xdef\consTE{0} \xdef\consTQ{-1}
\xdef\consTH{-1} \xdef\consTR{-1} \xdef\consTK{0} \xdef\consTM{-1} \xdef\consTI{0}
\xdef\consTL{-2} \xdef\consTV{0} \xdef\consTF{-2} \xdef\consTY{-3} \xdef\consTW{-5}
\xdef\consTB{0} \xdef\consTZ{-1} \xdef\consTX{0}
\xdef\consPC{-3} \xdef\consPS{1} \xdef\consPT{0} \xdef\consPP{6} \xdef\consPA{1}
\xdef\consPG{-1} \xdef\consPN{-1} \xdef\consPD{-1} \xdef\consPE{-1} \xdef\consPQ{0}
\xdef\consPH{0} \xdef\consPR{0} \xdef\consPK{-1} \xdef\consPM{-2} \xdef\consPI{-2}
\xdef\consPL{-3} \xdef\consPV{-1} \xdef\consPF{-5} \xdef\consPY{-5} \xdef\consPW{-6}
\xdef\consPB{-1} \xdef\consPZ{0} \xdef\consPX{-1}
\xdef\consAC{-2} \xdef\consAS{1} \xdef\consAT{1} \xdef\consAP{1} \xdef\consAA{2}
\xdef\consAG{1} \xdef\consAN{0} \xdef\consAD{0} \xdef\consAE{0} \xdef\consAQ{0}
\xdef\consAH{-1} \xdef\consAR{-2} \xdef\consAK{-1} \xdef\consAM{-1} \xdef\consAI{-1}
\xdef\consAL{-2} \xdef\consAV{0} \xdef\consAF{-4} \xdef\consAY{-3} \xdef\consAW{-6}
\xdef\consAB{0} \xdef\consAZ{0} \xdef\consAX{0}
\xdef\consGC{-3} \xdef\consGS{1} \xdef\consGT{0} \xdef\consGP{-1} \xdef\consGA{1}
\xdef\consGG{5} \xdef\consGN{0} \xdef\consGD{1} \xdef\consGE{0} \xdef\consGQ{-1}
\xdef\consGH{-2} \xdef\consGR{-3} \xdef\consGK{-2} \xdef\consGM{-3} \xdef\consGI{-3}
\xdef\consGL{-4} \xdef\consGV{-1} \xdef\consGF{-5} \xdef\consGY{-5} \xdef\consGW{-7}
\xdef\consGB{0} \xdef\consGZ{0} \xdef\consGX{-1}
\xdef\consNC{-4} \xdef\consNS{1} \xdef\consNT{0} \xdef\consNP{-1} \xdef\consNA{0}
\xdef\consNG{0} \xdef\consNN{2} \xdef\consND{2} \xdef\consNE{1} \xdef\consNQ{1}
\xdef\consNH{2} \xdef\consNR{0} \xdef\consNK{1} \xdef\consNM{-2} \xdef\consNI{-2}
\xdef\consNL{-3} \xdef\consNV{-2} \xdef\consNF{-4} \xdef\consNY{-2} \xdef\consNW{-4}
\xdef\consNB{2} \xdef\consNZ{1} \xdef\consNX{0}
\xdef\consDC{-5} \xdef\consDS{0} \xdef\consDT{0} \xdef\consDP{-1} \xdef\consDA{0}
\xdef\consDG{1} \xdef\consDN{2} \xdef\consDD{4} \xdef\consDE{3} \xdef\consDQ{2}
\xdef\consDH{1} \xdef\consDR{-1} \xdef\consDK{0} \xdef\consDM{-3} \xdef\consDI{-2}
\xdef\consDL{-4} \xdef\consDV{-2} \xdef\consDF{-6} \xdef\consDY{-4} \xdef\consDW{-7}
\xdef\consDB{3} \xdef\consDZ{3} \xdef\consDX{-1}
\xdef\consEC{-5} \xdef\consES{0} \xdef\consET{0} \xdef\consEP{-1} \xdef\consEA{0}
\xdef\consEG{0} \xdef\consEN{1} \xdef\consED{3} \xdef\consEE{4} \xdef\consEQ{2}
\xdef\consEH{1} \xdef\consER{-1} \xdef\consEK{0} \xdef\consEM{-2} \xdef\consEI{-2}
\xdef\consEL{-3} \xdef\consEV{-2} \xdef\consEF{-5} \xdef\consEY{-4} \xdef\consEW{-7}
\xdef\consEB{3} \xdef\consEZ{3} \xdef\consEX{-1}
\xdef\consQC{-5} \xdef\consQS{-1} \xdef\consQT{-1} \xdef\consQP{0} \xdef\consQA{0}
\xdef\consQG{-1} \xdef\consQN{1} \xdef\consQD{2} \xdef\consQE{2} \xdef\consQQ{4}
\xdef\consQH{3} \xdef\consQR{1} \xdef\consQK{1} \xdef\consQM{-1} \xdef\consQI{-2}
\xdef\consQL{-2} \xdef\consQV{-2} \xdef\consQF{-5} \xdef\consQY{-4} \xdef\consQW{-5}
\xdef\consQB{1} \xdef\consQZ{3} \xdef\consQX{-1}
\xdef\consHC{-3} \xdef\consHS{-1} \xdef\consHT{-1} \xdef\consHP{0} \xdef\consHA{-1}
\xdef\consHG{-2} \xdef\consHN{2} \xdef\consHD{1} \xdef\consHE{1} \xdef\consHQ{3}
\xdef\consHH{6} \xdef\consHR{2} \xdef\consHK{0} \xdef\consHM{-2} \xdef\consHI{-2}
\xdef\consHL{-2} \xdef\consHV{-2} \xdef\consHF{-2} \xdef\consHY{-5} \xdef\consHW{-7}
\xdef\consHB{1} \xdef\consHZ{2} \xdef\consHX{-1}
\xdef\consRC{-4} \xdef\consRS{0} \xdef\consRT{-1} \xdef\consRP{0} \xdef\consRA{-2}
\xdef\consRG{-3} \xdef\consRN{0} \xdef\consRD{-1} \xdef\consRE{-1} \xdef\consRQ{1}
\xdef\consRH{2} \xdef\consRR{6} \xdef\consRK{3} \xdef\consRM{0} \xdef\consRI{-2}
\xdef\consRL{-3} \xdef\consRV{-2} \xdef\consRF{-4} \xdef\consRY{-4} \xdef\consRW{2}
\xdef\consRB{-1} \xdef\consRZ{0} \xdef\consRX{-1}
\xdef\consKC{-5} \xdef\consKS{0} \xdef\consKT{0} \xdef\consKP{-1} \xdef\consKA{-1}
\xdef\consKG{-2} \xdef\consKN{1} \xdef\consKD{0} \xdef\consKE{0} \xdef\consKQ{1}
\xdef\consKH{0} \xdef\consKR{3} \xdef\consKK{5} \xdef\consKM{0} \xdef\consKI{-2}
\xdef\consKL{-3} \xdef\consKV{-2} \xdef\consKF{-5} \xdef\consKY{-4} \xdef\consKW{-3}
\xdef\consKB{1} \xdef\consKZ{-2} \xdef\consKX{-1}
\xdef\consMC{-5} \xdef\consMS{-2} \xdef\consMT{-1} \xdef\consMP{-2} \xdef\consMA{-1}
\xdef\consMG{-3} \xdef\consMN{-2} \xdef\consMD{-3} \xdef\consME{-2} \xdef\consMQ{-1}
\xdef\consMH{-2} \xdef\consMR{0} \xdef\consMK{0} \xdef\consMM{6} \xdef\consMI{2}
\xdef\consML{4} \xdef\consMV{2} \xdef\consMF{0} \xdef\consMY{-2} \xdef\consMW{-4}
\xdef\consMB{-2} \xdef\consMZ{-2} \xdef\consMX{-1}
\xdef\consIC{-2} \xdef\consIS{-1} \xdef\consIT{0} \xdef\consIP{-2} \xdef\consIA{-1}
\xdef\consIG{-3} \xdef\consIN{-2} \xdef\consID{-2} \xdef\consIE{-2} \xdef\consIQ{-2}
\xdef\consIH{-2} \xdef\consIR{-2} \xdef\consIK{-2} \xdef\consIM{2} \xdef\consII{5}
\xdef\consIL{2} \xdef\consIV{4} \xdef\consIF{1} \xdef\consIY{-1} \xdef\consIW{-5}
\xdef\consIB{-2} \xdef\consIZ{-2} \xdef\consIX{-1}
\xdef\consLC{-6} \xdef\consLS{-3} \xdef\consLT{-2} \xdef\consLP{-3} \xdef\consLA{-2}
\xdef\consLG{-4} \xdef\consLN{-3} \xdef\consLD{-4} \xdef\consLE{-3} \xdef\consLQ{-2}
\xdef\consLH{-2} \xdef\consLR{-3} \xdef\consLK{-3} \xdef\consLM{4} \xdef\consLI{2}
\xdef\consLL{6} \xdef\consLV{2} \xdef\consLF{2} \xdef\consLY{-1} \xdef\consLW{-2}
\xdef\consLB{-3} \xdef\consLZ{-3} \xdef\consLX{-1}
\xdef\consVC{-2} \xdef\consVS{-1} \xdef\consVT{0} \xdef\consVP{-1} \xdef\consVA{0}
\xdef\consVG{-1} \xdef\consVN{-2} \xdef\consVD{-2} \xdef\consVE{-2} \xdef\consVQ{-2}
\xdef\consVH{-2} \xdef\consVR{-2} \xdef\consVK{-2} \xdef\consVM{2} \xdef\consVI{4}
\xdef\consVL{2} \xdef\consVV{4} \xdef\consVF{-1} \xdef\consVY{-2} \xdef\consVW{-6}
\xdef\consVB{-2} \xdef\consVZ{-2} \xdef\consVX{-1}
\xdef\consFC{-4} \xdef\consFS{-3} \xdef\consFT{-2} \xdef\consFP{-5} \xdef\consFA{-4}
\xdef\consFG{-5} \xdef\consFN{-4} \xdef\consFD{-6} \xdef\consFE{-5} \xdef\consFQ{-5}
\xdef\consFH{-2} \xdef\consFR{-4} \xdef\consFK{-5} \xdef\consFM{0} \xdef\consFI{1}
\xdef\consFL{2} \xdef\consFV{-1} \xdef\consFF{9} \xdef\consFY{7} \xdef\consFW{0}
\xdef\consFB{-4} \xdef\consFZ{-5} \xdef\consFX{-2}
\xdef\consYC{0} \xdef\consYS{-3} \xdef\consYT{-3} \xdef\consYP{-5} \xdef\consYA{-3}
\xdef\consYG{-5} \xdef\consYN{-2} \xdef\consYD{-4} \xdef\consYE{-4} \xdef\consYQ{-4}
\xdef\consYH{0} \xdef\consYR{-4} \xdef\consYK{-4} \xdef\consYM{-2} \xdef\consYI{-1}
\xdef\consYL{-1} \xdef\consYV{-2} \xdef\consYF{7} \xdef\consYY{10} \xdef\consYW{0}
\xdef\consYB{-3} \xdef\consYZ{-4} \xdef\consYX{-2}
\xdef\consWC{-8} \xdef\consWS{-2} \xdef\consWT{-5} \xdef\consWP{-6} \xdef\consWA{-6}
\xdef\consWG{-7} \xdef\consWN{-4} \xdef\consWD{-7} \xdef\consWE{-7} \xdef\consWQ{-5}
\xdef\consWH{-3} \xdef\consWR{2} \xdef\consWK{-3} \xdef\consWM{-4} \xdef\consWI{-5}
\xdef\consWL{-2} \xdef\consWV{-6} \xdef\consWF{0} \xdef\consWY{0} \xdef\consWW{17}
\xdef\consWB{-5} \xdef\consWZ{-6} \xdef\consWX{-4}
\xdef\consBC{-4} \xdef\consBS{0} \xdef\consBT{0} \xdef\consBP{-1} \xdef\consBA{0}
\xdef\consBG{0} \xdef\consBN{2} \xdef\consBD{3} \xdef\consBE{3} \xdef\consBQ{1}
\xdef\consBH{1} \xdef\consBR{-1} \xdef\consBK{1} \xdef\consBM{-2} \xdef\consBI{-2}
\xdef\consBL{-3} \xdef\consBV{-2} \xdef\consBF{-4} \xdef\consBY{-3} \xdef\consBW{-5}
\xdef\consBB{3} \xdef\consBZ{2} \xdef\consBX{-1}
\xdef\consZC{-5} \xdef\consZS{0} \xdef\consZT{-1} \xdef\consZP{0} \xdef\consZA{0}
\xdef\consZG{0} \xdef\consZN{1} \xdef\consZD{3} \xdef\consZE{3} \xdef\consZQ{3}
\xdef\consZH{2} \xdef\consZR{0} \xdef\consZK{0} \xdef\consZM{-2} \xdef\consZI{-2}
\xdef\consZL{-3} \xdef\consZV{-2} \xdef\consZF{-5} \xdef\consZY{-4} \xdef\consZW{-6}
\xdef\consZB{2} \xdef\consZZ{3} \xdef\consZX{-1}
\xdef\consXC{-3} \xdef\consXS{0} \xdef\consXT{0} \xdef\consXP{-1} \xdef\consXA{0}
\xdef\consXG{-1} \xdef\consXN{0} \xdef\consXD{-1} \xdef\consXE{-1} \xdef\consXQ{-1}
\xdef\consXH{-1} \xdef\consXR{-1} \xdef\consXK{-1} \xdef\consXM{-1} \xdef\consXI{-1}
\xdef\consXL{-1} \xdef\consXV{-1} \xdef\consXF{-2} \xdef\consXY{-2} \xdef\consXW{-4}
\xdef\consXB{-1} \xdef\consXZ{-1} \xdef\consXX{-1}
\expandafter\xdef\csname cons..\endcsname{1}
\gappenalty{-8} \xdef\m@trixf@ctor{10}
\else
\xdef\temp@{PAM100} \xdef\m@trixf@ctor{10}
\ifx\first@\temp@
%%%% PAM100
\xdef\consCC{14} \xdef\consCS{-1} \xdef\consCT{-5} \xdef\consCP{-6} \xdef\consCA{-5}
\xdef\consCG{-8} \xdef\consCN{-8} \xdef\consCD{-11} \xdef\consCE{-11} \xdef\consCQ{-11}
\xdef\consCH{-6} \xdef\consCR{-6} \xdef\consCK{-11} \xdef\consCM{-11} \xdef\consCI{-5}
\xdef\consCL{-12} \xdef\consCV{-4} \xdef\consCF{-10} \xdef\consCY{-2} \xdef\consCW{-13}
\xdef\consCB{-6} \xdef\consCZ{-8} \xdef\consCX{-5}
\xdef\consSC{-1} \xdef\consSS{6} \xdef\consST{2} \xdef\consSP{1} \xdef\consSA{2}
\xdef\consSG{1} \xdef\consSN{2} \xdef\consSD{-1} \xdef\consSE{-2} \xdef\consSQ{-3}
\xdef\consSH{-4} \xdef\consSR{-1} \xdef\consSK{-2} \xdef\consSM{-4} \xdef\consSI{-4}
\xdef\consSL{-7} \xdef\consSV{-4} \xdef\consSF{-5} \xdef\consSY{-6} \xdef\consSW{-4}
\xdef\consSB{0} \xdef\consSZ{-2} \xdef\consSX{1}
\xdef\consTC{-5} \xdef\consTS{2} \xdef\consTT{7} \xdef\consTP{-1} \xdef\consTA{2}
\xdef\consTG{-3} \xdef\consTN{0} \xdef\consTD{-2} \xdef\consTE{-3} \xdef\consTQ{-3}
\xdef\consTH{-5} \xdef\consTR{-4} \xdef\consTK{-1} \xdef\consTM{-2} \xdef\consTI{-1}
\xdef\consTL{-5} \xdef\consTV{-1} \xdef\consTF{-6} \xdef\consTY{-6} \xdef\consTW{-10}
\xdef\consTB{-1} \xdef\consTZ{-2} \xdef\consTX{-1}
\xdef\consPC{-6} \xdef\consPS{1} \xdef\consPT{-1} \xdef\consPP{10} \xdef\consPA{1}
\xdef\consPG{-3} \xdef\consPN{-3} \xdef\consPD{-4} \xdef\consPE{-3} \xdef\consPQ{-1}
\xdef\consPH{-2} \xdef\consPR{-2} \xdef\consPK{-4} \xdef\consPM{-6} \xdef\consPI{-6}
\xdef\consPL{-5} \xdef\consPV{-4} \xdef\consPF{-9} \xdef\consPY{-11} \xdef\consPW{-11}
\xdef\consPB{-3} \xdef\consPZ{-1} \xdef\consPX{-2}
\xdef\consAC{-5} \xdef\consAS{2} \xdef\consAT{2} \xdef\consAP{1} \xdef\consAA{6}
\xdef\consAG{1} \xdef\consAN{-1} \xdef\consAD{-1} \xdef\consAE{0} \xdef\consAQ{-2}
\xdef\consAH{-5} \xdef\consAR{-5} \xdef\consAK{-4} \xdef\consAM{-3} \xdef\consAI{-3}
\xdef\consAL{-5} \xdef\consAV{0} \xdef\consAF{-7} \xdef\consAY{-6} \xdef\consAW{-11}
\xdef\consAB{-1} \xdef\consAZ{-1} \xdef\consAX{-1}
\xdef\consGC{-8} \xdef\consGS{1} \xdef\consGT{-3} \xdef\consGP{-3} \xdef\consGA{1}
\xdef\consGG{8} \xdef\consGN{-1} \xdef\consGD{-1} \xdef\consGE{-2} \xdef\consGQ{-5}
\xdef\consGH{-7} \xdef\consGR{-8} \xdef\consGK{-5} \xdef\consGM{-8} \xdef\consGI{-7}
\xdef\consGL{-8} \xdef\consGV{-4} \xdef\consGF{-8} \xdef\consGY{-11} \xdef\consGW{-13}
\xdef\consGB{-1} \xdef\consGZ{-2} \xdef\consGX{-2}
\xdef\consNC{-8} \xdef\consNS{2} \xdef\consNT{0} \xdef\consNP{-3} \xdef\consNA{-1}
\xdef\consNG{-1} \xdef\consNN{7} \xdef\consND{4} \xdef\consNE{1} \xdef\consNQ{-1}
\xdef\consNH{2} \xdef\consNR{-3} \xdef\consNK{1} \xdef\consNM{-5} \xdef\consNI{-4}
\xdef\consNL{-6} \xdef\consNV{-5} \xdef\consNF{-6} \xdef\consNY{-3} \xdef\consNW{-8}
\xdef\consNB{4} \xdef\consNZ{0} \xdef\consNX{-1}
\xdef\consDC{-11} \xdef\consDS{-1} \xdef\consDT{-2} \xdef\consDP{-4} \xdef\consDA{-1}
\xdef\consDG{-1} \xdef\consDN{4} \xdef\consDD{8} \xdef\consDE{5} \xdef\consDQ{1}
\xdef\consDH{-1} \xdef\consDR{-6} \xdef\consDK{-2} \xdef\consDM{-8} \xdef\consDI{-6}
\xdef\consDL{-9} \xdef\consDV{-6} \xdef\consDF{-11} \xdef\consDY{-9} \xdef\consDW{-13}
\xdef\consDB{4} \xdef\consDZ{3} \xdef\consDX{-2}
\xdef\consEC{-11} \xdef\consES{-2} \xdef\consET{-3} \xdef\consEP{-3} \xdef\consEA{0}
\xdef\consEG{-2} \xdef\consEN{1} \xdef\consED{5} \xdef\consEE{8} \xdef\consEQ{4}
\xdef\consEH{-2} \xdef\consER{-5} \xdef\consEK{-2} \xdef\consEM{-6} \xdef\consEI{-5}
\xdef\consEL{-7} \xdef\consEV{-5} \xdef\consEF{-11} \xdef\consEY{-7} \xdef\consEW{-14}
\xdef\consEB{3} \xdef\consEZ{4} \xdef\consEX{-2}
\xdef\consQC{-11} \xdef\consQS{-3} \xdef\consQT{-3} \xdef\consQP{-1} \xdef\consQA{-2}
\xdef\consQG{-5} \xdef\consQN{-1} \xdef\consQD{1} \xdef\consQE{4} \xdef\consQQ{9}
\xdef\consQH{4} \xdef\consQR{1} \xdef\consQK{-1} \xdef\consQM{-2} \xdef\consQI{-5}
\xdef\consQL{-3} \xdef\consQV{-5} \xdef\consQF{-10} \xdef\consQY{-9} \xdef\consQW{-11}
\xdef\consQB{0} \xdef\consQZ{5} \xdef\consQX{-2}
\xdef\consHC{-6} \xdef\consHS{-4} \xdef\consHT{-5} \xdef\consHP{-2} \xdef\consHA{-5}
\xdef\consHG{-7} \xdef\consHN{2} \xdef\consHD{-1} \xdef\consHE{-2} \xdef\consHQ{4}
\xdef\consHH{11} \xdef\consHR{1} \xdef\consHK{-3} \xdef\consHM{-7} \xdef\consHI{-7}
\xdef\consHL{-5} \xdef\consHV{-6} \xdef\consHF{-4} \xdef\consHY{-1} \xdef\consHW{-7}
\xdef\consHB{1} \xdef\consHZ{1} \xdef\consHX{-2}
\xdef\consRC{-6} \xdef\consRS{-1} \xdef\consRT{-4} \xdef\consRP{-2} \xdef\consRA{-5}
\xdef\consRG{-8} \xdef\consRN{-3} \xdef\consRD{-6} \xdef\consRE{-5} \xdef\consRQ{1}
\xdef\consRH{1} \xdef\consRR{10} \xdef\consRK{3} \xdef\consRM{-2} \xdef\consRI{-4}
\xdef\consRL{-7} \xdef\consRV{-6} \xdef\consRF{-7} \xdef\consRY{-10} \xdef\consRW{1}
\xdef\consRB{-3} \xdef\consRZ{-1} \xdef\consRX{-2}
\xdef\consKC{-11} \xdef\consKS{-2} \xdef\consKT{-1} \xdef\consKP{-4} \xdef\consKA{-4}
\xdef\consKG{-5} \xdef\consKN{1} \xdef\consKD{-2} \xdef\consKE{-2} \xdef\consKQ{-1}
\xdef\consKH{-3} \xdef\consKR{3} \xdef\consKK{8} \xdef\consKM{1} \xdef\consKI{-4}
\xdef\consKL{-6} \xdef\consKV{-6} \xdef\consKF{-11} \xdef\consKY{-10} \xdef\consKW{-9}
\xdef\consKB{0} \xdef\consKZ{-1} \xdef\consKX{-2}
\xdef\consMC{-11} \xdef\consMS{-4} \xdef\consMT{-2} \xdef\consMP{-6} \xdef\consMA{-3}
\xdef\consMG{-8} \xdef\consMN{-5} \xdef\consMD{-8} \xdef\consME{-6} \xdef\consMQ{-2}
\xdef\consMH{-7} \xdef\consMR{-2} \xdef\consMK{1} \xdef\consMM{13} \xdef\consMI{2}
\xdef\consML{4} \xdef\consMV{1} \xdef\consMF{-2} \xdef\consMY{-8} \xdef\consMW{-11}
\xdef\consMB{-4} \xdef\consMZ{-2} \xdef\consMX{-2}
\xdef\consIC{-5} \xdef\consIS{-4} \xdef\consIT{-1} \xdef\consIP{-6} \xdef\consIA{-3}
\xdef\consIG{-7} \xdef\consIN{-4} \xdef\consID{-6} \xdef\consIE{-5} \xdef\consIQ{-5}
\xdef\consIH{-7} \xdef\consIR{-4} \xdef\consIK{-4} \xdef\consIM{2} \xdef\consII{9}
\xdef\consIL{2} \xdef\consIV{5} \xdef\consIF{0} \xdef\consIY{-4} \xdef\consIW{-12}
\xdef\consIB{-3} \xdef\consIZ{-3} \xdef\consIX{-2}
\xdef\consLC{-12} \xdef\consLS{-7} \xdef\consLT{-5} \xdef\consLP{-5} \xdef\consLA{-5}
\xdef\consLG{-8} \xdef\consLN{-6} \xdef\consLD{-9} \xdef\consLE{-7} \xdef\consLQ{-3}
\xdef\consLH{-5} \xdef\consLR{-7} \xdef\consLK{-6} \xdef\consLM{4} \xdef\consLI{2}
\xdef\consLL{9} \xdef\consLV{1} \xdef\consLF{0} \xdef\consLY{-5} \xdef\consLW{-7}
\xdef\consLB{-5} \xdef\consLZ{-4} \xdef\consLX{-3}
\xdef\consVC{-4} \xdef\consVS{-4} \xdef\consVT{-1} \xdef\consVP{-4} \xdef\consVA{0}
\xdef\consVG{-4} \xdef\consVN{-5} \xdef\consVD{-6} \xdef\consVE{-5} \xdef\consVQ{-5}
\xdef\consVH{-6} \xdef\consVR{-6} \xdef\consVK{-6} \xdef\consVM{1} \xdef\consVI{5}
\xdef\consVL{1} \xdef\consVV{8} \xdef\consVF{-5} \xdef\consVY{-6} \xdef\consVW{-14}
\xdef\consVB{-4} \xdef\consVZ{-3} \xdef\consVX{-2}
\xdef\consFC{-10} \xdef\consFS{-5} \xdef\consFT{-6} \xdef\consFP{-9} \xdef\consFA{-7}
\xdef\consFG{-8} \xdef\consFN{-6} \xdef\consFD{-11} \xdef\consFE{-11} \xdef\consFQ{-10}
\xdef\consFH{-4} \xdef\consFR{-7} \xdef\consFK{-11} \xdef\consFM{-2} \xdef\consFI{0}
\xdef\consFL{0} \xdef\consFV{-5} \xdef\consFF{12} \xdef\consFY{6} \xdef\consFW{-2}
\xdef\consFB{-6} \xdef\consFZ{-7} \xdef\consFX{-4}
\xdef\consYC{-2} \xdef\consYS{-6} \xdef\consYT{-6} \xdef\consYP{-11} \xdef\consYA{-6}
\xdef\consYG{-11} \xdef\consYN{-3} \xdef\consYD{-9} \xdef\consYE{-7} \xdef\consYQ{-9}
\xdef\consYH{-1} \xdef\consYR{-10} \xdef\consYK{-10} \xdef\consYM{-8} \xdef\consYI{-4}
\xdef\consYL{-5} \xdef\consYV{-6} \xdef\consYF{6} \xdef\consYY{13} \xdef\consYW{-2}
\xdef\consYB{-4} \xdef\consYZ{-6} \xdef\consYX{-4}
\xdef\consWC{-13} \xdef\consWS{-4} \xdef\consWT{-10} \xdef\consWP{-11} \xdef\consWA{-11}
\xdef\consWG{-13} \xdef\consWN{-8} \xdef\consWD{-13} \xdef\consWE{-14} \xdef\consWQ{-11}
\xdef\consWH{-7} \xdef\consWR{1} \xdef\consWK{-9} \xdef\consWM{-11} \xdef\consWI{-12}
\xdef\consWL{-7} \xdef\consWV{-14} \xdef\consWF{-2} \xdef\consWY{-2} \xdef\consWW{19}
\xdef\consWB{-6} \xdef\consWZ{-8} \xdef\consWX{-6}
\xdef\consBC{-6} \xdef\consBS{0} \xdef\consBT{-1} \xdef\consBP{-3} \xdef\consBA{-1}
\xdef\consBG{-1} \xdef\consBN{4} \xdef\consBD{4} \xdef\consBE{3} \xdef\consBQ{0}
\xdef\consBH{1} \xdef\consBR{-3} \xdef\consBK{0} \xdef\consBM{-4} \xdef\consBI{-3}
\xdef\consBL{-5} \xdef\consBV{-4} \xdef\consBF{-6} \xdef\consBY{-4} \xdef\consBW{-6}
\xdef\consBB{4} \xdef\consBZ{2} \xdef\consBX{-2}
\xdef\consZC{-8} \xdef\consZS{-2} \xdef\consZT{-2} \xdef\consZP{-1} \xdef\consZA{-1}
\xdef\consZG{-2} \xdef\consZN{0} \xdef\consZD{3} \xdef\consZE{4} \xdef\consZQ{5}
\xdef\consZH{1} \xdef\consZR{-1} \xdef\consZK{-1} \xdef\consZM{-2} \xdef\consZI{-3}
\xdef\consZL{-4} \xdef\consZV{-3} \xdef\consZF{-7} \xdef\consZY{-6} \xdef\consZW{-8}
\xdef\consZB{2} \xdef\consZZ{5} \xdef\consZX{-2}
\xdef\consXC{-5} \xdef\consXS{-1} \xdef\consXT{-1} \xdef\consXP{-2} \xdef\consXA{-1}
\xdef\consXG{-2} \xdef\consXN{-1} \xdef\consXD{-2} \xdef\consXE{-2} \xdef\consXQ{-2}
\xdef\consXH{-2} \xdef\consXR{-2} \xdef\consXK{-2} \xdef\consXM{-2} \xdef\consXI{-2}
\xdef\consXL{-3} \xdef\consXV{-2} \xdef\consXF{-4} \xdef\consXY{-4} \xdef\consXW{-6}
\xdef\consXB{-2} \xdef\consXZ{-2} \xdef\consXX{-2}
\expandafter\xdef\csname cons..\endcsname{1}
\gappenalty{-9} \xdef\m@trixf@ctor{10}
\else
\xdef\temp@{BLOSUM62}
\ifx\first@\temp@
%%%% BLOSUM62
\xdef\consCC{9} \xdef\consCS{-1} \xdef\consCT{-1} \xdef\consCP{-3} \xdef\consCA{0}
\xdef\consCG{-3} \xdef\consCN{-3} \xdef\consCD{-3} \xdef\consCE{-4} \xdef\consCQ{-3}
\xdef\consCH{-3} \xdef\consCR{-3} \xdef\consCK{-3} \xdef\consCM{-1} \xdef\consCI{-1}
\xdef\consCL{-1} \xdef\consCV{-1} \xdef\consCF{-2} \xdef\consCY{-2} \xdef\consCW{-2}
\xdef\consSC{-1} \xdef\consSS{4} \xdef\consST{1} \xdef\consSP{-1} \xdef\consSA{1}
\xdef\consSG{0} \xdef\consSN{1} \xdef\consSD{0} \xdef\consSE{0} \xdef\consSQ{0}
\xdef\consSH{-1} \xdef\consSR{-1} \xdef\consSK{0} \xdef\consSM{-1} \xdef\consSI{-2}
\xdef\consSL{-2} \xdef\consSV{-2} \xdef\consSF{-2} \xdef\consSY{-2} \xdef\consSW{-3}
\xdef\consTC{-1} \xdef\consTS{1} \xdef\consTT{4} \xdef\consTP{1} \xdef\consTA{-1}
\xdef\consTG{1} \xdef\consTN{0} \xdef\consTD{1} \xdef\consTE{0} \xdef\consTQ{0}
\xdef\consTH{0} \xdef\consTR{-1} \xdef\consTK{0} \xdef\consTM{-1} \xdef\consTI{-2}
\xdef\consTL{-2} \xdef\consTV{-2} \xdef\consTF{-2} \xdef\consTY{-2} \xdef\consTW{-3}
\xdef\consPC{-3} \xdef\consPS{-1} \xdef\consPT{1} \xdef\consPP{7} \xdef\consPA{-1}
\xdef\consPG{-2} \xdef\consPN{-1} \xdef\consPD{-1} \xdef\consPE{-1} \xdef\consPQ{-1}
\xdef\consPH{-2} \xdef\consPR{-2} \xdef\consPK{-1} \xdef\consPM{-2} \xdef\consPI{-3}
\xdef\consPL{-3} \xdef\consPV{-2} \xdef\consPF{-4} \xdef\consPY{-3} \xdef\consPW{-4}
\xdef\consAC{0} \xdef\consAS{1} \xdef\consAT{-1} \xdef\consAP{-1} \xdef\consAA{4}
\xdef\consAG{0} \xdef\consAN{-1} \xdef\consAD{-2} \xdef\consAE{-1} \xdef\consAQ{-1}
\xdef\consAH{-2} \xdef\consAR{-1} \xdef\consAK{-1} \xdef\consAM{-1} \xdef\consAI{-1}
\xdef\consAL{-1} \xdef\consAV{-2} \xdef\consAF{-2} \xdef\consAY{-2} \xdef\consAW{-3}
\xdef\consGC{-3} \xdef\consGS{0} \xdef\consGT{1} \xdef\consGP{-2} \xdef\consGA{0}
\xdef\consGG{6} \xdef\consGN{-2} \xdef\consGD{-1} \xdef\consGE{-2} \xdef\consGQ{-2}
\xdef\consGH{-2} \xdef\consGR{-2} \xdef\consGK{-2} \xdef\consGM{-3} \xdef\consGI{-4}
\xdef\consGL{-4} \xdef\consGV{0} \xdef\consGF{-3} \xdef\consGY{-3} \xdef\consGW{-2}
\xdef\consNC{-3} \xdef\consNS{1} \xdef\consNT{0} \xdef\consNP{-2} \xdef\consNA{-2}
\xdef\consNG{0} \xdef\consNN{6} \xdef\consND{1} \xdef\consNE{0} \xdef\consNQ{0}
\xdef\consNH{-1} \xdef\consNR{0} \xdef\consNK{0} \xdef\consNM{-2} \xdef\consNI{-3}
\xdef\consNL{-3} \xdef\consNV{-3} \xdef\consNF{-3} \xdef\consNY{-2} \xdef\consNW{-4}
\xdef\consDC{-3} \xdef\consDS{0} \xdef\consDT{1} \xdef\consDP{-1} \xdef\consDA{-2}
\xdef\consDG{-1} \xdef\consDN{1} \xdef\consDD{6} \xdef\consDE{2} \xdef\consDQ{0}
\xdef\consDH{-1} \xdef\consDR{-2} \xdef\consDK{-1} \xdef\consDM{-3} \xdef\consDI{-3}
\xdef\consDL{-4} \xdef\consDV{-3} \xdef\consDF{-3} \xdef\consDY{-3} \xdef\consDW{-4}
\xdef\consEC{-4} \xdef\consES{0} \xdef\consET{0} \xdef\consEP{-1} \xdef\consEA{-1}
\xdef\consEG{-2} \xdef\consEN{0} \xdef\consED{2} \xdef\consEE{5} \xdef\consEQ{2}
\xdef\consEH{0} \xdef\consER{0} \xdef\consEK{1} \xdef\consEM{-2} \xdef\consEI{-3}
\xdef\consEL{-3} \xdef\consEV{-3} \xdef\consEF{-3} \xdef\consEY{-2} \xdef\consEW{-3}
\xdef\consQC{-3} \xdef\consQS{0} \xdef\consQT{0} \xdef\consQP{-1} \xdef\consQA{-1}
\xdef\consQG{-2} \xdef\consQN{0} \xdef\consQD{0} \xdef\consQE{2} \xdef\consQQ{5}
\xdef\consQH{0} \xdef\consQR{1} \xdef\consQK{1} \xdef\consQM{0} \xdef\consQI{-3}
\xdef\consQL{-2} \xdef\consQV{-2} \xdef\consQF{-3} \xdef\consQY{-1} \xdef\consQW{-2}
\xdef\consHC{-3} \xdef\consHS{-1} \xdef\consHT{0} \xdef\consHP{-2} \xdef\consHA{-2}
\xdef\consHG{-2} \xdef\consHN{1} \xdef\consHD{1} \xdef\consHE{0} \xdef\consHQ{0}
\xdef\consHH{8} \xdef\consHR{0} \xdef\consHK{-1} \xdef\consHM{-2} \xdef\consHI{-3}
\xdef\consHL{-3} \xdef\consHV{-2} \xdef\consHF{-1} \xdef\consHY{2} \xdef\consHW{-2}
\xdef\consRC{-3} \xdef\consRS{-1} \xdef\consRT{-1} \xdef\consRP{-2} \xdef\consRA{-1}
\xdef\consRG{-2} \xdef\consRN{0} \xdef\consRD{-2} \xdef\consRE{0} \xdef\consRQ{1}
\xdef\consRH{0} \xdef\consRR{5} \xdef\consRK{2} \xdef\consRM{-1} \xdef\consRI{-3}
\xdef\consRL{-2} \xdef\consRV{-3} \xdef\consRF{-3} \xdef\consRY{-2} \xdef\consRW{-3}
\xdef\consKC{-3} \xdef\consKS{0} \xdef\consKT{0} \xdef\consKP{-1} \xdef\consKA{-1}
\xdef\consKG{-2} \xdef\consKN{0} \xdef\consKD{-1} \xdef\consKE{1} \xdef\consKQ{1}
\xdef\consKH{-1} \xdef\consKR{2} \xdef\consKK{5} \xdef\consKM{-1} \xdef\consKI{-3}
\xdef\consKL{-2} \xdef\consKV{-3} \xdef\consKF{-3} \xdef\consKY{-2} \xdef\consKW{-3}
\xdef\consMC{-1} \xdef\consMS{-1} \xdef\consMT{-1} \xdef\consMP{-2} \xdef\consMA{-1}
\xdef\consMG{-3} \xdef\consMN{-2} \xdef\consMD{-3} \xdef\consME{-2} \xdef\consMQ{0}
\xdef\consMH{-2} \xdef\consMR{-1} \xdef\consMK{-1} \xdef\consMM{5} \xdef\consMI{1}
\xdef\consML{2} \xdef\consMV{-2} \xdef\consMF{0} \xdef\consMY{-1} \xdef\consMW{-1}
\xdef\consIC{-1} \xdef\consIS{-2} \xdef\consIT{-2} \xdef\consIP{-3} \xdef\consIA{-1}
\xdef\consIG{-4} \xdef\consIN{-3} \xdef\consID{-3} \xdef\consIE{-3} \xdef\consIQ{-3}
\xdef\consIH{-3} \xdef\consIR{-3} \xdef\consIK{-3} \xdef\consIM{1} \xdef\consII{4}
\xdef\consIL{2} \xdef\consIV{1} \xdef\consIF{0} \xdef\consIY{-1} \xdef\consIW{-3}
\xdef\consLC{-1} \xdef\consLS{-2} \xdef\consLT{-2} \xdef\consLP{-3} \xdef\consLA{-1}
\xdef\consLG{-4} \xdef\consLN{-3} \xdef\consLD{-4} \xdef\consLE{-3} \xdef\consLQ{-2}
\xdef\consLH{-3} \xdef\consLR{-2} \xdef\consLK{-2} \xdef\consLM{2} \xdef\consLI{2}
\xdef\consLL{4} \xdef\consLV{3} \xdef\consLF{0} \xdef\consLY{-1} \xdef\consLW{-2}
\xdef\consVC{-1} \xdef\consVS{-2} \xdef\consVT{-2} \xdef\consVP{-2} \xdef\consVA{0}
\xdef\consVG{-3} \xdef\consVN{-3} \xdef\consVD{-3} \xdef\consVE{-2} \xdef\consVQ{-2}
\xdef\consVH{-3} \xdef\consVR{-3} \xdef\consVK{-2} \xdef\consVM{1} \xdef\consVI{3}
\xdef\consVL{1} \xdef\consVV{4} \xdef\consVF{-1} \xdef\consVY{-1} \xdef\consVW{-3}
\xdef\consFC{-2} \xdef\consFS{-2} \xdef\consFT{-2} \xdef\consFP{-4} \xdef\consFA{-2}
\xdef\consFG{-3} \xdef\consFN{-3} \xdef\consFD{-3} \xdef\consFE{-3} \xdef\consFQ{-3}
\xdef\consFH{-1} \xdef\consFR{-3} \xdef\consFK{-3} \xdef\consFM{0} \xdef\consFI{0}
\xdef\consFL{0} \xdef\consFV{-1} \xdef\consFF{6} \xdef\consFY{3} \xdef\consFW{1}
\xdef\consYC{-2} \xdef\consYS{-2} \xdef\consYT{-2} \xdef\consYP{-3} \xdef\consYA{-2}
\xdef\consYG{-3} \xdef\consYN{-2} \xdef\consYD{-3} \xdef\consYE{-2} \xdef\consYQ{-1}
\xdef\consYH{2} \xdef\consYR{-2} \xdef\consYK{-2} \xdef\consYM{-1} \xdef\consYI{-1}
\xdef\consYL{-1} \xdef\consYV{-1} \xdef\consYF{3} \xdef\consYY{7} \xdef\consYW{2}
\xdef\consWC{-2} \xdef\consWS{-3} \xdef\consWT{-3} \xdef\consWP{-4} \xdef\consWA{-3}
\xdef\consWG{-2} \xdef\consWN{-4} \xdef\consWD{-4} \xdef\consWE{-3} \xdef\consWQ{-2}
\xdef\consWH{-2} \xdef\consWR{-3} \xdef\consWK{-3} \xdef\consWM{-1} \xdef\consWI{-3}
\xdef\consWL{-2} \xdef\consWV{-3} \xdef\consWF{1} \xdef\consWY{2} \xdef\consWW{11}
\gappenalty{0} \xdef\m@trixf@ctor{10}
\else
\message{<Unknown residue weight matrix - using `identity'>} \weighttable{identity}
\fi
\fi
\fi
\fi
\fi
}
\def\setweight#1#2#3{%
\expandafter\xdef\csname cons#1#2\endcsname{#3}
\expandafter\xdef\csname cons#2#1\endcsname{#3}
}
\weighttable{identity}
\gappenalty{0}
\def\c@d@ns{%
\codon{A}{GCA,GCG,GCC,GCT,GCU,GCN}
\codon{B}{---}
\codon{C}{TGC,TGT,UGC,UGU,TGY}
\codon{D}{GAC,GAT,GAU,GAY}
\codon{E}{GAA,GAG,GAR}
\codon{F}{TTC,TTT,UUC,UUU,TTY}
\codon{G}{GGA,GGG,GGC,GGT,GGU,GGN}
\codon{H}{CAC,CAT,CAY}
\codon{I}{ATA,ATC,ATT,AUA,AUC,AUU,ATH}
\codon{J}{---}
\codon{K}{AAA,AAG,AAG,AAR}
\codon{L}{CTA,CTG,CTC,CTT,TTA,TTG,CUG,CUG,CUC,CUU,UUA,UUG,YTN}
\codon{M}{ATG,AUG,ATG}
\codon{N}{AAC,AAT,AAU,AAY}
\codon{O}{---}
\codon{P}{CCA,CCG,CCC,CCT,CCU,CCN}
\codon{Q}{CAA,CAG,CAR}
\codon{R}{AGA,AGG,CGA,CGG,CGC,CGT,CGU,MGN}
\codon{S}{TCT,TCC,TCG,TCA,AGT,AGC,UCU,UCC,UCG,UCA,AGU,WSN}
\codon{T}{ACT,ACC,ACG,ACA,ACU,ACN}
\codon{U}{---}
\codon{V}{GTA,GTG,GTC,GTT,GUA,GUG,GUC,GUU,GTN}
\codon{W}{TGG,UGG,TGG}
\codon{X}{---}
\codon{Y}{TAC,TAT,UAC,UAU,TAY}
\codon{Z}{---}
\codon{.}{TAA,TAG,TGA,UAA,UAG,UGA,TRR}
}
\definecolor{GreenYellow} {cmyk}{0.15,0,0.69,0}
\definecolor{Yellow} {cmyk}{0,0,1,0}
\definecolor{Goldenrod} {cmyk}{0,0.10,0.84,0}
\definecolor{Dandelion} {cmyk}{0,0.29,0.84,0}
\definecolor{Apricot} {cmyk}{0,0.32,0.52,0}
\definecolor{Peach} {cmyk}{0,0.50,0.70,0}
\definecolor{Melon} {cmyk}{0,0.46,0.50,0}
\definecolor{YellowOrange} {cmyk}{0,0.42,1,0}
\definecolor{Orange} {cmyk}{0,0.61,0.87,0}
\definecolor{BurntOrange} {cmyk}{0,0.51,1,0}
\definecolor{Bittersweet} {cmyk}{0,0.75,1,0.24}
\definecolor{RedOrange} {cmyk}{0,0.77,0.87,0}
\definecolor{Mahagony} {cmyk}{0,0.85,0.87,0.35}
\definecolor{Maroon} {cmyk}{0,0.87,0.68,0.32}
\definecolor{BrickRed} {cmyk}{0,0.89,0.94,0.28}
\definecolor{Red} {cmyk}{0,1,1,0}
\definecolor{OrangeRed} {cmyk}{0,1,0.50,0}
\definecolor{RubineRed} {cmyk}{0,1,0.13,0}
\definecolor{WildStrawberry}{cmyk}{0,0.96,0.39,0}
\definecolor{Salmon} {cmyk}{0,0.53,0.38,0}
\definecolor{CarnationPink} {cmyk}{0,0.63,0,0}
\definecolor{Magenta} {cmyk}{0,1,0,0}
\definecolor{VioletRed} {cmyk}{0,0.81,0,0}
\definecolor{Rhodamine} {cmyk}{0,0.82,0,0}
\definecolor{Mulberry} {cmyk}{0.34,0.90,0,0.02}
\definecolor{RedViolet} {cmyk}{0.07,0.90,0,0.34}
\definecolor{Fuchsia} {cmyk}{0.47,0.91,0,0.08}
\definecolor{Lavender} {cmyk}{0,0.48,0,0}
\definecolor{Thistle} {cmyk}{0.12,0.59,0,0}
\definecolor{Orchid} {cmyk}{0.32,0.64,0,0}
\definecolor{DarkOrchid} {cmyk}{0.40,0.80,0.20,0}
\definecolor{Purple} {cmyk}{0.45,0.86,0,0}
\definecolor{Plum} {cmyk}{0.50,1,0,0}
\definecolor{Violet} {cmyk}{0.79,0.88,0,0}
\definecolor{RoyalPurple} {cmyk}{0.75,0.90,0,0}
\definecolor{BlueViolet} {cmyk}{0.86,0.91,0,0.04}
\definecolor{Periwinkle} {cmyk}{0.57,0.55,0,0}
\definecolor{CadetBlue} {cmyk}{0.62,0.57,0.23,0}
\definecolor{CornflowerBlue}{cmyk}{0.65,0.13,0,0}
\definecolor{MidnightBlue} {cmyk}{0.98,0.13,0,0.43}
\definecolor{NavyBlue} {cmyk}{0.94,0.54,0,0}
\definecolor{RoyalBlue} {cmyk}{1,0.50,0,0}
\definecolor{Blue} {cmyk}{1,1,0,0}
\definecolor{Cerulean} {cmyk}{0.94,0.11,0,0}
\definecolor{Cyan} {cmyk}{1,0,0,0}
\definecolor{ProcessBlue} {cmyk}{0.96,0,0,0}
\definecolor{SkyBlue} {cmyk}{0.62,0,0.12,0}
\definecolor{Turquoise} {cmyk}{0.85,0,0.20,0}
\definecolor{TealBlue} {cmyk}{0.86,0,0.34,0.02}
\definecolor{Aquamarine} {cmyk}{0.82,0,0.30,0}
\definecolor{BlueGreen} {cmyk}{0.85,0,0.33,0}
\definecolor{Emerald} {cmyk}{1,0,0.50,0}
\definecolor{JungleGreen} {cmyk}{0.99,0,0.52,0}
\definecolor{SeaGreen} {cmyk}{0.69,0,0.50,0}
\definecolor{Green} {cmyk}{1,0,1,0}
\definecolor{ForestGreen} {cmyk}{0.91,0,0.88,0.12}
\definecolor{PineGreen} {cmyk}{0.92,0,0.59,0.25}
\definecolor{LimeGreen} {cmyk}{0.50,0,1,0}
\definecolor{YellowGreen} {cmyk}{0.44,0,0.74,0}
\definecolor{SpringGreen} {cmyk}{0.26,0,0.76,0}
\definecolor{OliveGreen} {cmyk}{0.64,0,0.95,0.40}
\definecolor{RawSienna} {cmyk}{0,0.72,1,0.45}
\definecolor{Sepia} {cmyk}{0,0.83,1,0.70}
\definecolor{Brown} {cmyk}{0,0.81,1,0.60}
\definecolor{Tan} {cmyk}{0.14,0.42,0.56,0}
\definecolor{White} {cmyk}{0,0,0,0}
\definecolor{Gray0} {cmyk}{0,0,0,0}
\definecolor{Gray5} {cmyk}{0,0,0,0.05}
\definecolor{Gray10} {cmyk}{0,0,0,0.10}
\definecolor{Gray15} {cmyk}{0,0,0,0.15}
\definecolor{Gray20} {cmyk}{0,0,0,0.20}
\definecolor{Gray25} {cmyk}{0,0,0,0.25}
\definecolor{Gray30} {cmyk}{0,0,0,0.30}
\definecolor{LightGray} {cmyk}{0,0,0,0.33}
\definecolor{Gray35} {cmyk}{0,0,0,0.35}
\definecolor{Gray40} {cmyk}{0,0,0,0.40}
\definecolor{Gray45} {cmyk}{0,0,0,0.45}
\definecolor{Gray50} {cmyk}{0,0,0,0.50}
\definecolor{Gray} {cmyk}{0,0,0,0.50}
\definecolor{GrayDefault} {cmyk}{0,0,0,0.50}
\definecolor{Gray55} {cmyk}{0,0,0,0.55}
\definecolor{Gray60} {cmyk}{0,0,0,0.60}
\definecolor{Gray65} {cmyk}{0,0,0,0.65}
\definecolor{DarkGray} {cmyk}{0,0,0,0.66}
\definecolor{Gray70} {cmyk}{0,0,0,0.70}
\definecolor{Gray75} {cmyk}{0,0,0,0.75}
\definecolor{Gray80} {cmyk}{0,0,0,0.80}
\definecolor{Gray85} {cmyk}{0,0,0,0.85}
\definecolor{Gray90} {cmyk}{0,0,0,0.90}
\definecolor{Gray95} {cmyk}{0,0,0,0.95}
\definecolor{Black} {cmyk}{0,0,0,1}
\definecolor{Gray100} {cmyk}{0,0,0,1}
\definecolor{TC0} {cmyk}{0.4,0.4,0,0}
\definecolor{TC1} {cmyk}{0.6,0,0.7,0}
\definecolor{TC2} {cmyk}{0.4,0,0.7,0}
\definecolor{TC3} {cmyk}{0.2,0,1,0}
\definecolor{TC4} {cmyk}{0,0,1,0}
\definecolor{TC5} {cmyk}{0,0.2,1,0}
\definecolor{TC6} {cmyk}{0,0.4,1,0}
\definecolor{TC7} {cmyk}{0,0.6,1,0}
\definecolor{TC8} {cmyk}{0,0.8,1,0}
\definecolor{TC9} {cmyk}{0,0.875,1,0}
\definecolor{TC99} {cmyk}{0,0,0,0}
\definecolor{LightGreenYellow} {cmyk}{0.08,0,0.35,0}
\definecolor{LightYellow} {cmyk}{0,0,0.50,0}
\definecolor{LightGoldenrod} {cmyk}{0,0.05,0.42,0}
\definecolor{LightDandelion} {cmyk}{0,0.15,0.42,0}
\definecolor{LightApricot} {cmyk}{0,0.16,0.26,0}
\definecolor{LightPeach} {cmyk}{0,0.25,0.35,0}
\definecolor{LightMelon} {cmyk}{0,0.23,0.25,0}
\definecolor{LightYellowOrange} {cmyk}{0,0.21,0.50,0}
\definecolor{LightOrange} {cmyk}{0,0.31,0.44,0}
\definecolor{LightBurntOrange} {cmyk}{0,0.26,0.50,0}
\definecolor{LightBittersweet} {cmyk}{0,0.38,0.50,0.12}
\definecolor{LightRedOrange} {cmyk}{0,0.39,0.44,0}
\definecolor{LightMahagony} {cmyk}{0,0.43,0.44,0.18}
\definecolor{LightMaroon} {cmyk}{0,0.44,0.34,0.16}
\definecolor{LightBrickRed} {cmyk}{0,0.45,0.47,0.14}
\definecolor{LightRed} {cmyk}{0,0.50,0.50,0}
\definecolor{LightOrangeRed} {cmyk}{0,0.50,0.25,0}
\definecolor{LightRubineRed} {cmyk}{0,0.50,0.07,0}
\definecolor{LightWildStrawberry}{cmyk}{0,0.48,0.20,0}
\definecolor{LightSalmon} {cmyk}{0,0.27,0.19,0}
\definecolor{LightCarnationPink} {cmyk}{0,0.32,0,0}
\definecolor{LightMagenta} {cmyk}{0,0.50,0,0}
\definecolor{LightVioletRed} {cmyk}{0,0.40,0,0}
\definecolor{LightRhodamine} {cmyk}{0,0.41,0,0}
\definecolor{LightMulberry} {cmyk}{0.17,0.45,0,0.01}
\definecolor{LightRedViolet} {cmyk}{0.04,0.45,0,0.17}
\definecolor{LightFuchsia} {cmyk}{0.24,0.46,0,0.04}
\definecolor{LightLavender} {cmyk}{0,0.24,0,0}
\definecolor{LightThistle} {cmyk}{0.06,0.30,0,0}
\definecolor{LightOrchid} {cmyk}{0.16,0.32,0,0}
\definecolor{LightDarkOrchid} {cmyk}{0.20,0.40,0.10,0}
\definecolor{LightPurple} {cmyk}{0.23,0.43,0,0}
\definecolor{LightPlum} {cmyk}{0.25,0.50,0,0}
\definecolor{LightViolet} {cmyk}{0.40,0.44,0,0}
\definecolor{LightRoyalPurple} {cmyk}{0.38,0.45,0,0}
\definecolor{LightBlueViolet} {cmyk}{0.43,0.46,0,0.02}
\definecolor{LightPeriwinkle} {cmyk}{0.29,0.28,0,0}
\definecolor{LightCadetBlue} {cmyk}{0.31,0.29,0.12,0}
\definecolor{LightCornflowerBlue}{cmyk}{0.33,0.07,0,0}
\definecolor{LightMidnightBlue} {cmyk}{0.49,0.07,0,0.22}
\definecolor{LightNavyBlue} {cmyk}{0.47,0.27,0,0}
\definecolor{LightRoyalBlue} {cmyk}{0.50,0.25,0,0}
\definecolor{LightBlue} {cmyk}{0.50,0.50,0,0}
\definecolor{LightCerulean} {cmyk}{0.47,0.06,0,0}
\definecolor{LightCyan} {cmyk}{0.50,0,0,0}
\definecolor{LightProcessBlue} {cmyk}{0.48,0,0,0}
\definecolor{LightSkyBlue} {cmyk}{0.31,0,0.06,0}
\definecolor{LightTurquoise} {cmyk}{0.43,0,0.10,0}
\definecolor{LightTealBlue} {cmyk}{0.43,0,0.17,0.01}
\definecolor{LightAquamarine} {cmyk}{0.41,0,0.15,0}
\definecolor{LightBlueGreen} {cmyk}{0.43,0,0.17,0}
\definecolor{LightEmerald} {cmyk}{0.50,0,0.25,0}
\definecolor{LightJungleGreen} {cmyk}{0.50,0,0.26,0}
\definecolor{LightSeaGreen} {cmyk}{0.35,0,0.25,0}
\definecolor{LightGreen} {cmyk}{0.50,0,0.50,0}
\definecolor{LightForestGreen} {cmyk}{0.46,0,0.44,0.06}
\definecolor{LightPineGreen} {cmyk}{0.46,0,0.30,0.13}
\definecolor{LightLimeGreen} {cmyk}{0.25,0,0.50,0}
\definecolor{LightYellowGreen} {cmyk}{0.22,0,0.37,0}
\definecolor{LightSpringGreen} {cmyk}{0.13,0,0.38,0}
\definecolor{LightOliveGreen} {cmyk}{0.32,0,0.48,0.20}
\definecolor{LightRawSienna} {cmyk}{0,0.36,0.50,0.23}
\definecolor{LightSepia} {cmyk}{0,0.44,0.50,0.35}
\definecolor{LightBrown} {cmyk}{0,0.41,0.50,0.30}
\definecolor{LightTan} {cmyk}{0.07,0.21,0.28,0}
\definecolor{LightWhite} {cmyk}{0,0,0,0}
\definecolor{LightGray0} {cmyk}{0,0,0,0}
\definecolor{LightGray5} {cmyk}{0,0,0,0.02}
\definecolor{LightGray10} {cmyk}{0,0,0,0.05}
\definecolor{LightGray15} {cmyk}{0,0,0,0.07}
\definecolor{LightGray20} {cmyk}{0,0,0,0.10}
\definecolor{LightGray25} {cmyk}{0,0,0,0.12}
\definecolor{LightGray30} {cmyk}{0,0,0,0.15}
\definecolor{LightLightGray} {cmyk}{0,0,0,0.16}
\definecolor{LightGray35} {cmyk}{0,0,0,0.17}
\definecolor{LightGray40} {cmyk}{0,0,0,0.20}
\definecolor{LightGray45} {cmyk}{0,0,0,0.22}
\definecolor{LightGray50} {cmyk}{0,0,0,0.25}
\definecolor{LightGray} {cmyk}{0,0,0,0.25}
\definecolor{LightGray55} {cmyk}{0,0,0,0.27}
\definecolor{LightGray60} {cmyk}{0,0,0,0.30}
\definecolor{LightGray65} {cmyk}{0,0,0,0.32}
\definecolor{LightDarkGray} {cmyk}{0,0,0,0.33}
\definecolor{LightGray70} {cmyk}{0,0,0,0.35}
\definecolor{LightGray75} {cmyk}{0,0,0,0.37}
\definecolor{LightGray80} {cmyk}{0,0,0,0.40}
\definecolor{LightGray85} {cmyk}{0,0,0,0.42}
\definecolor{LightGray90} {cmyk}{0,0,0,0.45}
\definecolor{LightGray95} {cmyk}{0,0,0,0.47}
\definecolor{LightBlack} {cmyk}{0,0,0,0.50}
\definecolor{LightGray100} {cmyk}{0,0,0,0.50}
\definecolor{LightTC0} {cmyk}{0.2,0.2,0,0}
\definecolor{LightTC1} {cmyk}{0.3,0,0.35,0}
\definecolor{LightTC2} {cmyk}{0.2,0,0.35,0}
\definecolor{LightTC3} {cmyk}{0.1,0,0.5,0}
\definecolor{LightTC4} {cmyk}{0,0,0.5,0}
\definecolor{LightTC5} {cmyk}{0,0.1,0.5,0}
\definecolor{LightTC6} {cmyk}{0,0.2,0.5,0}
\definecolor{LightTC7} {cmyk}{0,0.3,0.5,0}
\definecolor{LightTC8} {cmyk}{0,0.4,0.5,0}
\definecolor{LightTC99} {cmyk}{0,0,0,0}
\definecolor{LightLightGreenYellow} {cmyk}{0.04,0,0.17,0}
\definecolor{LightLightYellow} {cmyk}{0,0,0.25,0}
\definecolor{LightLightGoldenrod} {cmyk}{0,0.02,0.21,0}
\definecolor{LightLightDandelion} {cmyk}{0,0.07,0.21,0}
\definecolor{LightLightApricot} {cmyk}{0,0.08,0.13,0}
\definecolor{LightLightPeach} {cmyk}{0,0.12,0.17,0}
\definecolor{LightLightMelon} {cmyk}{0,0.11,0.12,0}
\definecolor{LightLightYellowOrange} {cmyk}{0,0.10,0.25,0}
\definecolor{LightLightOrange} {cmyk}{0,0.15,0.22,0}
\definecolor{LightLightBurntOrange} {cmyk}{0,0.13,0.25,0}
\definecolor{LightLightBittersweet} {cmyk}{0,0.19,0.25,0.06}
\definecolor{LightLightRedOrange} {cmyk}{0,0.14,0.22,0}
\definecolor{LightLightMahagony} {cmyk}{0,0.21,0.22,0.09}
\definecolor{LightLightMaroon} {cmyk}{0,0.22,0.17,0.08}
\definecolor{LightLightBrickRed} {cmyk}{0,0.22,0.23,0.07}
\definecolor{LightLightRed} {cmyk}{0,0.25,0.25,0}
\definecolor{LightLightOrangeRed} {cmyk}{0,0.25,0.12,0}
\definecolor{LightLightRubineRed} {cmyk}{0,0.25,0.03,0}
\definecolor{LightLightWildStrawberry}{cmyk}{0,0.24,0.10,0}
\definecolor{LightLightSalmon} {cmyk}{0,0.13,0.09,0}
\definecolor{LightLightCarnationPink} {cmyk}{0,0.16,0,0}
\definecolor{LightLightMagenta} {cmyk}{0,0.25,0,0}
\definecolor{LightLightVioletRed} {cmyk}{0,0.20,0,0}
\definecolor{LightLightRhodamine} {cmyk}{0,0.20,0,0}
\definecolor{LightLightMulberry} {cmyk}{0.08,0.22,0,0.005}
\definecolor{LightLightRedViolet} {cmyk}{0.02,0.22,0,0.08}
\definecolor{LightLightFuchsia} {cmyk}{0.12,0.23,0,0.02}
\definecolor{LightLightLavender} {cmyk}{0,0.12,0,0}
\definecolor{LightLightThistle} {cmyk}{0.03,0.15,0,0}
\definecolor{LightLightOrchid} {cmyk}{0.08,0.16,0,0}
\definecolor{LightLightDarkOrchid} {cmyk}{0.10,0.20,0.05,0}
\definecolor{LightLightPurple} {cmyk}{0.11,0.21,0,0}
\definecolor{LightLightPlum} {cmyk}{0.12,0.25,0,0}
\definecolor{LightLightViolet} {cmyk}{0.20,0.22,0,0}
\definecolor{LightLightRoyalPurple} {cmyk}{0.19,0.22,0,0}
\definecolor{LightLightBlueViolet} {cmyk}{0.21,0.23,0,0.01}
\definecolor{LightLightPeriwinkle} {cmyk}{0.14,0.14,0,0}
\definecolor{LightLightCadetBlue} {cmyk}{0.15,0.14,0.06,0}
\definecolor{LightLightCornflowerBlue}{cmyk}{0.16,0.03,0,0}
\definecolor{LightLightMidnightBlue} {cmyk}{0.24,0.03,0,0.11}
\definecolor{LightLightNavyBlue} {cmyk}{0.23,0.13,0,0}
\definecolor{LightLightRoyalBlue} {cmyk}{0.25,0.12,0,0}
\definecolor{LightLightBlue} {cmyk}{0.25,0.25,0,0}
\definecolor{LightLightCerulean} {cmyk}{0.23,0.03,0,0}
\definecolor{LightLightCyan} {cmyk}{0.25,0,0,0}
\definecolor{LightLightProcessBlue} {cmyk}{0.24,0,0,0}
\definecolor{LightLightSkyBlue} {cmyk}{0.15,0,0.03,0}
\definecolor{LightLightTurquoise} {cmyk}{0.21,0,0.05,0}
\definecolor{LightLightTealBlue} {cmyk}{0.21,0,0.08,0.005}
\definecolor{LightLightAquamarine} {cmyk}{0.20,0,0.07,0}
\definecolor{LightLightBlueGreen} {cmyk}{0.21,0,0.08,0}
\definecolor{LightLightEmerald} {cmyk}{0.25,0,0.12,0}
\definecolor{LightLightJungleGreen} {cmyk}{0.25,0,0.13,0}
\definecolor{LightLightSeaGreen} {cmyk}{0.17,0,0.12,0}
\definecolor{LightLightGreen} {cmyk}{0.25,0,0.25,0}
\definecolor{LightLightForestGreen} {cmyk}{0.23,0,0.22,0.03}
\definecolor{LightLightPineGreen} {cmyk}{0.23,0,0.15,0.06}
\definecolor{LightLightLimeGreen} {cmyk}{0.12,0,0.25,0}
\definecolor{LightLightYellowGreen} {cmyk}{0.11,0,0.18,0}
\definecolor{LightLightSpringGreen} {cmyk}{0.06,0,0.19,0}
\definecolor{LightLightOliveGreen} {cmyk}{0.16,0,0.24,0.10}
\definecolor{LightLightRawSienna} {cmyk}{0,0.18,0.25,0.11}
\definecolor{LightLightSepia} {cmyk}{0,0.22,0.25,0.17}
\definecolor{LightLightBrown} {cmyk}{0,0.20,0.25,0.15}
\definecolor{LightLightTan} {cmyk}{0.03,0.10,0.14,0}
\definecolor{LightLightWhite} {cmyk}{0,0,0,0}
\definecolor{LightLightGray0} {cmyk}{0,0,0,0}
\definecolor{LightLightGray5} {cmyk}{0,0,0,0.01}
\definecolor{LightLightGray10} {cmyk}{0,0,0,0.02}
\definecolor{LightLightGray15} {cmyk}{0,0,0,0.03}
\definecolor{LightLightGray20} {cmyk}{0,0,0,0.05}
\definecolor{LightLightGray25} {cmyk}{0,0,0,0.06}
\definecolor{LightLightGray30} {cmyk}{0,0,0,0.07}
\definecolor{LightLightLightGray} {cmyk}{0,0,0,0.08}
\definecolor{LightLightGray35} {cmyk}{0,0,0,0.09}
\definecolor{LightLightGray40} {cmyk}{0,0,0,0.10}
\definecolor{LightLightGray45} {cmyk}{0,0,0,0.11}
\definecolor{LightLightGray50} {cmyk}{0,0,0,0.12}
\definecolor{LightLightGray} {cmyk}{0,0,0,0.13}
\definecolor{LightLightGray55} {cmyk}{0,0,0,0.14}
\definecolor{LightLightGray60} {cmyk}{0,0,0,0.15}
\definecolor{LightLightGray65} {cmyk}{0,0,0,0.16}
\definecolor{LightLightDarkGray} {cmyk}{0,0,0,0.17}
\definecolor{LightLightGray70} {cmyk}{0,0,0,0.18}
\definecolor{LightLightGray75} {cmyk}{0,0,0,0.19}
\definecolor{LightLightGray80} {cmyk}{0,0,0,0.20}
\definecolor{LightLightGray85} {cmyk}{0,0,0,0.21}
\definecolor{LightLightGray90} {cmyk}{0,0,0,0.22}
\definecolor{LightLightGray95} {cmyk}{0,0,0,0.23}
\definecolor{LightLightBlack} {cmyk}{0,0,0,0.25}
\definecolor{LightLightGray100} {cmyk}{0,0,0,0.25}
\definecolor{LightLightTC0} {cmyk}{0.1,0.1,0,0}
\definecolor{LightLightTC1} {cmyk}{0.15,0,0.175,0}
\definecolor{LightLightTC2} {cmyk}{0.1,0,0.175,0}
\definecolor{LightLightTC3} {cmyk}{0.05,0,0.25,0}
\definecolor{LightLightTC4} {cmyk}{0,0,0.25,0}
\definecolor{LightLightTC5} {cmyk}{0,0.05,0.25,0}
\definecolor{LightLightTC6} {cmyk}{0,0.1,0.25,0}
\definecolor{LightLightTC7} {cmyk}{0,0.15,0.25,0}
\definecolor{LightLightTC8} {cmyk}{0,0.2,0.25,0}
\definecolor{LightLightTC99} {cmyk}{0,0,0,0}
\definecolor{LightLightLightGreenYellow} {cmyk}{0.02,0,0.08,0}
\definecolor{LightLightLightYellow} {cmyk}{0,0,0.12,0}
\definecolor{LightLightLightGoldenrod} {cmyk}{0,0.01,0.10,0}
\definecolor{LightLightLightDandelion} {cmyk}{0,0.03,0.10,0}
\definecolor{LightLightLightApricot} {cmyk}{0,0.04,0.06,0}
\definecolor{LightLightLightPeach} {cmyk}{0,0.06,0.08,0}
\definecolor{LightLightLightMelon} {cmyk}{0,0.05,0.06,0}
\definecolor{LightLightLightYellowOrange} {cmyk}{0,0.05,0.12,0}
\definecolor{LightLightLightOrange} {cmyk}{0,0.07,0.11,0}
\definecolor{LightLightLightBurntOrange} {cmyk}{0,0.06,0.12,0}
\definecolor{LightLightLightBittersweet} {cmyk}{0,0.09,0.12,0.03}
\definecolor{LightLightLightRedOrange} {cmyk}{0,0.07,0.11,0}
\definecolor{LightLightLightMahagony} {cmyk}{0,0.10,0.11,0.04}
\definecolor{LightLightLightMaroon} {cmyk}{0,0.11,0.08,0.04}
\definecolor{LightLightLightBrickRed} {cmyk}{0,0.11,0.11,0.03}
\definecolor{LightLightLightRed} {cmyk}{0,0.12,0.12,0}
\definecolor{LightLightLightOrangeRed} {cmyk}{0,0.12,0.06,0}
\definecolor{LightLightLightRubineRed} {cmyk}{0,0.12,0.01,0}
\definecolor{LightLightLightWildStrawberry}{cmyk}{0,0.12,0.05,0}
\definecolor{LightLightLightSalmon} {cmyk}{0,0.06,0.04,0}
\definecolor{LightLightLightCarnationPink} {cmyk}{0,0.08,0,0}
\definecolor{LightLightLightMagenta} {cmyk}{0,0.12,0,0}
\definecolor{LightLightLightLightMagenta} {cmyk}{0,0.06,0,0}
\definecolor{LightLightLightVioletRed} {cmyk}{0,0.10,0,0}
\definecolor{LightLightLightRhodamine} {cmyk}{0,0.10,0,0}
\definecolor{LightLightLightMulberry} {cmyk}{0.04,0.11,0,0.002}
\definecolor{LightLightLightRedViolet} {cmyk}{0.01,0.11,0,0.04}
\definecolor{LightLightLightFuchsia} {cmyk}{0.06,0.11,0,0.01}
\definecolor{LightLightLightLavender} {cmyk}{0,0.06,0,0}
\definecolor{LightLightLightThistle} {cmyk}{0.01,0.07,0,0}
\definecolor{LightLightLightOrchid} {cmyk}{0.04,0.08,0,0}
\definecolor{LightLightLightDarkOrchid} {cmyk}{0.05,0.10,0.02,0}
\definecolor{LightLightLightPurple} {cmyk}{0.05,0.10,0,0}
\definecolor{LightLightLightPlum} {cmyk}{0.06,0.12,0,0}
\definecolor{LightLightLightViolet} {cmyk}{0.10,0.11,0,0}
\definecolor{LightLightLightRoyalPurple} {cmyk}{0.09,0.11,0,0}
\definecolor{LightLightLightBlueViolet} {cmyk}{0.10,0.11,0,0.005}
\definecolor{LightLightLightPeriwinkle} {cmyk}{0.07,0.07,0,0}
\definecolor{LightLightLightCadetBlue} {cmyk}{0.07,0.07,0.03,0}
\definecolor{LightLightLightCornflowerBlue}{cmyk}{0.08,0.01,0,0}
\definecolor{LightLightLightMidnightBlue} {cmyk}{0.12,0.01,0,0.05}
\definecolor{LightLightLightNavyBlue} {cmyk}{0.11,0.06,0,0}
\definecolor{LightLightLightRoyalBlue} {cmyk}{0.12,0.06,0,0}
\definecolor{LightLightLightBlue} {cmyk}{0.12,0.12,0,0}
\definecolor{LightLightLightCerulean} {cmyk}{0.11,0.01,0,0}
\definecolor{LightLightLightCyan} {cmyk}{0.12,0,0,0}
\definecolor{LightLightLightProcessBlue} {cmyk}{0.12,0,0,0}
\definecolor{LightLightLightSkyBlue} {cmyk}{0.07,0,0.01,0}
\definecolor{LightLightLightTurquoise} {cmyk}{0.10,0,0.02,0}
\definecolor{LightLightLightTealBlue} {cmyk}{0.10,0,0.04,0.002}
\definecolor{LightLightLightAquamarine} {cmyk}{0.10,0,0.03,0}
\definecolor{LightLightLightBlueGreen} {cmyk}{0.10,0,0.04,0}
\definecolor{LightLightLightEmerald} {cmyk}{0.12,0,0.06,0}
\definecolor{LightLightLightJungleGreen} {cmyk}{0.12,0,0.06,0}
\definecolor{LightLightLightSeaGreen} {cmyk}{0.08,0,0.06,0}
\definecolor{LightLightLightGreen} {cmyk}{0.12,0,0.12,0}
\definecolor{LightLightLightForestGreen} {cmyk}{0.11,0,0.11,0.01}
\definecolor{LightLightLightPineGreen} {cmyk}{0.11,0,0.07,0.03}
\definecolor{LightLightLightLimeGreen} {cmyk}{0.06,0,0.12,0}
\definecolor{LightLightLightYellowGreen} {cmyk}{0.05,0,0.09,0}
\definecolor{LightLightLightSpringGreen} {cmyk}{0.03,0,0.09,0}
\definecolor{LightLightLightOliveGreen} {cmyk}{0.08,0,0.12,0.05}
\definecolor{LightLightLightRawSienna} {cmyk}{0,0.09,0.12,0.05}
\definecolor{LightLightLightSepia} {cmyk}{0,0.11,0.12,0.06}
\definecolor{LightLightLightBrown} {cmyk}{0,0.10,0.12,0.07}
\definecolor{LightLightLightTan} {cmyk}{0.01,0.05,0.07,0}
\definecolor{LightLightLightWhite} {cmyk}{0,0,0,0}
\definecolor{LightLightLightGray0} {cmyk}{0,0,0,0}
\definecolor{LightLightLightGray5} {cmyk}{0,0,0,0.005}
\definecolor{LightLightLightGray10} {cmyk}{0,0,0,0.01}
\definecolor{LightLightLightGray15} {cmyk}{0,0,0,0.015}
\definecolor{LightLightLightGray20} {cmyk}{0,0,0,0.025}
\definecolor{LightLightLightGray25} {cmyk}{0,0,0,0.03}
\definecolor{LightLightLightGray30} {cmyk}{0,0,0,0.035}
\definecolor{LightLightLightLightGray} {cmyk}{0,0,0,0.04}
\definecolor{LightLightLightGray35} {cmyk}{0,0,0,0.045}
\definecolor{LightLightLightGray40} {cmyk}{0,0,0,0.05}
\definecolor{LightLightLightGray45} {cmyk}{0,0,0,0.055}
\definecolor{LightLightLightGray50} {cmyk}{0,0,0,0.06}
\definecolor{LightLightLightGray} {cmyk}{0,0,0,0.065}
\definecolor{LightLightLightGray55} {cmyk}{0,0,0,0.07}
\definecolor{LightLightLightGray60} {cmyk}{0,0,0,0.075}
\definecolor{LightLightLightGray65} {cmyk}{0,0,0,0.08}
\definecolor{LightLightLightDarkGray} {cmyk}{0,0,0,0.085}
\definecolor{LightLightLightGray70} {cmyk}{0,0,0,0.09}
\definecolor{LightLightLightGray75} {cmyk}{0,0,0,0.095}
\definecolor{LightLightLightGray80} {cmyk}{0,0,0,0.10}
\definecolor{LightLightLightGray85} {cmyk}{0,0,0,0.105}
\definecolor{LightLightLightGray90} {cmyk}{0,0,0,0.11}
\definecolor{LightLightLightGray95} {cmyk}{0,0,0,0.115}
\definecolor{LightLightLightBlack} {cmyk}{0,0,0,0.12}
\definecolor{LightLightLightGray100} {cmyk}{0,0,0,0.125}
\definecolor{LightLightLightTC0} {cmyk}{0.05,0.05,0,0}
\definecolor{LightLightLightTC1} {cmyk}{0.075,0,0.086,0}
\definecolor{LightLightLightTC2} {cmyk}{0.05,0,0.086,0}
\definecolor{LightLightLightTC3} {cmyk}{0.025,0,0.125,0}
\definecolor{LightLightLightTC4} {cmyk}{0,0,0.125,0}
\definecolor{LightLightLightTC5} {cmyk}{0,0.025,0.125,0}
\definecolor{LightLightLightTC6} {cmyk}{0,0.05,0.125,0}
\definecolor{LightLightLightTC7} {cmyk}{0,0.0175,0.125,0}
\definecolor{LightLightLightTC8} {cmyk}{0,0.1,0.125,0}
\definecolor{LightLightLightTC99} {cmyk}{0,0,0,0}
\definecolor{BlueRed5} {rgb} {0.15,0.17,0.55}
\definecolor{BlueRed10} {rgb} {0.20,0.23,0.57}
\definecolor{BlueRed15} {rgb} {0.24,0.29,0.60}
\definecolor{BlueRed20} {rgb} {0.33,0.35,0.64}
\definecolor{BlueRed25} {rgb} {0.43,0.43,0.68}
\definecolor{BlueRed30} {rgb} {0.52,0.52,0.73}
\definecolor{BlueRed35} {rgb} {0.60,0.60,0.78}
\definecolor{BlueRed40} {rgb} {0.70,0.70,0.84}
\definecolor{BlueRed45} {rgb} {0.80,0.80,0.85}
\definecolor{BlueRed50} {rgb} {0.86,0.82,0.82}
\definecolor{BlueRed55} {rgb} {0.87,0.73,0.73}
\definecolor{BlueRed60} {rgb} {0.89,0.64,0.64}
\definecolor{BlueRed65} {rgb} {0.90,0.55,0.55}
\definecolor{BlueRed70} {rgb} {0.91,0.47,0.46}
\definecolor{BlueRed75} {rgb} {0.91,0.39,0.37}
\definecolor{BlueRed80} {rgb} {0.90,0.33,0.28}
\definecolor{BlueRed85} {rgb} {0.89,0.25,0.20}
\definecolor{BlueRed90} {rgb} {0.88,0.23,0.14}
\definecolor{BlueRed95} {rgb} {0.87,0.21,0.09}
\definecolor{BlueRed100} {rgb} {0.87,0.16,0.04}
\definecolor{RedBlue100} {rgb} {0.15,0.17,0.55}
\definecolor{RedBlue95} {rgb} {0.15,0.17,0.55}
\definecolor{RedBlue90} {rgb} {0.20,0.23,0.57}
\definecolor{RedBlue85} {rgb} {0.24,0.29,0.60}
\definecolor{RedBlue80} {rgb} {0.33,0.35,0.64}
\definecolor{RedBlue75} {rgb} {0.43,0.43,0.68}
\definecolor{RedBlue70} {rgb} {0.52,0.52,0.73}
\definecolor{RedBlue65} {rgb} {0.60,0.60,0.78}
\definecolor{RedBlue60} {rgb} {0.70,0.70,0.84}
\definecolor{RedBlue55} {rgb} {0.80,0.80,0.85}
\definecolor{RedBlue50} {rgb} {0.86,0.82,0.82}
\definecolor{RedBlue45} {rgb} {0.87,0.73,0.73}
\definecolor{RedBlue40} {rgb} {0.89,0.64,0.64}
\definecolor{RedBlue35} {rgb} {0.90,0.55,0.55}
\definecolor{RedBlue30} {rgb} {0.91,0.47,0.46}
\definecolor{RedBlue25} {rgb} {0.91,0.39,0.37}
\definecolor{RedBlue20} {rgb} {0.90,0.33,0.28}
\definecolor{RedBlue15} {rgb} {0.89,0.25,0.20}
\definecolor{RedBlue10} {rgb} {0.88,0.23,0.14}
\definecolor{RedBlue5} {rgb} {0.87,0.21,0.09}
\definecolor{GreenRed5} {rgb} {0,1,0}
\definecolor{GreenRed10} {rgb} {0.05,0.95,0}
\definecolor{GreenRed15} {rgb} {0.10,0.90,0}
\definecolor{GreenRed20} {rgb} {0.15,0.85,0}
\definecolor{GreenRed25} {rgb} {0.20,0.80,0}
\definecolor{GreenRed30} {rgb} {0.25,0.75,0}
\definecolor{GreenRed35} {rgb} {0.30,0.70,0}
\definecolor{GreenRed40} {rgb} {0.35,0.65,0}
\definecolor{GreenRed45} {rgb} {0.40,0.60,0}
\definecolor{GreenRed50} {rgb} {0.45,0.55,0}
\definecolor{GreenRed55} {rgb} {0.50,0.50,0}
\definecolor{GreenRed60} {rgb} {0.55,0.45,0}
\definecolor{GreenRed65} {rgb} {0.60,0.40,0}
\definecolor{GreenRed70} {rgb} {0.65,0.35,0}
\definecolor{GreenRed75} {rgb} {0.70,0.30,0}
\definecolor{GreenRed80} {rgb} {0.75,0.25,0}
\definecolor{GreenRed85} {rgb} {0.80,0.20,0}
\definecolor{GreenRed90} {rgb} {0.85,0.15,0}
\definecolor{GreenRed95} {rgb} {0.90,0.10,0}
\definecolor{GreenRed100} {rgb} {0.95,0.05,0}
\definecolor{RedGreen100} {rgb} {0.05,0.95,0}
\definecolor{RedGreen95} {rgb} {0.10,0.90,0}
\definecolor{RedGreen90} {rgb} {0.15,0.85,0}
\definecolor{RedGreen85} {rgb} {0.20,0.80,0}
\definecolor{RedGreen80} {rgb} {0.25,0.75,0}
\definecolor{RedGreen75} {rgb} {0.30,0.70,0}
\definecolor{RedGreen70} {rgb} {0.35,0.65,0}
\definecolor{RedGreen65} {rgb} {0.40,0.60,0}
\definecolor{RedGreen60} {rgb} {0.45,0.55,0}
\definecolor{RedGreen55} {rgb} {0.50,0.50,0}
\definecolor{RedGreen50} {rgb} {0.55,0.45,0}
\definecolor{RedGreen45} {rgb} {0.60,0.40,0}
\definecolor{RedGreen40} {rgb} {0.65,0.35,0}
\definecolor{RedGreen35} {rgb} {0.70,0.30,0}
\definecolor{RedGreen30} {rgb} {0.75,0.25,0}
\definecolor{RedGreen25} {rgb} {0.80,0.20,0}
\definecolor{RedGreen20} {rgb} {0.85,0.15,0}
\definecolor{RedGreen15} {rgb} {0.90,0.10,0}
\definecolor{RedGreen10} {rgb} {0.95,0.05,0}
\definecolor{RedGreen5} {rgb} {1,0,0}
\definecolor{ColdHot5} {rgb} {0,0.08,1}
\definecolor{ColdHot10} {rgb} {0,0.29,1}
\definecolor{ColdHot15} {rgb} {0,0.49,1}
\definecolor{ColdHot20} {rgb} {0,0.70,1}
\definecolor{ColdHot25} {rgb} {0,0.90,1}
\definecolor{ColdHot30} {rgb} {0,1,0.87}
\definecolor{ColdHot35} {rgb} {0,1,0.68}
\definecolor{ColdHot40} {rgb} {0,1,0.46}
\definecolor{ColdHot45} {rgb} {0,1,0.25}
\definecolor{ColdHot50} {rgb} {0,1,0.04}
\definecolor{ColdHot55} {rgb} {0.16,1,0}
\definecolor{ColdHot60} {rgb} {0.35,1,0}
\definecolor{ColdHot65} {rgb} {0.56,1,0}
\definecolor{ColdHot70} {rgb} {0.79,1,0}
\definecolor{ColdHot75} {rgb} {0.98,1,0}
\definecolor{ColdHot80} {rgb} {1,0.82,0}
\definecolor{ColdHot85} {rgb} {1,0.60,0}
\definecolor{ColdHot90} {rgb} {1,0.40,0}
\definecolor{ColdHot95} {rgb} {1,0.20,0}
\definecolor{ColdHot100} {rgb} {0.91,0,0}
\definecolor{HotCold100} {rgb} {0,0.08,1}
\definecolor{HotCold95} {rgb} {0,0.29,1}
\definecolor{HotCold90} {rgb} {0,0.49,1}
\definecolor{HotCold85} {rgb} {0,0.70,1}
\definecolor{HotCold80} {rgb} {0,0.90,1}
\definecolor{HotCold75} {rgb} {0,1,0.87}
\definecolor{HotCold70} {rgb} {0,1,0.68}
\definecolor{HotCold65} {rgb} {0,1,0.46}
\definecolor{HotCold60} {rgb} {0,1,0.25}
\definecolor{HotCold55} {rgb} {0,1,0.04}
\definecolor{HotCold50} {rgb} {0.16,1,0}
\definecolor{HotCold45} {rgb} {0.35,1,0}
\definecolor{HotCold40} {rgb} {0.56,1,0}
\definecolor{HotCold35} {rgb} {0.79,1,0}
\definecolor{HotCold30} {rgb} {0.98,1,0}
\definecolor{HotCold25} {rgb} {1,0.82,0}
\definecolor{HotCold20} {rgb} {1,0.60,0}
\definecolor{HotCold15} {rgb} {1,0.40,0}
\definecolor{HotCold10} {rgb} {1,0.20,0}
\definecolor{HotCold5} {rgb} {0.91,0,0}
\expandafter\def\csname BlueRed5\endcsname{[0.15,0.17,0.55]}
\expandafter\def\csname BlueRed10\endcsname{[0.20,0.23,0.57]}
\expandafter\def\csname BlueRed15\endcsname{[0.24,0.29,0.60]}
\expandafter\def\csname BlueRed20\endcsname{[0.33,0.35,0.64]}
\expandafter\def\csname BlueRed25\endcsname{[0.43,0.43,0.68]}
\expandafter\def\csname BlueRed30\endcsname{[0.52,0.52,0.73]}
\expandafter\def\csname BlueRed35\endcsname{[0.60,0.60,0.78]}
\expandafter\def\csname BlueRed40\endcsname{[0.70,0.70,0.84]}
\expandafter\def\csname BlueRed45\endcsname{[0.80,0.80,0.85]}
\expandafter\def\csname BlueRed50\endcsname{[0.86,0.82,0.82]}
\expandafter\def\csname BlueRed55\endcsname{[0.87,0.73,0.73]}
\expandafter\def\csname BlueRed60\endcsname{[0.89,0.64,0.64]}
\expandafter\def\csname BlueRed65\endcsname{[0.90,0.55,0.55]}
\expandafter\def\csname BlueRed70\endcsname{[0.91,0.47,0.46]}
\expandafter\def\csname BlueRed75\endcsname{[0.91,0.39,0.37]}
\expandafter\def\csname BlueRed80\endcsname{[0.90,0.33,0.28]}
\expandafter\def\csname BlueRed85\endcsname{[0.89,0.25,0.20]}
\expandafter\def\csname BlueRed90\endcsname{[0.88,0.23,0.14]}
\expandafter\def\csname BlueRed95\endcsname{[0.87,0.21,0.09]}
\expandafter\def\csname BlueRed100\endcsname{[0.87,0.16,0.04]}
\expandafter\def\csname RedBlue100\endcsname{[0.15,0.17,0.55]}
\expandafter\def\csname RedBlue95\endcsname{[0.15,0.17,0.55]}
\expandafter\def\csname RedBlue90\endcsname{[0.20,0.23,0.57]}
\expandafter\def\csname RedBlue85\endcsname{[0.24,0.29,0.60]}
\expandafter\def\csname RedBlue80\endcsname{[0.33,0.35,0.64]}
\expandafter\def\csname RedBlue75\endcsname{[0.43,0.43,0.68]}
\expandafter\def\csname RedBlue70\endcsname{[0.52,0.52,0.73]}
\expandafter\def\csname RedBlue65\endcsname{[0.60,0.60,0.78]}
\expandafter\def\csname RedBlue60\endcsname{[0.70,0.70,0.84]}
\expandafter\def\csname RedBlue55\endcsname{[0.80,0.80,0.85]}
\expandafter\def\csname RedBlue50\endcsname{[0.86,0.82,0.82]}
\expandafter\def\csname RedBlue45\endcsname{[0.87,0.73,0.73]}
\expandafter\def\csname RedBlue40\endcsname{[0.89,0.64,0.64]}
\expandafter\def\csname RedBlue35\endcsname{[0.90,0.55,0.55]}
\expandafter\def\csname RedBlue30\endcsname{[0.91,0.47,0.46]}
\expandafter\def\csname RedBlue25\endcsname{[0.91,0.39,0.37]}
\expandafter\def\csname RedBlue20\endcsname{[0.90,0.33,0.28]}
\expandafter\def\csname RedBlue15\endcsname{[0.89,0.25,0.20]}
\expandafter\def\csname RedBlue10\endcsname{[0.88,0.23,0.14]}
\expandafter\def\csname RedBlue5\endcsname{[0.87,0.21,0.09]}
\expandafter\def\csname GreenRed5\endcsname{[0,1,0]}
\expandafter\def\csname GreenRed10\endcsname{[0.05,0.95,0]}
\expandafter\def\csname GreenRed15\endcsname{[0.10,0.90,0]}
\expandafter\def\csname GreenRed20\endcsname{[0.15,0.85,0]}
\expandafter\def\csname GreenRed25\endcsname{[0.20,0.80,0]}
\expandafter\def\csname GreenRed30\endcsname{[0.25,0.75,0]}
\expandafter\def\csname GreenRed35\endcsname{[0.30,0.70,0]}
\expandafter\def\csname GreenRed40\endcsname{[0.35,0.65,0]}
\expandafter\def\csname GreenRed45\endcsname{[0.40,0.60,0]}
\expandafter\def\csname GreenRed50\endcsname{[0.45,0.55,0]}
\expandafter\def\csname GreenRed55\endcsname{[0.50,0.50,0]}
\expandafter\def\csname GreenRed60\endcsname{[0.55,0.45,0]}
\expandafter\def\csname GreenRed65\endcsname{[0.60,0.40,0]}
\expandafter\def\csname GreenRed70\endcsname{[0.65,0.35,0]}
\expandafter\def\csname GreenRed75\endcsname{[0.70,0.30,0]}
\expandafter\def\csname GreenRed80\endcsname{[0.75,0.25,0]}
\expandafter\def\csname GreenRed85\endcsname{[0.80,0.20,0]}
\expandafter\def\csname GreenRed90\endcsname{[0.85,0.15,0]}
\expandafter\def\csname GreenRed95\endcsname{[0.90,0.10,0]}
\expandafter\def\csname GreenRed100\endcsname{[0.95,0.05,0]}
\expandafter\def\csname RedGreen100\endcsname{[0.05,0.95,0]}
\expandafter\def\csname RedGreen95\endcsname{[0.10,0.90,0]}
\expandafter\def\csname RedGreen90\endcsname{[0.15,0.85,0]}
\expandafter\def\csname RedGreen85\endcsname{[0.20,0.80,0]}
\expandafter\def\csname RedGreen80\endcsname{[0.25,0.75,0]}
\expandafter\def\csname RedGreen75\endcsname{[0.30,0.70,0]}
\expandafter\def\csname RedGreen70\endcsname{[0.35,0.65,0]}
\expandafter\def\csname RedGreen65\endcsname{[0.40,0.60,0]}
\expandafter\def\csname RedGreen60\endcsname{[0.45,0.55,0]}
\expandafter\def\csname RedGreen55\endcsname{[0.50,0.50,0]}
\expandafter\def\csname RedGreen50\endcsname{[0.55,0.45,0]}
\expandafter\def\csname RedGreen45\endcsname{[0.60,0.40,0]}
\expandafter\def\csname RedGreen40\endcsname{[0.65,0.35,0]}
\expandafter\def\csname RedGreen35\endcsname{[0.70,0.30,0]}
\expandafter\def\csname RedGreen30\endcsname{[0.75,0.25,0]}
\expandafter\def\csname RedGreen25\endcsname{[0.80,0.20,0]}
\expandafter\def\csname RedGreen20\endcsname{[0.85,0.15,0]}
\expandafter\def\csname RedGreen15\endcsname{[0.90,0.10,0]}
\expandafter\def\csname RedGreen10\endcsname{[0.95,0.05,0]}
\expandafter\def\csname RedGreen5\endcsname{[1,0,0]}
\expandafter\def\csname ColdHot5\endcsname{[0,0.08,1]}
\expandafter\def\csname ColdHot10\endcsname{[0,0.29,1]}
\expandafter\def\csname ColdHot15\endcsname{[0,0.49,1]}
\expandafter\def\csname ColdHot20\endcsname{[0,0.70,1]}
\expandafter\def\csname ColdHot25\endcsname{[0,0.90,1]}
\expandafter\def\csname ColdHot30\endcsname{[0,1,0.87]}
\expandafter\def\csname ColdHot35\endcsname{[0,1,0.68]}
\expandafter\def\csname ColdHot40\endcsname{[0,1,0.46]}
\expandafter\def\csname ColdHot45\endcsname{[0,1,0.25]}
\expandafter\def\csname ColdHot50\endcsname{[0,1,0.04]}
\expandafter\def\csname ColdHot55\endcsname{[0.16,1,0]}
\expandafter\def\csname ColdHot60\endcsname{[0.35,1,0]}
\expandafter\def\csname ColdHot65\endcsname{[0.56,1,0]}
\expandafter\def\csname ColdHot70\endcsname{[0.79,1,0]}
\expandafter\def\csname ColdHot75\endcsname{[0.98,1,0]}
\expandafter\def\csname ColdHot80\endcsname{[1,0.82,0]}
\expandafter\def\csname ColdHot85\endcsname{[1,0.60,0]}
\expandafter\def\csname ColdHot90\endcsname{[1,0.40,0]}
\expandafter\def\csname ColdHot95\endcsname{[1,0.20,0]}
\expandafter\def\csname ColdHot100\endcsname{[0.91,0,0]}
\expandafter\def\csname HotCold100\endcsname{[0,0.08,1]}
\expandafter\def\csname HotCold95\endcsname{[0,0.29,1]}
\expandafter\def\csname HotCold90\endcsname{[0,0.49,1]}
\expandafter\def\csname HotCold85\endcsname{[0,0.70,1]}
\expandafter\def\csname HotCold80\endcsname{[0,0.90,1]}
\expandafter\def\csname HotCold75\endcsname{[0,1,0.87]}
\expandafter\def\csname HotCold70\endcsname{[0,1,0.68]}
\expandafter\def\csname HotCold65\endcsname{[0,1,0.46]}
\expandafter\def\csname HotCold60\endcsname{[0,1,0.25]}
\expandafter\def\csname HotCold55\endcsname{[0,1,0.04]}
\expandafter\def\csname HotCold50\endcsname{[0.16,1,0]}
\expandafter\def\csname HotCold45\endcsname{[0.35,1,0]}
\expandafter\def\csname HotCold40\endcsname{[0.56,1,0]}
\expandafter\def\csname HotCold35\endcsname{[0.79,1,0]}
\expandafter\def\csname HotCold30\endcsname{[0.98,1,0]}
\expandafter\def\csname HotCold25\endcsname{[1,0.82,0]}
\expandafter\def\csname HotCold20\endcsname{[1,0.60,0]}
\expandafter\def\csname HotCold15\endcsname{[1,0.40,0]}
\expandafter\def\csname HotCold10\endcsname{[1,0.20,0]}
\expandafter\def\csname HotCold5\endcsname{[0.91,0,0]}
\def\make@lower{%
\if\first@ A\xdef\first@{a}\else \if\first@ B\xdef\first@{b}\else
\if\first@ C\xdef\first@{c}\else \if\first@ D\xdef\first@{d}\else
\if\first@ E\xdef\first@{e}\else \if\first@ F\xdef\first@{f}\else
\if\first@ G\xdef\first@{g}\else \if\first@ H\xdef\first@{h}\else
\if\first@ I\xdef\first@{i}\else \if\first@ J\xdef\first@{j}\else
\if\first@ K\xdef\first@{k}\else \if\first@ L\xdef\first@{l}\else
\if\first@ M\xdef\first@{m}\else \if\first@ N\xdef\first@{n}\else
\if\first@ O\xdef\first@{o}\else \if\first@ P\xdef\first@{p}\else
\if\first@ Q\xdef\first@{q}\else \if\first@ R\xdef\first@{r}\else
\if\first@ S\xdef\first@{s}\else \if\first@ T\xdef\first@{t}\else
\if\first@ U\xdef\first@{u}\else \if\first@ V\xdef\first@{v}\else
\if\first@ W\xdef\first@{w}\else \if\first@ X\xdef\first@{x}\else
\if\first@ Y\xdef\first@{y}\else \if\first@ Z\xdef\first@{z}\else
\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi}
\def\make@upper{%
\if\first@ a\xdef\first@{A}\else \if\first@ b\xdef\first@{B}\else
\if\first@ c\xdef\first@{C}\else \if\first@ d\xdef\first@{D}\else
\if\first@ e\xdef\first@{E}\else \if\first@ f\xdef\first@{F}\else
\if\first@ g\xdef\first@{G}\else \if\first@ h\xdef\first@{H}\else
\if\first@ i\xdef\first@{I}\else \if\first@ j\xdef\first@{J}\else
\if\first@ k\xdef\first@{K}\else \if\first@ l\xdef\first@{L}\else
\if\first@ m\xdef\first@{M}\else \if\first@ n\xdef\first@{N}\else
\if\first@ o\xdef\first@{O}\else \if\first@ p\xdef\first@{P}\else
\if\first@ q\xdef\first@{Q}\else \if\first@ r\xdef\first@{R}\else
\if\first@ s\xdef\first@{S}\else \if\first@ t\xdef\first@{T}\else
\if\first@ u\xdef\first@{U}\else \if\first@ v\xdef\first@{V}\else
\if\first@ w\xdef\first@{W}\else \if\first@ x\xdef\first@{X}\else
\if\first@ y\xdef\first@{Y}\else \if\first@ z\xdef\first@{Z}\else
\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi}
\def\type@get#1 MSF: #2 Type: #3 #4@{\seqtype{#3}}
\def\inf@@get#1 #2 #3 #4 #5 #6@{%
\def\first@{#1}
\def\second@{#2}
\def\third@{#3}
\xdef\fourth@{#4 @}
\expandafter\check@letter\fourth@
\ifnumber
\def\fourth@{#4}
\else
\xdef\fourth@{#5 @}
\expandafter\check@letter\fourth@
\ifnumber
\def\fourth@{#5}
\else
\def\fourth@{99999999}
\fi
\fi
\def\fifth@{#5}
\def\last@{#6}}
\def\check@char#1{\letterfalse \ifnum\catcode`#1=11 \lettertrue \fi
\numberfalse \ifnum\catcode`#1=12 \numbertrue \fi
\xdef\code@num{\the\catcode`#1}
\xdef\char@num{`#1}}
\def\check@letter#1#2@{\letterfalse\ifnum\catcode`#1=11 \lettertrue\fi%
\numberfalse\ifnum\catcode`#1=12 \numbertrue\fi}
\def\seq@get#1 #2@{\def\first@{#1} \def\seq@line{#2}}
\def\res@get#1#2@{\def\first@{#1} \def\seq@line{#2&@}}
\def\tot@get#1#2@{%
\xdef\first@{#1}
\expandafter\xdef\csname seq\the\triple@count\endcsname{#2&@}}
\def\dis@get#1#2@{%
\xdef\first@{#1}
\expandafter\xdef\csname res\the\triple@count\endcsname{#1}
\expandafter\xdef\csname seq\the\triple@count\endcsname{#2&@}}
\def\firstchar@get#1#2@{\def\first@{#1}\def\third@{#2@}}
\def\residue@get#1#2@{\xdef\first@{#1}
\xdef\char@num{`#1}
\expandafter\xdef\csname res\the\loopcount\endcsname{\first@}
\expandafter\xdef\csname sequence\the\loopcount\endcsname{#2@}}
\def\remove@fromseq#1@{\expandafter\xdef\csname sequence\the\loopcount\endcsname{#1}}
\def\get@temp#1@{\xdef\temp@{#1}}
\def\TC@get#1#2@{\xdef\char@num{`#1}
\ifnum\char@num=45 \xdef\TC@first@{*}
\else
\ifnum\char@num>57 \xdef\TC@first@{*}
\else
\xdef\TC@first@{#1}
\fi
\fi
\expandafter\xdef\csname TC@num\the\loopcount\endcsname{\TC@first@}
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{#2@}}
\def\sublogo@get#1 @{\xdef\first@{#1}}
\def\re@write#1,#2@{%
\xdef\third@{#2,@}
\xdef\first@{\csname hide@@@seq#1\endcsname}
\ifx\first@\last@
\else
\xdef\first@{#1&}
\ifx\first@\ampers@nd \else \advance\innerloopcount by 1 \fi
\if\second@ e \xdef\second@{\csname @rd#1\endcsname}
\else \xdef\second@{\second@,\csname @rd#1\endcsname}\fi
\fi
}
\def\order@set#1,#2@{%
\xdef\second@{#2,@}
\expandafter\xdef\csname @rd#1\endcsname{\the\loopcount}
\expandafter\xdef\csname res@count\the\loopcount\endcsname{%
\csname pos#1\endcsname}
\expandafter\xdef\csname hide@seq\the\loopcount\endcsname{%
\csname hide@@seq#1\endcsname}
\expandafter\xdef\csname hide@name\the\loopcount\endcsname{%
\csname hide@@name#1\endcsname}
\expandafter\xdef\csname hide@number\the\loopcount\endcsname{%
\csname hide@@number#1\endcsname}
\expandafter\xdef\csname seq@start\the\loopcount\endcsname{%
\csname seq@@start#1\endcsname}
\expandafter\xdef\csname seq@len\the\loopcount\endcsname{%
\csname seq@@len#1\endcsname}
\expandafter\xdef\csname seqname\the\loopcount\endcsname{%
\csname seq@name#1\endcsname}
\expandafter\xdef\csname newseqname\the\loopcount\endcsname{%
\csname newseq@name#1\endcsname}
\expandafter\xdef\csname seq@gap\the\loopcount\endcsname{%
\csname seq@@gap#1\endcsname}
\expandafter\xdef\csname name@col\the\loopcount\endcsname{%
\csname name@@col#1\endcsname}
\expandafter\xdef\csname number@col\the\loopcount\endcsname{%
\csname number@@col#1\endcsname}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{%
\csname stack@@reg#1\endcsname}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
\csname stack@@tintreg#1\endcsname}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
\csname stack@@emphreg#1\endcsname}
\expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{%
\csname stack@@lowerreg#1\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@@framereg#1\endcsname}
\expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{%
\csname stack@@shadingreg#1\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
\csname stack@@top#1\endcsname}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{%
\csname stack@@ttop#1\endcsname}
\expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{%
\csname stack@@tttop#1\endcsname}
\expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{%
\csname stack@@ttttop#1\endcsname}
\expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{%
\csname stack@@bottom#1\endcsname}
\expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{%
\csname stack@@bbottom#1\endcsname}
\expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{%
\csname stack@@bbbottom#1\endcsname}
\expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{%
\csname stack@@bbbbottom#1\endcsname}
}
\def\reorder@seqs#1{%
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\xdef\csname pos\the\loopcount\endcsname{%
\csname res@count\the\loopcount\endcsname}
\expandafter\xdef\csname hide@@seq\the\loopcount\endcsname{%
\csname hide@seq\the\loopcount\endcsname}
\expandafter\xdef\csname hide@@name\the\loopcount\endcsname{%
\csname hide@name\the\loopcount\endcsname}
\expandafter\xdef\csname hide@@number\the\loopcount\endcsname{%
\csname hide@number\the\loopcount\endcsname}
\expandafter\xdef\csname seq@@start\the\loopcount\endcsname{%
\csname seq@start\the\loopcount\endcsname}
\expandafter\xdef\csname seq@@len\the\loopcount\endcsname{%
\csname seq@len\the\loopcount\endcsname}
\expandafter\xdef\csname seq@name\the\loopcount\endcsname{%
\csname seqname\the\loopcount\endcsname}
\expandafter\xdef\csname newseq@name\the\loopcount\endcsname{%
\csname newseqname\the\loopcount\endcsname}
\expandafter\xdef\csname seq@@gap\the\loopcount\endcsname{%
\csname seq@gap\the\loopcount\endcsname}
\expandafter\xdef\csname name@@col\the\loopcount\endcsname{%
\csname name@col\the\loopcount\endcsname}
\expandafter\xdef\csname number@@col\the\loopcount\endcsname{%
\csname number@col\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@reg\the\loopcount\endcsname{%
\csname stack@reg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@tintreg\the\loopcount\endcsname{%
\csname stack@tintreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@emphreg\the\loopcount\endcsname{%
\csname stack@emphreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@lowerreg\the\loopcount\endcsname{%
\csname stack@lowerreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@shadingreg\the\loopcount\endcsname{%
\csname stack@shadingreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@top\the\loopcount\endcsname{%
\csname stack@top\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@ttop\the\loopcount\endcsname{%
\csname stack@ttop\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@tttop\the\loopcount\endcsname{%
\csname stack@tttop\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@ttttop\the\loopcount\endcsname{%
\csname stack@ttttop\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@bottom\the\loopcount\endcsname{%
\csname stack@bottom\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@bbottom\the\loopcount\endcsname{%
\csname stack@bbottom\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@bbbottom\the\loopcount\endcsname{%
\csname stack@bbbottom\the\loopcount\endcsname}
\expandafter\xdef\csname stack@@bbbbottom\the\loopcount\endcsname{%
\csname stack@bbbbottom\the\loopcount\endcsname}
\ifnum\loopcount<\killseq@count \repeat
\xdef\third@{#1}
\loopcount=0 \innerloopcount=0 \xdef\last@{kill} \xdef\second@{e}
\loop
\advance\loopcount by 1
\expandafter\re@write\third@
\ifnum\loopcount<\seq@count \repeat
\ifnum\innerloopcount<\killseq@count
\@latex@error{Not enough sequences specified in `orderseqs'
(\the\innerloopcount/\the\killseq@count)}\@ehc
\fi
\loopcount=0 \xdef\second@{\second@,@}
\loop
\advance\loopcount by 1
\expandafter\order@set\second@
\ifnum\loopcount<\killseq@count \repeat
\ifnum\cons@num>0 \xdef\cons@num{\csname @rd\cons@num\endcsname} \fi
\ifnum\rule@num>0 \xdef\rule@num{\csname @rd\rule@num\endcsname} \fi
\ifnum\divref@>0 \xdef\divref@{\csname @rd\divref@\endcsname} \fi
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\xdef\csname pos\the\loopcount\endcsname{0}
\ifnum\loopcount<\killseq@count \repeat
}
\def\group@get#1,#2@{%
\def\group@set{\expandafter\residue@get\second@
\ifnum\char@num>96 \make@upper \fi
\ifx\first@\ampers@nd
\else \expandafter\xdef\csname \prfx grp\first@\endcsname{\the\loopcount}
\xdef\second@{\csname sequence\the\loopcount\endcsname} \group@set
\fi}
\xdef\second@{#1 &@} \xdef\third@{#2&,@} \group@set}
\def\get@item#1,#2@{\xdef\first@{#2@}\xdef\first@@{#2}\xdef\fourth@{#1}}
\def\get@first@@#1-#2@{\xdef\first@@{#1}}
\def\get@digit#1,#2@{%
\def\check@series##1-##2##3@{%
\xdef\first@@{##2}\xdef\fourth@{##1}\xdef\fourth@@{##3}}
\xdef\first@{#2@}
\xdef\fourth@{#1-&@}
\expandafter\check@series\fourth@
\ifx\first@@\ampers@nd
\else
\xdef\first@@{\first@@\fourth@@-&@}
\expandafter\get@first@@\first@@
\loopcount=\fourth@
\ifnum\first@@>\fourth@
\advance\loopcount by 1
\xdef\first@{\the\loopcount-\first@@,#2@}
\else
\ifnum\first@@<\fourth@
\advance\loopcount by -1
\xdef\first@{\the\loopcount-\first@@,#2@}
\fi
\fi
\fi
}
\def\donot@shade{%
\expandafter\check@letter\first@
\ifletter
\expandafter\get@item\first@
\xdef\first@{\fourth@}
\get@name@number
\xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill}
\ifx\third@\second@
\else
\expandafter\xdef\csname hide@seq\first@\endcsname{noshade}
\fi
\xdef\first@{\first@@ @}
\donot@shade
\else
\expandafter\get@digit\first@
\ifx\fourth@\ampers@nd
\else
\xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill}
\ifx\third@\second@
\else
\expandafter\xdef\csname hide@seq\fourth@\endcsname{noshade}
\fi
\donot@shade
\fi
\fi}
\def\clear@res@nums#1{%
\temp@count=65
\loop
\xdef\first@@{\csname ch@r@\the\temp@count\endcsname}
\expandafter\xdef\csname res@num\first@@ #1\endcsname{0}
\advance\temp@count by 1
\ifnum\temp@count>90\else\repeat
\expandafter\xdef\csname res@num\d@t #1\endcsname{0}
\expandafter\xdef\csname res@num\questi@n #1\endcsname{0}
}
\def\setsubfamily@{%
\expandafter\check@letter\first@
\ifletter
\expandafter\get@item\first@
\xdef\first@{\fourth@}
\get@name@number
\advance\res@count by 1
\expandafter\xdef\csname subfamily@num\first@\endcsname{\subfamily@count}
\xdef\first@{\first@@ @}
\setsubfamily@
\else
\expandafter\get@digit\first@
\ifx\fourth@\ampers@nd
\else
\advance\res@count by 1
\expandafter\xdef\csname subfamily@num\fourth@\endcsname{\subfamily@count}
\setsubfamily@
\fi
\fi
}
\def\hideseq@{%
\expandafter\check@letter\first@
\ifletter
\expandafter\get@item\first@
\xdef\first@{\fourth@}
\get@name@number
\xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill}
\ifx\third@\second@
\else
\expandafter\xdef\csname hide@seq\first@\endcsname{true}
\fi
\xdef\first@{\first@@ @}
\hideseq@
\else
\expandafter\get@digit\first@
\ifx\fourth@\ampers@nd
\else
\xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill}
\ifx\third@\second@
\else
\expandafter\xdef\csname hide@seq\fourth@\endcsname{true}
\fi
\hideseq@
\fi
\fi}
\def\hidename@{%
\expandafter\check@letter\first@
\ifletter
\expandafter\get@item\first@
\xdef\first@{\fourth@}
\get@name@number
\expandafter\xdef\csname hide@name\first@\endcsname{yes}
\xdef\first@{\first@@ @}
\hidename@
\else
\expandafter\get@digit\first@
\ifx\fourth@\ampers@nd
\else
\expandafter\xdef\csname hide@name\fourth@\endcsname{yes}
\hidename@
\fi
\fi}
\def\hidenumber@{%
\expandafter\check@letter\first@
\ifletter
\expandafter\get@item\first@
\xdef\first@{\fourth@}
\get@name@number
\expandafter\xdef\csname hide@number\first@\endcsname{yes}
\xdef\first@{\first@@ @}
\hidenumber@
\else
\expandafter\get@digit\first@
\ifx\fourth@\ampers@nd
\else
\expandafter\xdef\csname hide@number\fourth@\endcsname{yes}
\hidenumber@
\fi
\fi}
\def\namecolor@{%
\expandafter\check@letter\first@
\ifletter
\expandafter\get@item\first@
\xdef\first@{\fourth@}
\get@name@number
\expandafter\xdef\csname name@col\first@\endcsname{\third@}
\xdef\first@{\first@@ @}
\namecolor@
\else
\expandafter\get@digit\first@
\ifx\fourth@\ampers@nd
\else
\expandafter\xdef\csname name@col\fourth@\endcsname{\third@}
\namecolor@
\fi
\fi}
\def\numbercolor@{%
\expandafter\check@letter\first@
\ifletter
\expandafter\get@item\first@
\xdef\first@{\fourth@}
\get@name@number
\expandafter\xdef\csname number@col\first@\endcsname{\third@}
\xdef\first@{\first@@ @}
\numbercolor@
\else
\expandafter\get@digit\first@
\ifx\fourth@\ampers@nd
\else
\expandafter\xdef\csname number@col\fourth@\endcsname{\third@}
\numbercolor@
\fi
\fi}
\def\killseq@{%
\expandafter\check@letter\first@
\ifletter
\expandafter\get@item\first@
\xdef\first@{\fourth@}
\get@name@number
\ifnum\first@>\seq@count
\else
\ifnum\killseq@count>1
\xdef\third@{\csname hide@seq\first@\endcsname} \xdef\second@{kill}
\ifx\third@\second@
\else
\expandafter\xdef\csname hide@seq\first@\endcsname{kill}
\expandafter\xdef\csname hide@@@seq\first@\endcsname{kill}
\ifnum\first@=\cons@num \xdef\cons@num{0} \fi
\advance\killseq@count by -1
\seq@percent=100 \divide\seq@percent by \killseq@count
\fi
\fi\fi
\xdef\first@{\first@@ @}
\killseq@
\else
\expandafter\get@digit\first@
\ifx\fourth@\ampers@nd
\else
\ifnum\fourth@>\seq@count
\else
\ifnum\killseq@count>1
\xdef\third@{\csname hide@seq\fourth@\endcsname} \xdef\second@{kill}
\ifx\third@\second@
\else
\expandafter\xdef\csname hide@seq\fourth@\endcsname{kill}
\expandafter\xdef\csname hide@@@seq\fourth@\endcsname{kill}
\ifnum\fourth@=\cons@num \xdef\cons@num{0} \fi
\advance\killseq@count by -1
\seq@percent=100 \divide\seq@percent by \killseq@count
\fi
\fi\fi
\killseq@
\fi
\fi}
\def\kill@loop{%
\advance\innerloopcount by 1
\xdef\first@{\csname hide@seq\the\innerloopcount\endcsname}
\ifx\first@\second@ \kill@loop \fi}
\def\kill@seqnow{%
\xdef\first@{\csname hide@seq\the\loopcount\endcsname} \xdef\second@{kill}
\innerloopcount=\loopcount
\ifx\first@\second@
\kill@loop
\expandafter\xdef\csname hide@seq\the\loopcount\endcsname{%
\csname hide@seq\the\innerloopcount\endcsname}
\expandafter\xdef\csname seqname\the\loopcount\endcsname{%
\csname seqname\the\innerloopcount\endcsname}
\expandafter\xdef\csname newseqname\the\loopcount\endcsname{%
\csname newseqname\the\innerloopcount\endcsname}
\expandafter\xdef\csname seq@gap\the\loopcount\endcsname{%
\csname seq@gap\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{%
\csname stack@reg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{%
\csname stack@tintreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{%
\csname stack@emphreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{%
\csname stack@lowerreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{%
\csname stack@framereg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{%
\csname stack@shadingreg\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{%
\csname stack@top\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{%
\csname stack@ttop\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{%
\csname stack@tttop\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{%
\csname stack@ttttop\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{%
\csname stack@bottom\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{%
\csname stack@bbottom\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{%
\csname stack@bbbottom\the\innerloopcount\endcsname}
\expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{%
\csname stack@bbbbottom\the\innerloopcount\endcsname}
\expandafter\xdef\csname res@count\the\loopcount\endcsname{%
\csname res@count\the\innerloopcount\endcsname}
\expandafter\xdef\csname hide@seq\the\innerloopcount\endcsname{kill}
\ifnum\loopcount=\rule@num \hideruler \fi
\fi
\expandafter\xdef\csname @rd\the\innerloopcount\endcsname{\the\loopcount}
\advance\loopcount by 1
\ifnum\loopcount>\killseq@count
\ifnum\rule@num>0\xdef\rule@num{\csname @rd\rule@num\endcsname}\fi
\ifnum\cons@num>0\xdef\cons@num{\csname @rd\cons@num\endcsname}\fi
\else
\kill@seqnow
\fi}
\def\get@sim#1#2@{\xdef\sim@char{#1} \xdef\last@{#2 &@}}
\def\getsim@char{%
\advance\innerloopcount by 1
\ifnum\innerloopcount>\m@x
\else
\expandafter\get@sim\last@
\ifx\second@\sim@char \xdef\third@{2} \innerloopcount=\m@x \fi
\getsim@char
\fi}
\def\get@count(#1)#2@{\xdef\last@{#2 &@} \xdef\m@x{#1}}
\def\get@nums#1..#2@{\xdef\first@{#1} \xdef\second@{#2}}
\def\func@shading#1{%
\clearfuncgroups
\xdef\temp@{#1}
\xdef\second@{charge}
\ifx\temp@\second@
\ifgerm@n
\funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up}
\funcgroup{basisch ($+$)}{KRH}{White}{Blue}{upper}{up}
\else
\ifsp@nish
\funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up}
\funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up}
\else
\funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up}
\funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up}
\fi
\fi
\else
\xdef\second@{hydropathy}
\ifx\temp@\second@
\ifgerm@n
\funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up}
\funcgroup{basisch ($+$)}{KRH}{White}{Blue}{upper}{up}
\funcgroup{polar ungeladen}{YSTGNQC}{Black}{Yellow}{upper}{up}
\funcgroup{hydrophob unpolar}{AFPMWVIL}{White}{Green}{upper}{up}
\else
\ifsp@nish
\funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up}
\funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up}
\funcgroup{polar sin carga}{YSTGNQC}{Black}{Yellow}{upper}{up}
\funcgroup{hidrof\'obico no polar}{AFPMWVIL}{White}{Green}{upper}{up}
\else
\funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up}
\funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up}
\funcgroup{polar uncharged}{YSTGNQC}{Black}{Yellow}{upper}{up}
\funcgroup{hydrophobic nonpolar}{AFPMWVIL}{White}{Green}{upper}{up}
\fi
\fi
\else
\xdef\second@{chemical}
\ifx\temp@\second@
\ifgerm@n
\funcgroup{sauer ($-$)}{DE}{White}{Red}{upper}{up}
\funcgroup{aliphatisch}{AGVIL}{White}{Black}{upper}{up}
\funcgroup{aliphatisch (klein)}{AG}{White}{Gray}{upper}{up}
\funcgroup{Amid}{NQ}{White}{Green}{upper}{up}
\funcgroup{aromatisch}{FYW}{White}{Brown}{upper}{up}
\funcgroup{basisch (+)}{KRH}{White}{Blue}{upper}{up}
\funcgroup{Hydroxyl}{ST}{Black}{Magenta}{upper}{up}
\funcgroup{Imin}{P}{Black}{Orange}{upper}{up}
\funcgroup{Schwefel}{CM}{Black}{Yellow}{upper}{up}
\else
\ifsp@nish
\funcgroup{\'acido ($-$)}{DE}{White}{Red}{upper}{up}
\funcgroup{alif\'atico}{AGVIL}{White}{Black}{upper}{up}
\funcgroup{alif\'atico (parvo)}{AG}{White}{Gray}{upper}{up}
\funcgroup{amida}{NQ}{White}{Green}{upper}{up}
\funcgroup{arom\'atico}{FYW}{White}{Brown}{upper}{up}
\funcgroup{b\'asico ($+$)}{KRH}{White}{Blue}{upper}{up}
\funcgroup{hidr\'oxido}{ST}{Black}{Magenta}{upper}{up}
\funcgroup{imino}{P}{Black}{Orange}{upper}{up}
\funcgroup{azufre}{CM}{Black}{Yellow}{upper}{up}
\else
\funcgroup{acidic ($-$)}{DE}{White}{Red}{upper}{up}
\funcgroup{aliphatic}{AGVIL}{White}{Black}{upper}{up}
\funcgroup{aliphatic (small)}{AG}{White}{Gray}{upper}{up}
\funcgroup{amide}{NQ}{White}{Green}{upper}{up}
\funcgroup{aromatic}{FYW}{White}{Brown}{upper}{up}
\funcgroup{basic ($+$)}{KRH}{White}{Blue}{upper}{up}
\funcgroup{hydroxyl}{ST}{Black}{Magenta}{upper}{up}
\funcgroup{imino}{P}{Black}{Orange}{upper}{up}
\funcgroup{sulfur}{CM}{Black}{Yellow}{upper}{up}
\fi
\fi
\else
\xdef\second@{structure}
\ifx\temp@\second@
\ifgerm@n
\funcgroup{extern}{DEHKNQR}{Black}{Orange}{upper}{up}
\funcgroup{ambivalent}{ACGPSTWY}{Black}{Yellow}{upper}{up}
\funcgroup{intern}{FILMV}{White}{Green}{upper}{up}
\else
\ifsp@nish
\funcgroup{externo}{DEHKNQR}{Black}{Orange}{upper}{up}
\funcgroup{ambivalente}{ACGPSTWY}{Black}{Yellow}{upper}{up}
\funcgroup{interno}{FILMV}{White}{Green}{upper}{up}
\else
\funcgroup{external}{DEHKNQR}{Black}{Orange}{upper}{up}
\funcgroup{ambivalent}{ACGPSTWY}{Black}{Yellow}{upper}{up}
\funcgroup{internal}{FILMV}{White}{Green}{upper}{up}
\fi
\fi
\else
\xdef\second@{standard area}
\ifx\temp@\second@
\ifgerm@n
\funcgroup{\ 88,1 (G); Standard Seitenkettenfl\"ache %
(\AA$^2$)}%
{G}{Black}{BrickRed}{upper}{up}
\funcgroup{118,2 (A); 129,8 (S)}{AS}{Black}{Orange}{upper}{up}
\funcgroup{146,1 (C); 146,8 (P)}%
{CP}{Black}{Yellow}{upper}{up}
\funcgroup{152,5 (T); 158,7 (D); 164,5 (V); 165,5 (N)}%
{TDVN}{Black}{YellowGreen}{upper}{up}
\funcgroup{181,0 (I); 186,2 (E)}{IE}{White}{PineGreen}{upper}{up}
\funcgroup{193,1 (L); 193,2 (Q); 202,5 (H); 203,3 (M)}%
{LQHM}{Black}{SkyBlue}{upper}{up}
\funcgroup{222,8 (F); 225,8 (K)}{FK}{White}{RoyalPurple}{upper}{up}
\funcgroup{238,8 (Y)}{Y}{White}{RedViolet}{upper}{up}
\funcgroup{256,0 (R); 266,2 (W)}{RW}{White}{Black}{upper}{up}
\else
\ifsp@nish
\funcgroup{\ 88.1 (G); Superficie est\'andar de la cadena lateral (\AA$^2$)}%
{G}{Black}{BrickRed}{upper}{up}
\funcgroup{118.2 (A); 129.8 (S)}{AS}{Black}{Orange}{upper}{up}
\funcgroup{146.1 (C); 146.8 (P)}%
{CP}{Black}{Yellow}{upper}{up}
\funcgroup{152.5 (T); 158.7 (D); 164.5 (V); 165.5 (N)}%
{TDVN}{Black}{YellowGreen}{upper}{up}
\funcgroup{181.0 (I); 186.2 (E)}{IE}{White}{PineGreen}{upper}{up}
\funcgroup{193.1 (L); 193.2 (Q); 202.5 (H); 203.3 (M)}%
{LQHM}{Black}{SkyBlue}{upper}{up}
\funcgroup{222.8 (F); 225.8 (K)}{FK}{White}{RoyalPurple}{upper}{up}
\funcgroup{238.8 (Y)}{Y}{White}{RedViolet}{upper}{up}
\funcgroup{256.0 (R); 266.2 (W)}{RW}{White}{Black}{upper}{up}
\else
\funcgroup{\ 88.1 (G); Standard sidechain area (\AA$^2$)}%
{G}{Black}{BrickRed}{upper}{up}
\funcgroup{118.2 (A); 129.8 (S)}{AS}{Black}{Orange}{upper}{up}
\funcgroup{146.1 (C); 146.8 (P)}%
{CP}{Black}{Yellow}{upper}{up}
\funcgroup{152.5 (T); 158.7 (D); 164.5 (V); 165.5 (N)}%
{TDVN}{Black}{YellowGreen}{upper}{up}
\funcgroup{181.0 (I); 186.2 (E)}{IE}{White}{PineGreen}{upper}{up}
\funcgroup{193.1 (L); 193.2 (Q); 202.5 (H); 203.3 (M)}%
{LQHM}{Black}{SkyBlue}{upper}{up}
\funcgroup{222.8 (F); 225.8 (K)}{FK}{White}{RoyalPurple}{upper}{up}
\funcgroup{238.8 (Y)}{Y}{White}{RedViolet}{upper}{up}
\funcgroup{256.0 (R); 266.2 (W)}{RW}{White}{Black}{upper}{up}
\fi
\fi
\else
\xdef\second@{accessible area}
\ifx\temp@\second@
\ifgerm@n
\funcgroup{\ 13,9 (C); Zug\"angliche Seitenkettenfl\"ache %
(\AA$^2$)}%
{CIV}{Black}{BrickRed}{upper}{up}
\funcgroup{\ 23,0 (I); 23,5 (V); 25,2 (G)}%
{IVG}{Black}{Orange}{upper}{up}
\funcgroup{\ 28,7 (F); 29,0 (L); 30,5 (M); 31,5 (A)}%
{FLMA}{Black}{Yellow}{upper}{up}
\funcgroup{\ 41,7 (W); 44,2 (S); 46,0 (T); 46,7 (H)}%
{WSTH}{Black}{YellowGreen}{upper}{up}
\funcgroup{\ 53,7 (P)}{P}{White}{PineGreen}{upper}{up}
\funcgroup{\ 59,1 (Y); 60,9 (D); 62,2 (N)}%
{YDN}{Black}{SkyBlue}{upper}{up}
\funcgroup{\ 72,3 (E); 74,0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up}
\funcgroup{\ 93,8 (R)}{R}{White}{RedViolet}{upper}{up}
\funcgroup{110,3 (K)}{K}{White}{Black}{upper}{up}
\else
\ifsp@nish
\funcgroup{\ 13.9 (C); Superficie accesible de la cadena lateral (\AA$^2$)}%
{CIV}{Black}{BrickRed}{upper}{up}
\funcgroup{\ 23.0 (I); 23.5 (V); 25.2 (G)}%
{IVG}{Black}{Orange}{upper}{up}
\funcgroup{\ 28.7 (F); 29.0 (L); 30.5 (M); 31.5 (A)}%
{FLMA}{Black}{Yellow}{upper}{up}
\funcgroup{\ 41.7 (W); 44.2 (S); 46.0 (T); 46.7 (H)}%
{WSTH}{Black}{YellowGreen}{upper}{up}
\funcgroup{\ 53.7 (P)}{P}{White}{PineGreen}{upper}{up}
\funcgroup{\ 59.1 (Y); 60.9 (D); 62.2 (N)}%
{YDN}{Black}{SkyBlue}{upper}{up}
\funcgroup{\ 72.3 (E); 74.0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up}
\funcgroup{\ 93.8 (R)}{R}{White}{RedViolet}{upper}{up}
\funcgroup{110.3 (K)}{K}{White}{Black}{upper}{up}
\else
\funcgroup{\ 13.9 (C); Accessible sidechain area (\AA$^2$)}%
{CIV}{Black}{BrickRed}{upper}{up}
\funcgroup{\ 23.0 (I); 23.5 (V); 25.2 (G)}%
{IVG}{Black}{Orange}{upper}{up}
\funcgroup{\ 28.7 (F); 29.0 (L); 30.5 (M); 31.5 (A)}%
{FLMA}{Black}{Yellow}{upper}{up}
\funcgroup{\ 41.7 (W); 44.2 (S); 46.0 (T); 46.7 (H)}%
{WSTH}{Black}{YellowGreen}{upper}{up}
\funcgroup{\ 53.7 (P)}{P}{White}{PineGreen}{upper}{up}
\funcgroup{\ 59.1 (Y); 60.9 (D); 62.2 (N)}%
{YDN}{Black}{SkyBlue}{upper}{up}
\funcgroup{\ 72.3 (E); 74.0 (Q)}{EQ}{White}{RoyalPurple}{upper}{up}
\funcgroup{\ 93.8 (R)}{R}{White}{RedViolet}{upper}{up}
\funcgroup{110.3 (K)}{K}{White}{Black}{upper}{up}
\fi
\fi
\else
\xdef\second@{rasmol}
\ifx\temp@\second@
\funcgroup{Asp, Glu}{DE}{Red}{White}{upper}{up}
\funcgroup{Arg, Lys, His}{KRH}{Blue}{White}{upper}{up}
\funcgroup{Phe, Tyr, Trp}{FYW}{MidnightBlue}{White}{upper}{up}
\funcgroup{Ala, Gly}{AG}{Gray}{White}{upper}{up}
\funcgroup{Cys, Met}{CM}{Yellow}{White}{upper}{up}
\funcgroup{Ser, Thr}{ST}{Orange}{White}{upper}{up}
\funcgroup{Asn, Gln}{NQ}{Cyan}{White}{upper}{up}
\funcgroup{Leu, Val, Ile}{LVI}{Green}{White}{upper}{up}
\funcgroup{Pro}{P}{Apricot}{White}{upper}{up}
\else
\message{<Unknown shading mode - clearing `funcgroups'>}
\fi\fi\fi\fi\fi\fi\fi
}
\def\shadeallresidues{\all@fshadetrue}
\def\get@fromstack#1;#2;#3;#4;#5@{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\third@{#3} \xdef\fourth@{#4} \xdef\last@{#5@}
}
\def\getregion@fromstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@reg\temp@\endcsname}
\expandafter\get@fromstack\first@
\expandafter\xdef\csname style\temp@\endcsname{\first@}
\expandafter\xdef\csname start\temp@\endcsname{\second@}
\expandafter\xdef\csname stop\temp@\endcsname{\third@}
\expandafter\xdef\csname all\temp@\endcsname{\fourth@}
\expandafter\xdef\csname stack@reg\temp@\endcsname{\last@}
}
\def\sort@stack{%
\expandafter\get@fromstack\last@
\ifx\first@\ampers@nd
\xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;&;&;&;&;@}
\else
\ifnum\st@rt<\second@
\xdef\tmpstack{\tmpstack\the\loopcount;\st@rt;\st@p;\@ll;%
\first@;\second@;\third@;\fourth@;\last@}
\else
\xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;}
\sort@stack
\fi\fi
}
\def\get@regions#1..#2,#3@{%
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
\xdef\last@{\csname stack@reg\seq@\endcsname}
\xdef\tmpstack{}
\sort@stack
\expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack}
}
\def\get@fromemphstack#1;#2;#3;#4@{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\third@{#3} \xdef\last@{#4@}
}
\def\getregion@fromemphstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@emphreg\temp@\endcsname}
\expandafter\get@fromemphstack\first@
\expandafter\xdef\csname emphstart\temp@\endcsname{\first@}
\expandafter\xdef\csname emphstop\temp@\endcsname{\second@}
\expandafter\xdef\csname emphall\temp@\endcsname{\third@}
\expandafter\xdef\csname stack@emphreg\temp@\endcsname{\last@}
}
\def\sort@emphstack{%
\expandafter\get@fromemphstack\last@
\ifx\first@\ampers@nd
\xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@}
\else
\ifnum\st@rt<\second@
\xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@}
\else
\xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@emphstack
\fi\fi
}
\def\get@emphregions#1..#2,#3@{%
\regionalemphtrue
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
\xdef\last@{\csname stack@emphreg\seq@\endcsname}
\xdef\tmpstack{}
\sort@emphstack
\expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
}
\def\getregion@fromlowerstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@lowerreg\temp@\endcsname}
\expandafter\get@fromemphstack\first@
\expandafter\xdef\csname lowerstart\temp@\endcsname{\first@}
\expandafter\xdef\csname lowerstop\temp@\endcsname{\second@}
\expandafter\xdef\csname lowerall\temp@\endcsname{\third@}
\expandafter\xdef\csname stack@lowerreg\temp@\endcsname{\last@}
}
\def\sort@lowerstack{%
\expandafter\get@fromemphstack\last@
\ifx\first@\ampers@nd
\xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;&;&;&;@}
\else
\ifnum\st@rt<\second@
\xdef\tmpstack{\tmpstack\st@rt;\st@p;\@ll;\first@;\second@;\third@;\last@}
\else
\xdef\tmpstack{\tmpstack\first@;\second@;\third@;} \sort@lowerstack
\fi\fi
}
\def\get@lowerregions#1..#2,#3@{%
\regionallowertrue
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
\xdef\last@{\csname stack@lowerreg\seq@\endcsname}
\xdef\tmpstack{}
\sort@lowerstack
\expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack}
}
\def\get@fromdomstack#1;#2;#3@{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\last@{#3@}
}
\def\sort@domstack{%
\expandafter\get@fromdomstack\last@
\ifx\first@\ampers@nd
\xdef\tmpstack{\tmpstack\st@rt;\st@p;&;&;@}
\else
\ifnum\st@rt<\second@
\xdef\tmpstack{\tmpstack\st@rt;\st@p;\first@;\second@;\last@}
\else
\xdef\tmpstack{\tmpstack\first@;\second@;} \sort@domstack
\fi\fi
}
\def\get@domainregions#1..#2,#3@{%
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
\xdef\last@{\stack@dom}
\xdef\tmpstack{}
\sort@domstack
\xdef\stack@dom{\tmpstack}
}
\def\get@domain{%
\expandafter\get@fromdomstack\last@
\ifx\first@\ampers@nd
\else
\loopcount=\first@
\loop
\xdef\domain@num@list{\domain@num@list \the\loopcount,}
\advance\loopcount by 1
\ifnum\loopcount>\second@\else\repeat
\get@domain
\fi
}
\def\getregion@fromtintstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@tintreg\temp@\endcsname}
\expandafter\get@fromemphstack\first@
\expandafter\xdef\csname tintstart\temp@\endcsname{\first@}
\expandafter\xdef\csname tintstop\temp@\endcsname{\second@}
\expandafter\xdef\csname tintall\temp@\endcsname{\third@}
\expandafter\xdef\csname stack@tintreg\temp@\endcsname{\last@}
}
\def\get@tintregions#1..#2,#3@{%
\regionaltinttrue
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
\xdef\last@{\csname stack@tintreg\seq@\endcsname}
\xdef\tmpstack{}
\sort@emphstack
\expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack}
}
\def\getregion@fromframestack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@framereg\temp@\endcsname}
\expandafter\get@fromemphstack\first@
\expandafter\xdef\csname framestart\temp@\endcsname{\first@}
\expandafter\xdef\csname framestop\temp@\endcsname{\second@}
\expandafter\xdef\csname framestyle\temp@\endcsname{\third@}
\expandafter\xdef\csname stack@framereg\temp@\endcsname{\last@}
}
\def\get@frameregions#1..#2,#3@{%
\frame@true
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
\xdef\last@{\csname stack@framereg\seq@\endcsname}
\xdef\tmpstack{}
\sort@emphstack
\expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
}
\def\getregion@fromshadingstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@shadingreg\temp@\endcsname}
\expandafter\get@fromemphstack\first@
\expandafter\xdef\csname shadingstart\temp@\endcsname{\first@}
\expandafter\xdef\csname shadingstop\temp@\endcsname{\second@}
\expandafter\xdef\csname shadingstyle\temp@\endcsname{\third@}
\expandafter\xdef\csname stack@shadingreg\temp@\endcsname{\last@}
}
\def\get@shadingregions#1..#2,#3@{%
\shading@true
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
\xdef\last@{\csname stack@shadingreg\seq@\endcsname}
\xdef\tmpstack{}
\sort@emphstack
\expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack}
}
\def\getregion@fromfstack#1{%
\xdef\temp@{#1}
\xdef\first@{\csname stack@\bottop@\temp@\endcsname}
\expandafter\get@fromstack\first@
\expandafter\xdef\csname text\bottop@\temp@\endcsname{\first@}
\expandafter\xdef\csname start\bottop@\temp@\endcsname{\second@}
\expandafter\xdef\csname stop\bottop@\temp@\endcsname{\third@}
\ifx\fourth@\ampers@nd \xdef\fourth@{///} \fi
\expandafter\xdef\csname style\bottop@\temp@\endcsname{\fourth@}
\expandafter\xdef\csname stack@\bottop@\temp@\endcsname{\last@}
}
\def\sort@fstack{%
\expandafter\get@fromstack\last@
\ifx\first@\ampers@nd
\xdef\tmpstack{\tmpstack\f@text@;\st@rt;\st@p;\style@;&;&;&;&;@}
\else
\ifnum\st@rt<\second@
\xdef\tmpstack{\tmpstack\f@text@;\st@rt;\st@p;\style@;%
\first@;\second@;\third@;\fourth@;\last@}
\else
\xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;}
\sort@fstack
\fi\fi
}
\def\get@fregions#1..#2,#3@{%
\xdef\st@rt{#1}
\ifx\temp@\y@
\xdef\st@p{#1}
\else
\xdef\st@p{#2}
\fi
\xdef\list@{#3}
\xdef\last@{\csname stack@\bottop@\seq@\endcsname}
\xdef\tmpstack{}
\sort@fstack
\expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
}
\def\getarrow@shape#1#2#3#4&{%
\xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}
\if\first@@ v
\if\second@@ =
\else \xdef\style@{\first@@ v\third@@#4} \fi
\else
\if\first@@ v
\if\second@@ =
\else \xdef\style@{\first@@ v\third@@#4} \fi
\else
\if\third@@ v
\if\second@@ =
\else \xdef\style@{\first@@ v\third@@#4} \fi
\else
\if\third@@ v
\if\second@@ =
\else \xdef\style@{\first@@ v\third@@#4} \fi
\fi\fi\fi\fi
}
\def\get@shape#1#2#3{%
\xdef\first@@{#1}\xdef\second@@{#2}\xdef\third@@{#3}%
\if\second@@ v \xdef\second@@{arrow}%
\fi%
\if\second@@ = \xdef\second@@{doublearrow}%
\fi%
}
\def\getstyle@left#1#2#3#4@{%
\ifstop@
\xdef\style@@{\csname fstyle\bottop@\the\loopcount\endcsname}
\else
\xdef\style@@{#2}
\xdef\temp@{-}
\ifx\style@@\temp@ \xdef\style@@{#1#2-#4}
\else
\xdef\temp@{v}
\ifx\style@@\temp@ \xdef\style@@{#1#2-#4}
\else
\xdef\temp@{=}
\ifx\style@@\temp@ \xdef\style@@{#1#2=#4}
\else
\xdef\style@@{\csname fstyle\bottop@\the\loopcount\endcsname}
\fi\fi\fi\fi
}
\def\getstyle@right#1#2#3#4@{%
\xdef\style@@{#2}
\xdef\temp@{-}
\ifx\style@@\temp@
\expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{-#2#3#4}
\fi
\xdef\temp@{v}
\ifx\style@@\temp@
\expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{-#2#3#4}
\fi
\xdef\temp@{=}
\ifx\style@@\temp@
\expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{=#2#3#4}
\fi
}
\def\opt@color#1[#2]#3&{\xdef\fourth@{#1}\xdef\f@color{#2}}
\def\graph@opt@color#1[#2]:#3[#4][#5]#6&{%
\xdef\fourth@{#1}
\xdef\f@color{#2}
\xdef\ffourth@{#3}
\xdef\ff@color{#4}
\xdef\fffourth@{#5}}
\def\arrow@col@width#1[#2][#3]#4&{\xdef\fourth@{#1}\xdef\f@color{#2}\xdef\rule@@thick{#3}}
\def\second@color#1,&{\xdef\back@color{#1}}
\def\two@opt@color#1,#2@{%
\xdef\sixth@{#1}%
\xdef\seventh@{#2}%
\ifx\first@\ampers@nd%
\else%
\xdef\frame@color{#1}%
\ifx\seventh@\ampers@nd%
\xdef\back@color{#1}%
\xdef\backtext@color{White}%
\else%
\expandafter\second@color\seventh@%
\fi%
\fi%
}
\def\test@get#1#2@{%
\xdef\temp@{#1} \xdef\third@@{#2@}
\ifx\temp@\ampers@nd
\else
\if \temp@ X
\xdef\temp@{\second@@}
\fi
\ifx\temp@\second@@
\xdef\third@@{\second@@}
\else
\expandafter\test@get\third@@
\fi
\fi
}
\def\get@@second@#1#2@{\xdef\second@@{#1}\xdef\first@@{#2@}}
\def\get@@third@#1]#2@{\xdef\third@@{#1&@}\xdef\fifth@@{#2@}}
\def\get@third@#1#2@{\xdef\third@@{#1}\xdef\fifth@@{#2@}}
\def\find@motif{%
\expandafter\get@@second@\first@@
\ifx\second@@\ampers@nd
\else
\ifx\second@@\d@t
\else
\advance\temp@count by 1
\if \third@@ X
\xdef\third@@{\second@@}
\fi
\ifx\third@@\br@cket
\expandafter\get@@third@\fifth@@
\expandafter\test@get\third@@
\fi
\ifx\second@@\third@@
\ifx\nineth@@\n@
\xdef\st@rt{\the\temp@count}
\xdef\st@p{n}
\fi
\xdef\nineth@@{y}
\expandafter\get@third@\fifth@@
\ifx\third@@\ampers@nd
\xdef\st@p{\the\temp@count}
\xdef\list@{}
\xdef\tmpstack{}
\xdef\temp@{shade}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@reg\seq@\endcsname}
\loopcount=\style@
\sort@stack
\expandafter\xdef\csname stack@reg\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{emph}
\ifx\temp@\temp@@
\regionalemphtrue
\xdef\last@{\csname stack@emphreg\seq@\endcsname}
\sort@emphstack
\expandafter\xdef\csname stack@emphreg\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{lower}
\ifx\temp@\temp@@
\regionallowertrue
\xdef\last@{\csname stack@lowerreg\seq@\endcsname}
\sort@lowerstack
\expandafter\xdef\csname stack@lowerreg\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{tint}
\ifx\temp@\temp@@
\regionaltinttrue
\xdef\last@{\csname stack@tintreg\seq@\endcsname}
\sort@emphstack
\expandafter\xdef\csname stack@tintreg\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{frame}
\ifx\temp@\temp@@
\frame@true
\xdef\last@{\csname stack@framereg\seq@\endcsname}
\sort@emphstack
\expandafter\xdef\csname stack@framereg\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{shading}
\ifx\temp@\temp@@
\shading@true
\xdef\last@{\csname stack@shadingreg\seq@\endcsname}
\sort@emphstack
\expandafter\xdef\csname stack@shadingreg\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{ttttop}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@ttttop\seq@\endcsname}
\sort@fstack
\expandafter\xdef\csname stack@ttttop\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{tttop}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@tttop\seq@\endcsname}
\sort@fstack
\expandafter\xdef\csname stack@tttop\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{ttop}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@ttop\seq@\endcsname}
\sort@fstack
\expandafter\xdef\csname stack@ttop\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{top}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@top\seq@\endcsname}
\sort@fstack
\expandafter\xdef\csname stack@top\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{bottom}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@bottom\seq@\endcsname}
\sort@fstack
\expandafter\xdef\csname stack@bottom\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{bbottom}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@bbottom\seq@\endcsname}
\sort@fstack
\expandafter\xdef\csname stack@bbottom\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{bbbottom}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@bbbottom\seq@\endcsname}
\sort@fstack
\expandafter\xdef\csname stack@bbbottom\seq@\endcsname{\tmpstack}
\else
\xdef\temp@{bbbbottom}
\ifx\temp@\temp@@
\xdef\last@{\csname stack@bbbbottom\seq@\endcsname}
\sort@fstack
\expandafter\xdef\csname stack@bbbbottom\seq@\endcsname{\tmpstack}
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
\xdef\nineth@@{n}
\fi
\else
\ifx\nineth@@\y@
\xdef\first@@{\second@@\first@@}
\advance\temp@count by -1
\fi
\xdef\nineth@@{n} \xdef\st@p{n}
\xdef\fifth@@{\m@tif} \expandafter\get@third@\fifth@@
\fi
\fi
\find@motif
\fi
}
\def\prep@motif{%
\def\get@motif@specs##1,##2,##3,##4,##5,&{%
\xdef\seq@{##1} \xdef\temp@@{##2} \xdef\@ll{##3} \def\fourth@@{##4} \xdef\fifth@@{##5&@}
}
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{\csname style\the\loopcount\endcsname;%
\csname start\the\loopcount\endcsname;%
\csname stop\the\loopcount\endcsname;%
\csname all\the\loopcount\endcsname;%
\csname stack@reg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{\csname emphstart\the\loopcount\endcsname;%
\csname emphstop\the\loopcount\endcsname;%
\csname emphall\the\loopcount\endcsname;%
\csname stack@emphreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{\csname lowerstart\the\loopcount\endcsname;%
\csname lowerstop\the\loopcount\endcsname;%
\csname lowerall\the\loopcount\endcsname;%
\csname stack@lowerreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{\csname tintstart\the\loopcount\endcsname;%
\csname tintstop\the\loopcount\endcsname;%
\csname tintall\the\loopcount\endcsname;%
\csname stack@tintreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{\csname framestart\the\loopcount\endcsname;%
\csname framestop\the\loopcount\endcsname;%
\csname framestyle\the\loopcount\endcsname;%
\csname stack@framereg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{\csname shadingstart\the\loopcount\endcsname;%
\csname shadingstop\the\loopcount\endcsname;%
\csname shadingstyle\the\loopcount\endcsname;%
\csname stack@shadingreg\the\loopcount\endcsname}
\expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{\csname textttttop\the\loopcount\endcsname;%
\csname startttttop\the\loopcount\endcsname;%
\csname stopttttop\the\loopcount\endcsname;%
\csname stylettttop\the\loopcount\endcsname;%
\csname stack@ttttop\the\loopcount\endcsname}
\expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{\csname texttttop\the\loopcount\endcsname;%
\csname starttttop\the\loopcount\endcsname;%
\csname stoptttop\the\loopcount\endcsname;%
\csname styletttop\the\loopcount\endcsname;%
\csname stack@tttop\the\loopcount\endcsname}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{\csname textttop\the\loopcount\endcsname;%
\csname startttop\the\loopcount\endcsname;%
\csname stopttop\the\loopcount\endcsname;%
\csname stylettop\the\loopcount\endcsname;%
\csname stack@ttop\the\loopcount\endcsname}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{\csname texttop\the\loopcount\endcsname;%
\csname starttop\the\loopcount\endcsname;%
\csname stoptop\the\loopcount\endcsname;%
\csname styletop\the\loopcount\endcsname;%
\csname stack@top\the\loopcount\endcsname}
\expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{\csname textbottom\the\loopcount\endcsname;%
\csname startbottom\the\loopcount\endcsname;%
\csname stopbottom\the\loopcount\endcsname;%
\csname stylebottom\the\loopcount\endcsname;%
\csname stack@bottom\the\loopcount\endcsname}
\expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{\csname textbbottom\the\loopcount\endcsname;%
\csname startbbottom\the\loopcount\endcsname;%
\csname stopbbottom\the\loopcount\endcsname;%
\csname stylebbottom\the\loopcount\endcsname;%
\csname stack@bbottom\the\loopcount\endcsname}
\expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{\csname textbbbottom\the\loopcount\endcsname;%
\csname startbbbottom\the\loopcount\endcsname;%
\csname stopbbbottom\the\loopcount\endcsname;%
\csname stylebbbottom\the\loopcount\endcsname;%
\csname stack@bbbottom\the\loopcount\endcsname}
\expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{\csname textbbbbottom\the\loopcount\endcsname;%
\csname startbbbbottom\the\loopcount\endcsname;%
\csname stopbbbbottom\the\loopcount\endcsname;%
\csname stylebbbbottom\the\loopcount\endcsname;%
\csname stack@bbbbottom\the\loopcount\endcsname}
\ifnum\loopcount<\seq@num\repeat
\temp@@count=0
\loop
\advance\temp@@count by 1
\xdef\first@@{\csname motif\the\temp@@count\endcsname}
\expandafter\get@motif@specs\first@@
\xdef\first@@{\csname sequence\seq@\endcsname &@}
\temp@count=\csname res@count\seq@\endcsname
\xdef\f@text@{\@ll}
\xdef\style@{\fourth@@}
\xdef\m@tif{\fifth@@} \expandafter\get@third@\fifth@@
\xdef\nineth@@{n} \xdef\st@p{n}
\find@motif
\ifnum\temp@@count<\motif@num\repeat
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\getregion@fromstack{\the\loopcount}
\expandafter\getregion@fromtintstack{\the\loopcount}
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
\expandafter\getregion@fromshadingstack{\the\loopcount}
\xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
\ifnum\loopcount<\seq@num\repeat
}
\def\test@motif#1#2@{%
\xdef\temp@{shade}
\ifx\temp@\temp@@ \xdef\style@{\the\loopcount} \fi
\xdef\temp@{emph}
\ifx\temp@\temp@@ \xdef\style@{0} \fi
\xdef\temp@{lower}
\ifx\temp@\temp@@ \xdef\style@{0} \fi
\xdef\temp@{tint}
\ifx\temp@\temp@@ \xdef\style@{0} \fi
\xdef\temp@{frame}
\ifx\temp@\temp@@ \xdef\style@{0} \fi
\xdef\temp@{shading}
\ifx\temp@\temp@@ \xdef\style@{0} \fi
\xdef\temp@{#1#2}
\xdef\first@{#1}
\ifx\first@\br@cket
\xdef\label@motif{y}
\temp@count=\motif@num
\advance\temp@count by 1
\xdef\motif@num{\the\temp@count}
\expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@}
\xdef\list@{&}
\else
\expandafter\check@char\first@
\ifletter
\xdef\label@motif{y}
\temp@count=\motif@num
\advance\temp@count by 1
\xdef\motif@num{\the\temp@count}
\expandafter\xdef\csname motif\the\temp@count\endcsname{\seq@,\temp@@,\@ll,\style@,\temp@}
\xdef\list@{&}
\fi
\fi
}
\def\test@PDB#1:#2,#3,#4,#5,#6@{%
\xdef\last@{#1[,]&}\expandafter\opt@color\last@
\xdef\PDB@distance{no}
\ifx\f@color\comm@
\else
\xdef\f@color{\f@color .&&@}
\expandafter\coord@get\f@color
\xdef\temp@{\c@@rd @}
\expandafter\check@letter\temp@
\ifletter
\else
\temp@count=\c@@rd
\multiply\temp@count by \temp@count
\xdef\PDB@distance{\the\temp@count}
\fi
\fi
\xdef\PDB@hitpos{0}
\xdef\PDB@stack{}
\xdef\PDB@name{#2}
\xdef\PDB@type{point}
\ifx\fourth@\PDB@type
\xdef\PDB@{y}
\xdef\last@{#3[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum@a{\fourth@}
\ifx\f@color\C@lpha
\xdef\PDB@back@side@a{CA}
\else
\xdef\PDB@back@side@a{side}
\fi
\xdef\PDB@refnum@b{0} \xdef\PDB@back@side@b{x}
\xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
\ifx\PDB@distance\n@ \xdef\PDB@distance{3600}\fi
\load@PDB
\expandafter\get@item\PDB@stack \xdef\list@{\first@@}
\else
\xdef\PDB@type{line}
\ifx\fourth@\PDB@type
\xdef\PDB@{y}
\xdef\last@{#3[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum{\fourth@}
\ifx\f@color\C@lpha
\xdef\PDB@back@side{CA}
\else
\xdef\PDB@back@side{side}
\fi
\xdef\last@{#4[,]&}\expandafter\opt@color\last@
\ifnum\PDB@refnum<\fourth@
\xdef\PDB@refnum@a{\PDB@refnum}
\xdef\PDB@refnum@b{\fourth@}
\xdef\PDB@back@side@a{\PDB@back@side}
\ifx\f@color\C@lpha
\xdef\PDB@back@side@b{CA}
\else
\xdef\PDB@back@side@b{side}
\fi
\else
\xdef\PDB@refnum@b{\PDB@refnum}
\xdef\PDB@refnum@a{\fourth@}
\xdef\PDB@back@side@b{\PDB@back@side}
\ifx\f@color\C@lpha
\xdef\PDB@back@side@a{CA}
\else
\xdef\PDB@back@side@a{side}
\fi
\fi
\xdef\PDB@refnum@c{0} \xdef\PDB@back@side@c{x}
\ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
\load@PDB
\expandafter\get@item\PDB@stack \xdef\list@{\first@@}
\else
\xdef\PDB@type{plane}
\ifx\fourth@\PDB@type
\xdef\PDB@{y}
\xdef\last@{#3[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum{\fourth@}
\ifx\f@color\C@lpha
\xdef\PDB@back@side{CA}
\else
\xdef\PDB@back@side{side}
\fi
\xdef\last@{#4[,]&}\expandafter\opt@color\last@
\ifnum\PDB@refnum<\fourth@
\xdef\PDB@refnum@a{\PDB@refnum}
\xdef\PDB@refnum@b{\fourth@}
\xdef\PDB@back@side@a{\PDB@back@side}
\ifx\f@color\C@lpha
\xdef\PDB@back@side@b{CA}
\else
\xdef\PDB@back@side@b{side}
\fi
\else
\xdef\PDB@refnum@b{\PDB@refnum}
\xdef\PDB@refnum@a{\fourth@}
\xdef\PDB@back@side@b{\PDB@back@side}
\ifx\f@color\C@lpha
\xdef\PDB@back@side@a{CA}
\else
\xdef\PDB@back@side@a{side}
\fi
\fi
\xdef\last@{#5[,]&}\expandafter\opt@color\last@
\xdef\PDB@refnum{\fourth@}
\ifx\f@color\C@lpha
\xdef\PDB@back@side{CA}
\else
\xdef\PDB@back@side{side}
\fi
\ifnum\PDB@refnum>\PDB@refnum@b
\xdef\PDB@refnum@c{\PDB@refnum}
\xdef\PDB@back@side@c{\PDB@back@side}
\else
\ifnum\PDB@refnum>\PDB@refnum@a
\xdef\PDB@refnum@c{\PDB@refnum@b}
\xdef\PDB@back@side@c{\PDB@back@side@b}
\xdef\PDB@refnum@b{\PDB@refnum}
\xdef\PDB@back@side@b{\PDB@back@side}
\else
\xdef\PDB@refnum@c{\PDB@refnum@b}
\xdef\PDB@back@side@c{\PDB@back@side@b}
\xdef\PDB@refnum@b{\PDB@refnum@a}
\xdef\PDB@back@side@b{\PDB@back@side@a}
\xdef\PDB@refnum@a{\PDB@refnum}
\xdef\PDB@back@side@a{\PDB@back@side}
\fi
\fi
\ifx\PDB@distance\n@ \xdef\PDB@distance{100}\fi
\load@PDB
\expandafter\get@item\PDB@stack \xdef\list@{\first@@}
\else
\xdef\temp@{\list@ @}
\expandafter\test@motif\temp@
\fi
\fi
\fi
}
\def\test@fill#1:#2:#3&{%
\xdef\last@{#1[,][,]&}\expandafter\arrow@col@width\last@%
\xdef\second@@{\fourth@}%
\xdef\last@{///}%
\ifx\fourth@\last@%
\xdef\second@@{empty}%
\else
\xdef\last@{translate}%
\ifx\fourth@\last@%
\xdef\second@@{translate}%
\xdef\fill@char{#2[,]&}%
\expandafter\opt@color\fill@char%
\xdef\fill@char{\fourth@}%
\else
\xdef\last@{fill}%
\ifx\fourth@\last@
\xdef\second@@{fill}%
\xdef\fill@char{#2[,]&}%
\expandafter\opt@color\fill@char%
\xdef\fill@char{\fourth@}%
\else
\xdef\last@{bar}%
\ifx\fourth@\last@
\xdef\second@@{bar}%
\xdef\b@r{bar}%
\ifx\f@color\comm@
\xdef\g@min{,}\xdef\g@max{,}%
\else
\xdef\f@color{\f@color @}%
\expandafter\get@item\f@color%
\xdef\g@min{\fourth@} \xdef\g@max{\first@@}%
\xdef\pm@shift{\fourth@}%
\fi%
\xdef\fill@char{#2[,]&}%
\expandafter\opt@color\fill@char%
\ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi%
\xdef\fill@char{\fourth@}%
\xdef\box@color{\f@color,&@}%
\expandafter\two@opt@color\box@color%
\else
\xdef\last@{color}%
\ifx\fourth@\last@
\xdef\second@@{color}%
\ifx\f@color\comm@
\xdef\g@min{,}\xdef\g@max{,}%
\else
\xdef\f@color{\f@color @}%
\expandafter\get@item\f@color%
\xdef\g@min{\fourth@} \xdef\g@max{\first@@}%
\fi%
\xdef\fill@char{#2[,]&}%
\expandafter\opt@color\fill@char%
\ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi%
\xdef\fill@char{\fourth@}%
\else
\xdef\last@{box}%
\ifx\fourth@\last@%
\xdef\second@@{box}%
\ifx\f@color\comm@\xdef\f@color{White}\fi%
\xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@%
\ifnumber%
\ifx\rule@@thick\comm@%
\xdef\rule@@thick{\f@color}%
\xdef\box@color{White,&@}%
\else%
\xdef\seventh@{\rule@@thick}%
\xdef\rule@@thick{\f@color}%
\xdef\box@color{\seventh@,&@}%
\fi%
\else%
\xdef\box@color{\f@color,&@}%
\fi%
\expandafter\two@opt@color\box@color%
\xdef\fill@char{#2[,]&}%
\expandafter\opt@color\fill@char%
\xdef\fill@char{\fourth@}%
\else
\xdef\last@{plotcolor}%
\ifx\fourth@\last@%
\xdef\second@@{plotcolor}%
\ifx\f@color\comm@%
\xdef\pm@shift{0}%
\else%
\xdef\pm@shift{\f@color}%
\fi%
\xdef\fill@char{#2[,]&}%
\expandafter\opt@color\fill@char%
\xdef\fill@char{\fourth@}%
\else
\xdef\last@{plotbar}%
\ifx\fourth@\last@%
\xdef\second@@{plotbar}%
\xdef\b@r{bar}%
\ifx\f@color\comm@
\xdef\pm@shift{0}%
\else
\xdef\pm@shift{\f@color}%
\fi%
\xdef\fill@char{#2[,]&}%
\expandafter\opt@color\fill@char%
\ifx\f@color\comm@\xdef\f@color{GrayDefault}\fi%
\xdef\fill@char{\fourth@}%
\xdef\box@color{\f@color,&@}%
\expandafter\two@opt@color\box@color%
\else
\xdef\arrow@color{\f@color}%
\ifx\arrow@color\comm@\xdef\arrow@color{Black}\fi%
\xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@%
\ifnumber%
\ifx\rule@@thick\comm@%
\xdef\rule@@thick{\f@color}%
\xdef\arrow@color{Black}%
\else%
\xdef\seventh@{\rule@@thick}%
\xdef\rule@@thick{\f@color}%
\xdef\arrow@color{\seventh@}%
\fi%
\fi%
\xdef\fill@char{#2[,]&}%
\expandafter\opt@color\fill@char%
\xdef\fill@char{\fourth@}%
\ifx\f@color\comm@\xdef\f@color{Black,White}\fi%
\xdef\backtext@color{White}%
\xdef\f@color{\f@color,&@}%
\expandafter\two@opt@color\f@color%
\xdef\f@color{\arrow@color}%
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\xdef\seventh@{\f@color @}\expandafter\check@letter\seventh@%
\ifnumber%
\ifx\rule@@thick\comm@%
\xdef\rule@@thick{\f@color}%
\xdef\f@color{Black}%
\else%
\xdef\seventh@{\rule@@thick}%
\xdef\rule@@thick{\f@color}%
\xdef\f@color{\seventh@}%
\fi%
\fi%
\ifx\rule@@thick\comm@\xdef\rule@@thick{\the\rule@thick}\fi%
\ifx\f@color\comm@\xdef\f@color{Black}\fi}
\def\clear@groups{%
\expandafter\xdef\csname \prfx grpA\endcsname{ -1}
\expandafter\xdef\csname \prfx grpB\endcsname{ -2}
\expandafter\xdef\csname \prfx grpC\endcsname{ -3}
\expandafter\xdef\csname \prfx grpD\endcsname{ -4}
\expandafter\xdef\csname \prfx grpE\endcsname{ -5}
\expandafter\xdef\csname \prfx grpF\endcsname{ -6}
\expandafter\xdef\csname \prfx grpG\endcsname{ -7}
\expandafter\xdef\csname \prfx grpH\endcsname{ -8}
\expandafter\xdef\csname \prfx grpI\endcsname{ -9}
\expandafter\xdef\csname \prfx grpJ\endcsname{-10}
\expandafter\xdef\csname \prfx grpK\endcsname{-11}
\expandafter\xdef\csname \prfx grpL\endcsname{-12}
\expandafter\xdef\csname \prfx grpM\endcsname{-13}
\expandafter\xdef\csname \prfx grpN\endcsname{-14}
\expandafter\xdef\csname \prfx grpO\endcsname{-15}
\expandafter\xdef\csname \prfx grpP\endcsname{-16}
\expandafter\xdef\csname \prfx grpQ\endcsname{-17}
\expandafter\xdef\csname \prfx grpR\endcsname{-18}
\expandafter\xdef\csname \prfx grpS\endcsname{-19}
\expandafter\xdef\csname \prfx grpT\endcsname{-20}
\expandafter\xdef\csname \prfx grpU\endcsname{-21}
\expandafter\xdef\csname \prfx grpV\endcsname{-22}
\expandafter\xdef\csname \prfx grpW\endcsname{-23}
\expandafter\xdef\csname \prfx grpX\endcsname{-24}
\expandafter\xdef\csname \prfx grpY\endcsname{-25}
\expandafter\xdef\csname \prfx grpZ\endcsname{-26}
\expandafter\xdef\csname \prfx grp-\endcsname{-999}
\expandafter\xdef\csname \prfx grp.\endcsname{-999}
\expandafter\xdef\csname \prfx grp=\endcsname{-999}
}
\def\inactivate@chars{%
\catcode`\#=12
\catcode`\"=12
\catcode`\~=12
\catcode`\^=12
\catcode`\_=12
}
\def\numcount{\the\loopcount}
\def\Alphacount{\@Alph\loopcount}
\def\alphacount{\@alph\loopcount}
\def\romancount{\@roman\loopcount}
\def\Romancount{\@Roman\loopcount}
\def\cut@name#1.#2@{\global\xdef\file@n@me{#1}}
\def\coord@get#1.#2#3@{%
\xdef\temp@{#2}
\ifx\temp@\ampers@nd \xdef\temp@{0} \fi
\xdef\c@@rd{#1\temp@}
}
\def\struc@get#1 #2 #3 #4 #5 #6 #7 #8 #9@{%
\xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3} \xdef\fourth@{#4}
\xdef\fifth@{#5} \xdef\sixth@{#6} \xdef\seventh@{#7}\xdef\eighth@{#8}
\xdef\nineth@{#9}}
\def\get@PHD#1|#2|#3@{\xdef\PHD@line{\PHD@line #2}}
\def\write@PHDsec{%
\expandafter\get@sim\last@
\ifx\sim@char\c@mp
\def\end@{\the\innerloopcount}
\advance\innerloopcount by 1
\else
\ifnum\end@<\begin@ \xdef\end@{\begin@}\fi
\if\c@mp .
\else
\if\c@mp L
\else
\if\c@mp H
\ifx\show@Hsec\yes
\loopcount=\first@
\advance\loopcount by 1
\xdef\first@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Hsec}{\begin@..\end@}%
{\label@Hsec}{\text@Hsec}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Hsec}{\st@rt}{\begin@..\end@}%
{\label@Hsec}{\text@Hsec}}\fi
\fi
\else
\if\c@mp E
\ifx\show@Esec\yes
\loopcount=\second@
\advance\loopcount by 1
\xdef\second@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Esec}{\begin@..\end@}%
{\label@Esec}{\text@Esec}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Esec}{\st@rt}{\begin@..\end@}%
{\label@Esec}{\text@Esec}}\fi
\fi
\fi\fi\fi\fi
\xdef\c@mp{\sim@char}
\advance\innerloopcount by 1
\xdef\begin@{\the\innerloopcount}
\fi
\ifx\sim@char\ampers@nd\else\write@PHDsec\fi
}
\def\write@PHDtopo{%
\expandafter\get@sim\last@
\ifx\sim@char\c@mp
\def\end@{\the\innerloopcount}
\advance\innerloopcount by 1
\else
\ifnum\end@<\begin@ \xdef\end@{\begin@}\fi
\if\c@mp .
\else
\if\c@mp L
\else
\if\c@mp T
\ifx\show@TMtop\yes
\loopcount=\first@
\advance\loopcount by 1
\xdef\first@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@TMtop}{\begin@..\end@}%
{\label@TMtop}{\text@TMtop}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@TMtop}{\st@rt}{\begin@..\end@}%
{\label@TMtop}{\text@TMtop}}\fi
\fi
\else
\if\c@mp i
\ifx\show@itop\yes
\loopcount=\second@
\advance\loopcount by 1
\xdef\second@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@itop}{\begin@..\end@}%
{\label@itop}{\text@itop}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@itop}{\st@rt}{\begin@..\end@}%
{\label@itop}{\text@itop}}\fi
\fi
\else
\if\c@mp o
\ifx\show@etop\yes
\loopcount=\second@
\advance\loopcount by 1
\xdef\second@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@etop}{\begin@..\end@}%
{\label@etop}{\text@etop}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@etop}{\st@rt}{\begin@..\end@}%
{\label@etop}{\text@etop}}\fi
\fi
\fi\fi\fi\fi\fi
\xdef\c@mp{\sim@char}
\advance\innerloopcount by 1
\xdef\begin@{\the\innerloopcount}
\fi
\ifx\sim@char\ampers@nd\else\write@PHDtopo\fi
}
\def\include@T@coffee{%
\bgroup
\immediate\openin\structurefile = \TC@first@\relax
\ifeof\structurefile
\PackageError{TeXshade}
{File `\TC@first@' not found}
{\MessageBreak
The file you specified is missing or you have \MessageBreak
misspelled it. \MessageBreak\MessageBreak
No T-Coffee shading will be displayed (using "similar"). \MessageBreak
Type <return> to proceed. \MessageBreak
Type X <return> to quit. \MessageBreak
}
\immediate\closein\structurefile\egroup
\simmodetrue \funcmodefalse \T@coffeefalse
\else
\message{<T-Coffee shading>}
\xdef\first@{} \xdef\temp@{*}
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\ifx\first@\temp@ \xdef\temp@{y}
\read\structurefile to \readline
\read\structurefile to \readline
\fi
\fi
\ifx\temp@\y@ \else\repeat
\loopcount=0
\xdef\temp@{cons}
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\if\second@ :
\advance\loopcount by 1\relax
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
\fi
\fi
\ifx\first@\temp@\expandafter\xdef\csname T@coffee0\endcsname{} \else\repeat
\xdef\temp@{\the\loopcount}
\loopcount=0
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\advance\loopcount by 1
\ifnum\loopcount=\temp@ \loopcount=0 \fi
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname \third@}
\fi
\ifeof\structurefile \else\repeat
\closein\structurefile
\loopcount=0
\loop
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
\advance\loopcount by 1
\ifnum\loopcount=\temp@ \else\repeat
\egroup
\def\n@m@tch{{$\bullet$}}
\expandafter\def\csname fg@color0\endcsname{TC0}
\expandafter\def\csname fg@color1\endcsname{TC1}
\expandafter\def\csname fg@color2\endcsname{TC2}
\expandafter\def\csname fg@color3\endcsname{TC3}
\expandafter\def\csname fg@color4\endcsname{TC4}
\expandafter\def\csname fg@color5\endcsname{TC5}
\expandafter\def\csname fg@color6\endcsname{TC6}
\expandafter\def\csname fg@color7\endcsname{TC7}
\expandafter\def\csname fg@color8\endcsname{TC8}
\expandafter\def\csname fg@color9\endcsname{TC9}
\expandafter\def\csname fg@textcolor0\endcsname{Black}
\expandafter\def\csname fg@textcolor1\endcsname{Black}
\expandafter\def\csname fg@textcolor2\endcsname{Black}
\expandafter\def\csname fg@textcolor3\endcsname{Black}
\expandafter\def\csname fg@textcolor4\endcsname{Black}
\expandafter\def\csname fg@textcolor5\endcsname{Black}
\expandafter\def\csname fg@textcolor6\endcsname{Black}
\expandafter\def\csname fg@textcolor7\endcsname{Black}
\expandafter\def\csname fg@textcolor8\endcsname{Black}
\expandafter\def\csname fg@textcolor9\endcsname{Black}
\fi
}
\def\include@DSSP{%
\xdef\first@{\csname optiondssp\the\loopcount\endcsname}
\xdef\bottop@{\csname bottopdssp\the\loopcount\endcsname}
\xdef\st@rt{\csname doseqdssp\the\loopcount\endcsname}
\xdef\structurefilename{\csname filenamedssp\the\loopcount\endcsname}
\bgroup
\xdef\file@n@me{\structurefilename .@}
\expandafter\cut@name\file@n@me
\xdef\file@n@me{\file@n@me.sec}
\ifx\first@\file@n@me
\else
\immediate\openin\alignfile = \file@n@me\relax
\ifeof\alignfile \xdef\first@{make new} \fi
\immediate\closein\alignfile
\fi
\xdef\temp@{make new}
\ifx\first@\temp@
\def\par{}
\inactivate@chars
\immediate\openin\structurefile = \structurefilename\relax
\ifeof\structurefile
\PackageError{TeXshade}
{File `\structurefilename' not found}
{\MessageBreak
The `DSSP' file you specified is missing or you have \MessageBreak
misspelled it. \MessageBreak\MessageBreak
No labels for secondary structures will be displayed. \MessageBreak
Type <return> to proceed. \MessageBreak
Type X <return> to quit. \MessageBreak
}
\immediate\closein\structurefile\egroup
\else
\message{[\structurefilename] ->}
\xdef\second@{} \xdef\temp@{RESIDUE}
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\ifx\second@\temp@ \xdef\temp@{AA}\fi
\ifx\third@\temp@ \else\repeat
\immediate\openout\featurefile = \file@n@me
\xdef\c@mp{+}
\xdef\begin@{\csname seq@start\st@rt\endcsname}
\xdef\end@{\csname seq@start\st@rt\endcsname}
\xdef\st@rt@{\begin@}
\expandafter\innerloopcount=\csname seq@start\st@rt\endcsname
\advance\innerloopcount by -1
\xdef\first@@{0} \xdef\second@@{0} \xdef\third@@{0}
\xdef\fourth@@{0} \xdef\fifth@@{0} \xdef\sixth@@{0}
\xdef\seventh@@{0}
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\if\c@mp + \xdef\c@mp{\fifth@}\fi
\ifx\fifth@\c@mp
\ifx\fc@DSSP\y@
\temp@count=\first@
\else
\temp@count=\second@
\fi
\advance\temp@count by \st@rt@
\advance\temp@count by -1
\xdef\end@{\the\temp@count}
\else
\ifnum\begin@>0
\ifnum\end@<\begin@ \xdef\end@{\begin@}\fi
\if\c@mp C
\else
\if\c@mp H
\ifx\show@Hdssp\yes
\loopcount=\first@@
\advance\loopcount by 1
\xdef\first@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Hdssp}{\begin@..\end@}%
{\label@Hdssp}{\text@Hdssp}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Hdssp}{\st@rt}{\begin@..\end@}%
{\label@Hdssp}{\text@Hdssp}}\fi
\fi
\else
\if\c@mp G
\ifx\show@Gdssp\yes
\loopcount=\second@@
\advance\loopcount by 1
\xdef\second@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Gdssp}{\begin@..\end@}%
{\label@Gdssp}{\text@Gdssp}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Gdssp}{\st@rt}{\begin@..\end@}%
{\label@Gdssp}{\text@Gdssp}}\fi
\fi
\else
\if\c@mp I
\ifx\show@Idssp\yes
\loopcount=\third@@
\advance\loopcount by 1
\xdef\third@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Idssp}{\begin@..\end@}%
{\label@Idssp}{\text@Idssp}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Idssp}{\st@rt}{\begin@..\end@}%
{\label@Idssp}{\text@Idssp}}\fi
\fi
\else
\if\c@mp E
\ifx\show@Edssp\yes
\loopcount=\fourth@@
\advance\loopcount by 1
\xdef\fourth@@{\the\loopcount}
\advance\innerloopcount by 1
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Edssp}{\begin@..\end@}%
{\label@Edssp}{\text@Edssp}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Edssp}{\st@rt}{\begin@..\end@}%
{\label@Edssp}{\text@Edssp}}\fi
\fi
\else
\if\c@mp B
\ifx\show@Bdssp\yes
\loopcount=\fifth@@
\advance\loopcount by 1
\xdef\fifth@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Bdssp}{\begin@..\end@}%
{\label@Bdssp}{\text@Bdssp}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Bdssp}{\st@rt}{\begin@..\end@}%
{\label@Bdssp}{\text@Bdssp}}\fi
\fi
\else
\if\c@mp T
\ifx\show@Tdssp\yes
\loopcount=\sixth@@
\advance\loopcount by 1
\xdef\sixth@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Tdssp}{\begin@..\end@}%
{\label@Tdssp}{\text@Tdssp}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Tdssp}{\st@rt}{\begin@..\end@}%
{\label@Tdssp}{\text@Tdssp}}\fi
\fi
\else
\if\c@mp S
\ifx\show@Sdssp\yes
\loopcount=\seventh@@
\advance\loopcount by 1
\xdef\seventh@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Sdssp}{\begin@..\end@}%
{\label@Sdssp}{\text@Sdssp}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Sdssp}{\st@rt}{\begin@..\end@}%
{\label@Sdssp}{\text@Sdssp}}\fi
\fi
\fi\fi\fi\fi\fi\fi\fi\fi
\fi
\xdef\c@mp{\fifth@}
\ifx\fc@DSSP\y@
\temp@count=\first@
\else
\temp@count=\second@
\fi
\advance\temp@count by \st@rt@
\advance\temp@count by -1
\xdef\begin@{\the\temp@count}
\fi
\fi
\ifeof\structurefile \else\repeat
\closein\structurefile
\immediate\closeout\featurefile
\egroup
\input{\file@n@me}
\fi
\else
\egroup
\message{using existing file:}
\input{\file@n@me}
\fi
}
\def\include@HMMTOP{%
\def\get@HMMTOP@TMs##1-##2 ##3@{%
\xdef\temp@@{\temp@@\fourth@@##1\fourth@@##2}
\xdef\structureline{##3 @}
}
\def\get@HMMTOP{%
\ifnum\temp@count<\fifth@
\advance\temp@count by 1
\expandafter\get@HMMTOP@TMs\structureline
\get@HMMTOP
\fi
}
\def\rem@ve@TM@info Transmembrane helices: ##1@{%
\xdef\structureline{##1 @}
\temp@count=0
\get@HMMTOP
}
\xdef\bottop@{\csname bottopHMMTOP\the\loopcount\endcsname}
\xdef\st@rt{\csname doseqHMMTOP\the\loopcount\endcsname}
\xdef\first@{\csname optionHMMTOP\the\loopcount\endcsname}
\xdef\structurefilename{\csname filenameHMMTOP\the\loopcount\endcsname}
\bgroup
\xdef\file@n@me{\structurefilename .@}
\expandafter\cut@name\file@n@me
\xdef\file@n@me{\file@n@me.top}
\ifx\first@\file@n@me
\else
\immediate\openin\alignfile = \file@n@me\relax
\ifeof\alignfile \xdef\first@{make new} \fi
\immediate\closein\alignfile
\fi
\xdef\temp@{make new}
\ifx\first@\temp@
\def\par{}
\inactivate@chars
\immediate\openin\structurefile = \structurefilename\relax
\ifeof\structurefile
\PackageError{TeXshade}
{File `\structurefilename' not found}
{\MessageBreak
The `HMMTOP' file you specified is missing or you have \MessageBreak
misspelled it. \MessageBreak\MessageBreak
No labels for secondary structures will be displayed. \MessageBreak
Type <return> to proceed. \MessageBreak
Type X <return> to quit. \MessageBreak
}
\immediate\closein\structurefile\egroup
\else
\message{[\structurefilename] ->}
\immediate\openout\featurefile = \file@n@me
\xdef\first@{\csname fileseqHMMTOP\the\loopcount\endcsname @}
\expandafter\check@letter\first@
\ifletter
\xdef\st@p{\csname fileseqHMMTOP\the\loopcount\endcsname}
\else
\xdef\first@{\csname fileseqHMMTOP\the\loopcount\endcsname}
\ifnum\first@=0
\xdef\st@p{0}
\else
\xdef\st@p{\csname fileseqHMMTOP\the\loopcount\endcsname}
\fi
\fi
\xdef\temp@{yes} \innerloopcount=0
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\ifx\first@\@HP
\ifx\temp@\yes \xdef\temp@{\readline} \fi
\ifletter
\ifx\st@p\third@ \xdef\temp@{\readline} \fi
\else
\ifnum\st@p=0
\expandafter\ifx\csname seqname\st@rt\endcsname\third@
\xdef\temp@{\readline} \xdef\st@p{-1}
\else
\expandafter\ifx\csname newseqname\st@rt\endcsname\third@
\xdef\temp@{\readline} \xdef\st@p{-1}
\fi
\fi
\else
\advance\innerloopcount by 1
\ifnum\st@p=\innerloopcount \xdef\temp@{\readline} \fi
\fi
\fi
\else
\xdef\first@@{Protein:}
\ifx\first@\first@@
\xdef\second@@{\second@}
\xdef\temp@@{>HP:} \xdef\fourth@@{ }
\read\structurefile to \readline
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\xdef\temp@@{\temp@@\fourth@@\second@\fourth@@\second@@}
\read\structurefile to \readline
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\xdef\temp@@{\temp@@\fourth@@\second@}
\read\structurefile to \readline
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\xdef\temp@@{\temp@@\fourth@@\fifth@}
\read\structurefile to \readline
\xdef\structureline{\readline @}
\expandafter\rem@ve@TM@info\structureline
\xdef\temp@@{\temp@@\fourth@@}
\ifx\temp@\yes \xdef\temp@{\temp@@} \fi
\ifletter
\ifx\st@p\third@ \xdef\temp@{\temp@@} \fi
\else
\ifnum\st@p=0
\expandafter\ifx\csname seqname\st@rt\endcsname\second@@
\xdef\temp@{\temp@@}
\else
\expandafter\ifx\csname newseqname\st@rt\endcsname\second@@
\xdef\temp@{\temp@@}
\fi
\fi
\else
\advance\innerloopcount by 1
\ifnum\st@p=\innerloopcount \xdef\temp@{\temp@@} \fi
\fi
\fi
\fi
\fi
\fi
\ifeof\structurefile \else\repeat
\xdef\seq@line{\temp@ @}
\innerloopcount=0
\loop
\advance\innerloopcount by 1
\expandafter\seq@get\seq@line
\xdef\seq@line{\seq@line @}
\ifnum\innerloopcount=4 \xdef\c@mp{\first@} \fi
\ifnum\innerloopcount=5 \xdef\st@p{\first@} \else \repeat
\xdef\first@{IN}
\ifx\c@mp\first@ \xdef\c@mp{i} \else \xdef\c@mp{e} \fi
\xdef\begin@{1} \xdef\first@@{0} \xdef\second@@{0}
\innerloopcount=0
\loop
\advance\innerloopcount by 1
\expandafter\seq@get\seq@line
\xdef\seq@line{\seq@line @}
\temp@count=\first@
\advance\temp@count by -1
\xdef\end@{\the\temp@count}
\loopcount=\second@@
\advance\loopcount by 1
\xdef\second@@{\the\loopcount}
\if\c@mp i
\ifx\show@i@HMMTOP\yes
\immediate\write\featurefile{%
\string\feature{\bottop@i@HMMTOP}{\st@rt}{\begin@..\end@}%
{\label@i@HMMTOP}{\text@i@HMMTOP}}\fi
\xdef\c@mp{e}
\else
\ifx\show@e@HMMTOP\yes
\immediate\write\featurefile{%
\string\feature{\bottop@e@HMMTOP}{\st@rt}{\begin@..\end@}%
{\label@e@HMMTOP}{\text@e@HMMTOP}}\fi
\xdef\c@mp{i}
\fi
\advance\temp@count by 1
\xdef\begin@{\the\temp@count}
\expandafter\seq@get\seq@line
\xdef\seq@line{\seq@line @}
\xdef\end@{\first@}
\loopcount=\first@@
\advance\loopcount by 1
\xdef\first@@{\the\loopcount}
\ifx\show@TM@HMMTOP\yes
\immediate\write\featurefile{%
\string\feature{\bottop@TM@HMMTOP}{\st@rt}{\begin@..\end@}%
{\label@TM@HMMTOP}{\text@TM@HMMTOP}}\fi
\temp@count=\end@ \advance\temp@count by 1 \xdef\begin@{\the\temp@count}
\ifnum\innerloopcount=\st@p\else\repeat
\closein\structurefile
\immediate\closeout\featurefile
\egroup
\input{\file@n@me}
\fi
\else
\egroup
\message{using existing file:}
\input{\file@n@me}
\fi
}
\def\include@stride{%
\xdef\first@{\csname optionstride\the\loopcount\endcsname}
\xdef\bottop@{\csname bottopstride\the\loopcount\endcsname}
\xdef\st@rt{\csname doseqstride\the\loopcount\endcsname}
\xdef\structurefilename{\csname filenamestride\the\loopcount\endcsname}
\bgroup
\xdef\file@n@me{\structurefilename .@}
\expandafter\cut@name\file@n@me
\xdef\file@n@me{\file@n@me.sec}
\ifx\first@\file@n@me
\else
\immediate\openin\alignfile = \file@n@me\relax
\ifeof\alignfile \xdef\first@{make new} \fi
\immediate\closein\alignfile
\fi
\xdef\temp@{make new}
\ifx\first@\temp@
\def\par{}
\inactivate@chars
\immediate\openin\structurefile = \structurefilename\relax
\ifeof\structurefile
\PackageError{TeXshade}
{File `\structurefilename' not found}
{\MessageBreak
The `STRIDE' file you specified is missing or you have \MessageBreak
misspelled it. \MessageBreak\MessageBreak
No labels for secondary structures will be displayed. \MessageBreak
Type <return> to proceed. \MessageBreak
Type X <return> to quit. \MessageBreak
}
\immediate\closein\structurefile\egroup
\else
\message{[\structurefilename] ->}
\immediate\openout\featurefile = \file@n@me
\xdef\c@mp{+}
\xdef\begin@{\csname seq@start\st@rt\endcsname}
\xdef\end@{\csname seq@start\st@rt\endcsname}
\xdef\st@rt@{\begin@}
\expandafter\innerloopcount=\csname seq@start\st@rt\endcsname
\advance\innerloopcount by -1
\xdef\first@@{0} \xdef\second@@{0} \xdef\third@@{0}
\xdef\fourth@@{0} \xdef\fifth@@{0} \xdef\sixth@@{0}
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\ifx\first@\@asg
\if\c@mp + \xdef\c@mp{\sixth@}\fi
\ifx\sixth@\c@mp
\temp@count=\fifth@
\advance\temp@count by \st@rt@
\advance\temp@count by -1
\xdef\end@{\the\temp@count}
\else
\ifnum\begin@>0
\ifnum\end@<\begin@ \xdef\end@{\begin@}\fi
\if\c@mp C
\else
\if\c@mp H
\ifx\show@Hstride\yes
\loopcount=\first@@
\advance\loopcount by 1
\xdef\first@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Hstride}{\begin@..\end@}%
{\label@Hstride}{\text@Hstride}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Hstride}{\st@rt}{\begin@..\end@}%
{\label@Hstride}{\text@Hstride}}\fi
\fi
\else
\if\c@mp G
\ifx\show@Gstride\yes
\loopcount=\second@@
\advance\loopcount by 1
\xdef\second@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Gstride}{\begin@..\end@}%
{\label@Gstride}{\text@Gstride}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Gstride}{\st@rt}{\begin@..\end@}%
{\label@Gstride}{\text@Gstride}}\fi
\fi
\else
\if\c@mp I
\ifx\show@Istride\yes
\loopcount=\third@@
\advance\loopcount by 1
\xdef\third@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Istride}{\begin@..\end@}%
{\label@Istride}{\text@Istride}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Istride}{\st@rt}{\begin@..\end@}%
{\label@Istride}{\text@Istride}}\fi
\fi
\else
\if\c@mp E
\ifx\show@Estride\yes
\loopcount=\fourth@@
\advance\loopcount by 1
\xdef\fourth@@{\the\loopcount}
\advance\innerloopcount by 1
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Estride}{\begin@..\end@}%
{\label@Estride}{\text@Estride}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Estride}{\st@rt}{\begin@..\end@}%
{\label@Estride}{\text@Estride}}\fi
\fi
\else
\if\c@mp B
\ifx\show@Bstride\yes
\loopcount=\fifth@@
\advance\loopcount by 1
\xdef\fifth@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Bstride}{\begin@..\end@}%
{\label@Bstride}{\text@Bstride}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Bstride}{\st@rt}{\begin@..\end@}%
{\label@Bstride}{\text@Bstride}}\fi
\fi
\else
\if\c@mp T
\ifx\show@Tstride\yes
\loopcount=\sixth@@
\advance\loopcount by 1
\xdef\sixth@@{\the\loopcount}
\ifx\m@p\yes
\immediate\write\featurefile{%
\string\feature{\bottop@Tstride}{\begin@..\end@}%
{\label@Tstride}{\text@Tstride}}
\else
\immediate\write\featurefile{%
\string\feature{\bottop@Tstride}{\st@rt}{\begin@..\end@}%
{\label@Tstride}{\text@Tstride}}\fi
\fi
\fi\fi\fi\fi\fi\fi\fi
\fi
\xdef\c@mp{\sixth@}
\temp@count=\fifth@
\advance\temp@count by \st@rt@
\advance\temp@count by -1
\xdef\begin@{\the\temp@count}
\fi
\fi
\fi
\ifeof\structurefile \else\repeat
\closein\structurefile
\immediate\closeout\featurefile
\egroup
\input{\file@n@me}
\fi
\else
\egroup
\message{using existing file:}
\input{\file@n@me}
\fi
}
\def\include@PHD{%
\xdef\first@{\csname optionphd\the\loopcount\endcsname}
\xdef\bottop@{\csname bottopphd\the\loopcount\endcsname}
\xdef\st@rt{\csname doseqphd\the\loopcount\endcsname}
\xdef\m@de{\csname modephd\the\loopcount\endcsname}
\xdef\structurefilename{\csname filenamephd\the\loopcount\endcsname}
\bgroup
\xdef\file@n@me{\structurefilename .@}
\expandafter\cut@name\file@n@me
\xdef\temp@{structure}
\ifx\m@de\temp@
\xdef\temp@{\file@n@me .sec}
\immediate\openin\alignfile = \temp@\relax
\ifeof\alignfile \xdef\first@{make new} \fi
\immediate\closein\alignfile
\else
\xdef\temp@{topology}
\ifx\m@de\temp@
\xdef\temp@{\file@n@me .top}
\immediate\openin\alignfile = \temp@\relax
\ifeof\alignfile \xdef\first@{make new} \fi
\immediate\closein\alignfile
\else
\message{<Unknown type - ignoring \noexpand\includePHD>}
\xdef\first@{ignore}
\fi\fi
\xdef\temp@{make new}
\ifx\first@\temp@
\def\par{}
\xdef\PHD@line{}
\inactivate@chars
\immediate\openin\structurefile=\structurefilename\relax
\ifeof\structurefile
\PackageError{TeXshade}%
{File `\structurefilename' not found}%
{\MessageBreak
The `PHD' file you specified is missing or you have \MessageBreak
misspelled it. \MessageBreak\MessageBreak
No labels for secondary structures will be displayed. \MessageBreak
Type <return> to proceed. \MessageBreak
Type X <return> to quit. \MessageBreak
}
\immediate\closein\structurefile\egroup
\else
\message{[\structurefilename] ->}
\loop
\read\structurefile to \readline
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\xdef\temp@{structure}
\ifx\m@de\temp@
\xdef\temp@{SUB}
\ifx\temp@\first@
\xdef\temp@{sec}
\ifx\temp@\second@
\xdef\third@{\third@ @}
\expandafter\get@PHD\third@
\fi
\else
\ifx\temp@\second@
\xdef\temp@{sec}
\ifx\temp@\third@
\xdef\fourth@{\fourth@ @}
\expandafter\get@PHD\fourth@
\fi
\fi
\fi
\else
\xdef\temp@{topology}
\ifx\m@de\temp@
\xdef\temp@{PHDThtm}
\ifx\temp@\first@
\xdef\second@{\second@ @}
\expandafter\get@PHD\second@
\fi
\fi\fi
\ifeof\structurefile \else\repeat
\closein\structurefile
\xdef\c@mp{+}
\xdef\begin@{\csname seq@start\st@rt\endcsname}
\xdef\end@{\csname seq@start\st@rt\endcsname}
\expandafter\innerloopcount=\csname seq@start\st@rt\endcsname
\advance\innerloopcount by -1
\xdef\first@{0} \xdef\second@{0} \xdef\third@{0}
\xdef\fourth@{0} \xdef\fifth@{0} \xdef\sixth@{0}
\xdef\last@{\PHD@line &@}
\xdef\temp@{structure}
\ifx\temp@\m@de
\xdef\file@n@me{\file@n@me .sec}
\immediate\openout\featurefile = \file@n@me\relax
\write@PHDsec
\fi
\xdef\temp@{topology}
\ifx\temp@\m@de
\xdef\file@n@me{\file@n@me .top}
\immediate\openout\featurefile = \file@n@me\relax
\write@PHDtopo
\fi
\immediate\closeout\featurefile
\egroup
\input{\file@n@me}
\fi
\else
\egroup
\xdef\temp@{ignore}
\ifx\temp@\first@
\else
\message{using existing file:}
\xdef\temp@{structure}
\ifx\temp@\m@de \xdef\file@n@me{\file@n@me .sec} \fi
\xdef\temp@{topology}
\ifx\temp@\m@de \xdef\file@n@me{\file@n@me .top} \fi
\input{\file@n@me}
\fi
\fi}
\def\show@DSSP{%
\expandafter\get@item\first@
\ifx\fourth@\ampers@nd
\else
\xdef\temp@{alpha}
\ifx\fourth@\temp@ \xdef\show@Hdssp{\second@}\fi
\xdef\temp@{3-10}
\ifx\fourth@\temp@ \xdef\show@Gdssp{\second@}\fi
\xdef\temp@{pi}
\ifx\fourth@\temp@ \xdef\show@Idssp{\second@}\fi
\xdef\temp@{beta}
\ifx\fourth@\temp@ \xdef\show@Edssp{\second@}\fi
\xdef\temp@{bridge}
\ifx\fourth@\temp@ \xdef\show@Bdssp{\second@}\fi
\xdef\temp@{turn}
\ifx\fourth@\temp@ \xdef\show@Tdssp{\second@}\fi
\xdef\temp@{bend}
\ifx\fourth@\temp@ \xdef\show@Sdssp{\second@}\fi
\show@DSSP
\fi}
\def\show@HMMTOP{%
\expandafter\get@item\first@
\ifx\fourth@\ampers@nd
\else
\xdef\temp@{internal}
\ifx\fourth@\temp@ \xdef\show@i@HMMTOP{\second@}\fi
\xdef\temp@{external}
\ifx\fourth@\temp@ \xdef\show@e@HMMTOP{\second@}\fi
\xdef\temp@{TM}
\ifx\fourth@\temp@ \xdef\show@TM@HMMTOP{\second@}\fi
\show@HMMTOP
\fi}
\def\show@STRIDE{%
\expandafter\get@item\first@
\ifx\fourth@\ampers@nd
\else
\xdef\temp@{alpha}
\ifx\fourth@\temp@ \xdef\show@Hstride{\second@}\fi
\xdef\temp@{3-10}
\ifx\fourth@\temp@ \xdef\show@Gstride{\second@}\fi
\xdef\temp@{pi}
\ifx\fourth@\temp@ \xdef\show@Istride{\second@}\fi
\xdef\temp@{beta}
\ifx\fourth@\temp@ \xdef\show@Estride{\second@}\fi
\xdef\temp@{bridge}
\ifx\fourth@\temp@ \xdef\show@Bstride{\second@}\fi
\xdef\temp@{turn}
\ifx\fourth@\temp@ \xdef\show@Tstride{\second@}\fi
\show@STRIDE
\fi}
\def\show@PHDtopo{%
\expandafter\get@item\first@
\ifx\fourth@\ampers@nd
\else
\xdef\temp@{internal}
\ifx\fourth@\temp@ \xdef\show@itop{\second@}\fi
\xdef\temp@{external}
\ifx\fourth@\temp@ \xdef\show@etop{\second@}\fi
\xdef\temp@{TM}
\ifx\fourth@\temp@ \xdef\show@TMtop{\second@}\fi
\show@PHDtopo
\fi}
\def\show@PHDsec{%
\expandafter\get@item\first@
\ifx\fourth@\ampers@nd
\else
\xdef\temp@{alpha}
\ifx\fourth@\temp@ \xdef\show@Hsec{\second@}\fi
\xdef\temp@{beta}
\ifx\fourth@\temp@ \xdef\show@Esec{\second@}\fi
\show@PHDsec
\fi}
\def\get@triplet#1,#2@{%
\xdef\third@{#1}
\ifx\third@\ampers@nd
\else
\expandafter\xdef\csname @\third@\endcsname{\first@}
\expandafter\xdef\csname rev@\first@\endcsname{\third@}
\xdef\fourth@{#2,&,@}
\expandafter\get@triplet\fourth@
\fi}
\def\get@dom@count#1,#2@{\res@count=#1 \xdef\temp@{#2 @}}
\def\get@name@number{%
\xdef\second@{n}
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\ifx\csname newseqname\the\loopcount\endcsname\first@
\xdef\first@{\the\loopcount} \loopcount=\seq@count
\xdef\second@{y}
\fi
\ifnum\loopcount=\seq@count \else \repeat
\ifx\second@\n@
\message{<Sequence name `\first@' was not found - using first sequence.>}
\xdef\first@{1}
\fi
}
\def\get@name@number@table{%
\xdef\second@{n}%
\loopcount=0%
\loop%
\advance\loopcount by 1%
\expandafter\ifx\csname newseqname\the\loopcount\endcsname\first@%
\xdef\first@{\the\loopcount}\loopcount=\seq@num%
\xdef\second@{y}%
\fi%
\ifnum\loopcount=\seq@num\else\repeat%
\ifx\second@\n@%
\message{<Sequence name `\first@' was not found - using first sequence.>}%
\xdef\first@{1}%
\fi%
}
\def\calc@distance@point{%
\loopcount=\xref@coord@a \advance\loopcount by -\x@coord\relax
\multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
\loopcount=\yref@coord@a \advance\loopcount by -\y@coord\relax
\multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
\loopcount=\zref@coord@a \advance\loopcount by -\z@coord\relax
\multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
\advance\loopcount by \y@distance\relax
\advance\loopcount by \x@distance\relax
\ifnum\loopcount > \PDB@distance \else
\loopcount=\PDB@hitpos \advance\loopcount by 1
\ifnum\loopcount=\PDB@pos
\else
\xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
\fi
\xdef\PDB@hitpos{\PDB@pos}
\fi
}
\def\calc@distance@line{%
\loopcount=\x@coord\relax \multiply\loopcount by \x@orient
\temp@count=\y@coord \relax \multiply\temp@count by \y@orient
\advance\loopcount by \temp@count
\temp@count=\z@coord \relax \multiply\temp@count by \z@orient
\advance\loopcount by \temp@count
\advance\loopcount by -\c@nst@
\xdef\z@hler{\the\loopcount}
\multiply\loopcount by \x@orient \divide\loopcount by \f@ct@r \advance\loopcount by \xref@coord@a
\advance\loopcount by -\x@coord
\multiply\loopcount by \loopcount \xdef\x@distance{\the\loopcount}
\loopcount=\z@hler
\multiply\loopcount by \y@orient \divide\loopcount by \f@ct@r \advance\loopcount by \yref@coord@a
\advance\loopcount by -\y@coord
\multiply\loopcount by \loopcount \xdef\y@distance{\the\loopcount}
\loopcount=\z@hler
\multiply\loopcount by \z@orient \divide\loopcount by \f@ct@r \advance\loopcount by \zref@coord@a
\advance\loopcount by -\z@coord
\multiply\loopcount by \loopcount \xdef\z@distance{\the\loopcount}
\advance\loopcount by \y@distance\relax
\advance\loopcount by \x@distance\relax
\ifnum\loopcount > \PDB@distance \else
\loopcount=\PDB@hitpos \advance\loopcount by 1
\ifnum\loopcount=\PDB@pos
\else
\xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
\fi
\xdef\PDB@hitpos{\PDB@pos}
\fi
}
\def\intr@@t{%
\loopcount=\r@@t
\temp@count=1
\loop
\advance\loopcount by \temp@count
\divide\loopcount by 2
\temp@count=\r@@t
\divide\temp@count by \loopcount
\ifnum\loopcount>\temp@count\repeat
}
\def\calc@distance@plane{%
\loopcount=\x@coord\relax
\multiply\loopcount by \x@orient
\temp@count=\y@coord \relax
\multiply\temp@count by \y@orient
\advance\loopcount by \temp@count
\temp@count=\z@coord \relax
\multiply\temp@count by \z@orient
\advance\loopcount by \temp@count
\advance\loopcount by \c@nst@
\divide\loopcount by \f@ct@r
\multiply\loopcount by \loopcount
\ifnum\loopcount > \PDB@distance \else
\loopcount=\PDB@hitpos \advance\loopcount by 1
\ifnum\loopcount=\PDB@pos
\else
\xdef\PDB@stack{\PDB@stack\PDB@hitpos,\PDB@pos..}
\fi
\xdef\PDB@hitpos{\PDB@pos}
\fi
}
\def\load@PDB{%
\bgroup
\immediate\openin\structurefile = \PDB@name\relax
\ifeof\structurefile
\PackageError{TeXshade}
{File `\PDB@name' not found}
{\MessageBreak
The file you specified is missing or you have \MessageBreak
misspelled it. \MessageBreak\MessageBreak
No PDB domain labeling will be displayed. \MessageBreak
Type <return> to proceed. \MessageBreak
Type X <return> to quit. \MessageBreak
}
\immediate\closein\structurefile\egroup
\else
\message{<reading PDB: \PDB@name>}
\xdef\first@{}
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\ifx\first@\@TOM
\ifx\PDB@back@side@a\C@lpha
\ifx\third@\C@lpha
\xdef\temp@@@{\fifth@ &&@}
\expandafter\check@letter\temp@@@
\ifnumber
\ifnum\fifth@=\PDB@refnum@a
\xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
\fi
\else
\ifnum\sixth@=\PDB@refnum@a
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
\xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
\fi
\fi
\fi
\else
\xdef\temp@@@{\fifth@ &&@}
\expandafter\check@letter\temp@@@
\ifnumber
\ifnum\fifth@=\PDB@refnum@a
\xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@a{\c@@rd}
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@a{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@a{\c@@rd}
\fi
\else
\ifnum\sixth@=\PDB@refnum@a
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@a{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@a{\c@@rd}
\xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@a{\c@@rd}
\fi
\fi
\fi
\ifx\PDB@back@side@b\C@lpha
\ifx\third@\C@lpha
\xdef\temp@@@{\fifth@ &&@}
\expandafter\check@letter\temp@@@
\ifnumber
\ifnum\fifth@=\PDB@refnum@b
\xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
\fi
\else
\ifnum\sixth@=\PDB@refnum@b
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
\xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
\fi
\fi
\fi
\else
\xdef\temp@@@{\fifth@ &&@}
\expandafter\check@letter\temp@@@
\ifnumber
\ifnum\fifth@=\PDB@refnum@b
\xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@b{\c@@rd}
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@b{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@b{\c@@rd}
\fi
\else
\ifnum\sixth@=\PDB@refnum@b
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@b{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@b{\c@@rd}
\xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@b{\c@@rd}
\fi
\fi
\fi
\ifx\PDB@back@side@c\C@lpha
\ifx\third@\C@lpha
\xdef\temp@@@{\fifth@ &&@}
\expandafter\check@letter\temp@@@
\ifnumber
\ifnum\fifth@=\PDB@refnum@c
\xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
\fi
\else
\ifnum\sixth@=\PDB@refnum@c
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
\xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
\fi
\fi
\fi
\else
\xdef\temp@@@{\fifth@ &&@}
\expandafter\check@letter\temp@@@
\ifnumber
\ifnum\fifth@=\PDB@refnum@c
\xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\xref@coord@c{\c@@rd}
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\yref@coord@c{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\zref@coord@c{\c@@rd}
\fi
\else
\ifnum\sixth@=\PDB@refnum@c
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\xref@coord@c{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\yref@coord@c{\c@@rd}
\xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\zref@coord@c{\c@@rd}
\fi
\fi
\fi
\fi
\fi
\ifeof\structurefile \else\repeat
\closein\structurefile
\ifx\PDB@type\@line@
\loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient{\the\loopcount}
\loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient{\the\loopcount}
\loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient{\the\loopcount}
\loopcount=\xref@coord@a \multiply\loopcount by \x@orient
\temp@count=\yref@coord@a \multiply\temp@count by \y@orient
\advance\loopcount by \temp@count
\temp@count=\zref@coord@a \multiply\temp@count by \z@orient
\advance\loopcount by \temp@count
\xdef\c@nst@{\the\loopcount}
\loopcount=\x@orient \multiply\loopcount by \x@orient
\temp@count=\y@orient \multiply\temp@count by \y@orient
\advance\loopcount by \temp@count
\temp@count=\z@orient \multiply\temp@count by \z@orient
\advance\loopcount by \temp@count
\xdef\f@ct@r{\the\loopcount}
\fi
\ifx\PDB@type\@plane@
\loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@b \xdef\x@orient@r{\the\loopcount}
\loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@b \xdef\y@orient@r{\the\loopcount}
\loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@b \xdef\z@orient@r{\the\loopcount}
\loopcount=\xref@coord@a \advance\loopcount by -\xref@coord@c \xdef\x@orient@s{\the\loopcount}
\loopcount=\yref@coord@a \advance\loopcount by -\yref@coord@c \xdef\y@orient@s{\the\loopcount}
\loopcount=\zref@coord@a \advance\loopcount by -\zref@coord@c \xdef\z@orient@s{\the\loopcount}
\loopcount=\y@orient@r \multiply\loopcount by \z@orient@s
\temp@count=\z@orient@r \multiply\temp@count by \y@orient@s
\advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\x@orient{\the\loopcount}
\loopcount=\z@orient@r \multiply\loopcount by \x@orient@s
\temp@count=\x@orient@r \multiply\temp@count by \z@orient@s
\advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\y@orient{\the\loopcount}
\loopcount=\x@orient@r \multiply\loopcount by \y@orient@s
\temp@count=\y@orient@r \multiply\temp@count by \x@orient@s
\advance\loopcount by -\temp@count \divide\loopcount by 100 \xdef\z@orient{\the\loopcount}
\loopcount=\x@orient \multiply\loopcount by \xref@coord@a
\temp@count=\y@orient \multiply\temp@count by \yref@coord@a
\advance\loopcount by \temp@count
\temp@count=\z@orient \multiply\temp@count by \zref@coord@a
\advance\loopcount by \temp@count
\multiply\loopcount by -1\relax
\xdef\c@nst@{\the\loopcount}
\loopcount=\x@orient \multiply\loopcount by \loopcount
\temp@count=\y@orient \multiply\temp@count by \temp@count
\advance\loopcount by \temp@count
\temp@count=\z@orient \multiply\temp@count by \temp@count
\advance\loopcount by \temp@count
\xdef\r@@t{\the\loopcount} \intr@@t
\xdef\f@ct@r{\the\loopcount}
\fi
\immediate\openin\structurefile = \PDB@name\relax
\xdef\first@{}
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\structureline{\readline & & & & & & & & &@}
\expandafter\struc@get\structureline
\ifx\first@\@TOM
\xdef\temp@@@{\fifth@ &&@}
\expandafter\check@letter\temp@@@
\ifnumber
\xdef\PDB@pos{\fifth@}
\xdef\sixth@{\sixth@ &.&&@} \expandafter\coord@get\sixth@ \xdef\x@coord{\c@@rd}
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\y@coord{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\z@coord{\c@@rd}
\else
\xdef\PDB@pos{\sixth@}
\xdef\seventh@{\seventh@ &.&&@} \expandafter\coord@get\seventh@ \xdef\x@coord{\c@@rd}
\xdef\eighth@{\eighth@ &.&&@} \expandafter\coord@get\eighth@ \xdef\y@coord{\c@@rd}
\xdef\nineth@{\nineth@ &.&&@} \expandafter\coord@get\nineth@ \xdef\z@coord{\c@@rd}
\fi
\ifnum\PDB@hitpos=\PDB@pos
\else
\ifx\PDB@type\@point@
\calc@distance@point
\else
\ifx\PDB@type\@line@
\calc@distance@line
\else
\ifx\PDB@type\@plane@
\calc@distance@plane
\fi
\fi
\fi
\fi
\fi
\fi
\ifeof\structurefile \xdef\PDB@stack{\PDB@stack\PDB@hitpos,&@}
\else\repeat
\closein\structurefile
\fi
\egroup
}
%%%%% Definition of user commands
\def\clearfuncgroups{\xdef\prfx{func} \clear@groups \xdef\fgroup@num{0}}
\clearfuncgroups
\def\germanlanguage{\germ@ntrue \sp@nishfalse \def\cons@name{Konsensus}}
\def\spanishlanguage{\germ@nfalse \sp@nishtrue \def\cons@name{consenso}}
\def\englishlanguage{\germ@nfalse \sp@nishfalse \def\cons@name{consensus}}
\def\showlegend{\legend@true}
\def\hidelegend{\legend@false}
\def\movelegend#1#2{%
\setlength\hspace@legend{#1}
\setlength\vspace@legend{#2}
}
\newcommand{\showcaption}[2][bottom]{\def\cap@pos{#1}\def\c@p{#2}}
\def\shortcaption#1{\def\c@pshort{#1}}
\def\funcgroup#1#2#3#4#5#6{%
\xdef\first@{#1}
\loopcount=0 \innerloopcount=0
\loop
\advance\loopcount by 1
\ifx\csname fgroup@name\the\loopcount\endcsname\first@
\innerloopcount=\loopcount \loopcount=\fgroup@num
\fi
\ifnum\loopcount<\fgroup@num \repeat
\ifnum\innerloopcount=0
\ifnum\fgroup@num<9
\innerloopcount=\fgroup@num
\advance\innerloopcount by 1 \xdef\fgroup@num{\the\innerloopcount}
\else \message{<Too many \noexpand\funcgroups>}
\fi
\fi
\ifnum\innerloopcount>0
\expandafter\xdef\csname fgroup@name\the\innerloopcount\endcsname{\first@}
\expandafter\xdef\csname fg@textcolor\the\innerloopcount\endcsname{#3}
\expandafter\xdef\csname fg@color\the\innerloopcount\endcsname{#4}
\expandafter\xdef\csname funcm@tch\the\innerloopcount\endcsname{#5}
\expandafter\def\csname func@style\the\innerloopcount\endcsname{%
\csname text#6\endcsname}
\xdef\prfx{func}
\xdef\third@{#2&,@} \loopcount=\innerloopcount
\expandafter\group@get\third@
\fi}
\def\pepgroups#1{%
\xdef\prfx{pep}
\clear@groups
\xdef\third@{#1&,@} \loopcount=0
\loop \expandafter\group@get\third@ \advance\loopcount by 1
\ifnum\loopcount<10 \repeat}
\def\DNAgroups#1{%
\xdef\prfx{DNA}
\clear@groups
\xdef\third@{#1&,@} \loopcount=0
\loop \expandafter\group@get\third@ \advance\loopcount by 1
\ifnum\loopcount<10 \repeat}
\def\pepsims#1#2{\xdef\prfx{pep}
\def\sim@set{\expandafter\residue@get\second@
\ifx\first@\ampers@nd
\else \advance\innerloopcount by 1
\expandafter\xdef\csname simpair\third@\first@\endcsname{1}
\expandafter\xdef\csname simpair\first@\third@\endcsname{1}
\xdef\second@{\csname sequence\the\loopcount\endcsname} \sim@set
\fi}
\xdef\first@{#1} \make@upper \xdef\third@{\first@}
\xdef\last@{#2} \xdef\second@{#2 &@} \innerloopcount=0 \sim@set
\expandafter\xdef\csname \prfx sim\third@\endcsname{%
(\the\innerloopcount)\last@}}
\def\DNAsims#1#2{\xdef\prfx{DNA}
\def\sim@set{\expandafter\residue@get\second@
\ifx\first@\ampers@nd
\else \advance\innerloopcount by 1
\xdef\second@{\csname sequence\the\loopcount\endcsname} \sim@set
\fi}
\xdef\first@{#1} \make@upper \xdef\third@{\first@}
\xdef\last@{#2} \xdef\second@{#2 &@} \innerloopcount=0 \sim@set
\expandafter\xdef\csname \prfx sim\third@\endcsname{%
(\the\innerloopcount)\last@}}
\def\fingerprint#1{%
\ifnum #1 >0
\residuesperline*{#1}
\def\finger@linenum{#1}
\shownames{left}
\hidenumbering
\rulersteps{100}
\nomatchresidues{}{Gray10}{}{}
\loopcount=0
\loop
\advance\loopcount by 1
\separationline{\the\loopcount}
\ifnum\loopcount<\seq@count\repeat
\fi}
\def\printPDBlist#1{%
\xdef\list@{}
\xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
\xdef\first@{\list@ &}
\ifx\first@\ampers@nd
\else
\xdef\first@{\list@ @}
\loop
\expandafter\get@item\first@
\fourth@
\ifx\first@@\ampers@nd\else{,\ }\repeat
\fi
}
\def\messagePDBlist#1{%
\xdef\list@{}
\xdef\temp@{#1,,,:,,,,@} \expandafter\test@PDB\temp@
\xdef\first@{\list@ &}
\ifx\first@\ampers@nd
\else
\message{(#1:}
\xdef\first@{\list@ @}%
\loop%
\expandafter\get@item\first@%
\message{\fourth@}%
\ifx\first@@\ampers@nd\else\repeat%
\message{)}
\fi
}
\def\shaderegion#1#2#3#4{%
\regionalshadetrue
\xdef\seq@{#1}
\xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
\xdef\first@{\seq@ @} \expandafter\check@letter\first@
\xdef\first@{\seq@}
\ifletter \get@name@number \xdef\seq@{\first@} \fi
\ifnum\seq@>\seq@count
\message{<Ignored `\seq@' in \noexpand\shaderegion or \noexpand\shadeblock>}
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\loopcount=\seq@regions
\advance\loopcount by 1
\xdef\seq@regions{\the\loopcount}
\expandafter\xdef\csname fgseqregion\the\loopcount\endcsname{#3}
\expandafter\xdef\csname bgseqregion\the\loopcount\endcsname{#4}
\xdef\list@{#2,&}
\xdef\temp@@{shade}
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\ifx\list@\ampers@nd
\else
\loop
\xdef\list@{\list@ @}
\expandafter\get@regions\list@
\ifx\list@\ampers@nd\else\repeat
\fi
\fi
}
\def\shadeblock#1#2#3#4{%
\xdef\seq@{#1}
\xdef\@ll{yes}
\shaderegion{#1}{#2}{#3}{#4}
\xdef\@ll{}
}
\def\tintregion#1#2{%
\xdef\seq@{#1}
\xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
\xdef\first@{\seq@ @} \expandafter\check@letter\first@
\xdef\first@{\seq@}
\ifletter \get@name@number \xdef\seq@{\first@} \fi
\ifnum\seq@>\seq@count
\message{<Ignored seq `\seq@' in \noexpand\tintregion or \noexpand\tintblock>}
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
\xdef\temp@@{tint} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\ifx\list@\ampers@nd
\else
\loop
\xdef\list@{\list@ @}
\expandafter\get@tintregions\list@
\ifx\list@\ampers@nd\else\repeat
\fi
\fi
}
\def\tintblock#1#2{%
\xdef\seq@{#1}
\xdef\@ll{yes}
\tintregion{#1}{#2}
\xdef\@ll{}
}
\def\tintdefault#1{%
\xdef\first@{#1}
\xdef\second@{strong}
\ifx\first@\second@
\xdef\light@{LightLightLight}
\else
\xdef\second@{medium}
\ifx\first@\second@
\xdef\light@{LightLight}
\else
\xdef\second@{weak}
\ifx\first@\second@
\xdef\light@{Light}
\else
\xdef\light@{LightLight}
\fi\fi\fi
}
\def\lowerregion#1#2{%
\xdef\seq@{#1}
\xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
\xdef\first@{\seq@ @} \expandafter\check@letter\first@
\xdef\first@{\seq@}
\ifletter \get@name@number \xdef\seq@{\first@} \fi
\ifnum\seq@>\seq@count
\message{<Ignored seq `\seq@' in \noexpand\lowerregion or \noexpand\lowerblock>}
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
\xdef\temp@@{lower} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\ifx\list@\ampers@nd
\else
\loop
\xdef\list@{\list@ @}
\expandafter\get@lowerregions\list@
\ifx\list@\ampers@nd\else\repeat
\fi
\fi
}
\def\lowerblock#1#2{%
\xdef\seq@{#1}
\xdef\@ll{yes}
\lowerregion{#1}{#2}
\xdef\@ll{}
}
\def\emphregion#1#2{%
\xdef\seq@{#1}
\xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
\xdef\first@{\seq@ @} \expandafter\check@letter\first@
\xdef\first@{\seq@}
\ifletter \get@name@number \xdef\seq@{\first@} \fi
\ifnum\seq@>\seq@count
\message{<Ignored seq `\seq@' in \noexpand\emphregion or \noexpand\emphblock>}
\else
\ifx\@ll\yes \xdef\@ll{y}\else \xdef\@ll{n}\fi
\xdef\list@{#2,&}
\xdef\temp@@{emph} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\ifx\list@\ampers@nd
\else
\loop
\xdef\list@{\list@ @}
\expandafter\get@emphregions\list@
\ifx\list@\ampers@nd\else\repeat
\fi
\fi
}
\def\emphblock#1#2{%
\xdef\seq@{#1}
\xdef\@ll{yes}
\emphregion{#1}{#2}
\xdef\@ll{}
}
\def\emphdefault#1{\def\res@style{\csname text#1\endcsname}}
\def\frameblock#1#2#3{%
\xdef\seq@{#1}
\xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
\xdef\first@{\seq@ @} \expandafter\check@letter\first@
\xdef\first@{\seq@}
\ifletter \get@name@number \xdef\seq@{\first@} \fi
\ifnum\seq@>\seq@count
\message{<Ignored seq `\seq@' in \noexpand\frameblock>}
\else
\xdef\@ll{#3}
\xdef\list@{#2,&}
\xdef\temp@@{frame} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\ifx\list@\ampers@nd
\else
\loop
\xdef\list@{\list@ @}
\expandafter\get@frameregions\list@
\ifx\list@\ampers@nd\else\repeat
\fi
\fi
}
\def\changeshadingcolors#1#2#3{%
\xdef\seq@{#1}
\xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
\xdef\first@{\seq@ @} \expandafter\check@letter\first@
\xdef\first@{\seq@}
\ifletter \get@name@number \xdef\seq@{\first@} \fi
\ifnum\seq@>\seq@count
\message{<Ignored seq `\seq@' in \noexpand\changeshadingcolors>}
\else
\xdef\@ll{#3}
\xdef\list@{#2,&}
\xdef\temp@@{shading} \loopcount=0
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\ifx\list@\ampers@nd
\else
\loop
\xdef\list@{\list@ @}
\expandafter\get@shadingregions\list@
\ifx\list@\ampers@nd\else\repeat
\fi
\fi
}
\def\bargraphstretch#1{\def\b@r@stretch{#1}}
\def\colorscalestretch#1{\def\sc@le@stretch{#1}}
\def\rm@@measure#1#2@{%
\xdef\test@{#1}
\ifx\test@\ampers@nd
\else
\expandafter\check@char\test@
\ifnumber\xdef\first@{\first@ #1}
\xdef\second@{#2 &@}
\expandafter\rm@@measure\second@
\fi
\fi
}
\def\rm@measure#1.#2@{\xdef\first@{#1.}\xdef\second@{#2 @}\xdef\third@{#1}\expandafter\rm@@measure\second@}
\def\pm@calc{%
\temp@@length=100000sp
\temp@@length=\g@min\temp@@length
\innerloopcount=\temp@@length
\xdef\min@{\the\innerloopcount}
\arrow@height=\temp@@length
\temp@@length=100000sp
\temp@@length=\g@max\temp@@length
\advance\temp@@length by -\arrow@height
\innerloopcount=\temp@@length
\divide\innerloopcount by 100
\ifnum\innerloopcount=0 \innerloopcount=1 \fi
\xdef\m@x{\the\innerloopcount}
\xdef\test@{\g@min pt}
\setlength\arrow@width{\test@}
\xdef\test@{\g@max pt}
\setlength\arrow@height{\test@}
\advance\arrow@height by -\arrow@width
\ifdim\arrow@width<0pt\temp@@length=-\arrow@width\xdef\test@{y}\else\temp@@length=\arrow@width\xdef\test@{n}\fi
\ifdim\arrow@height>0pt
\ifx\test@\n@ \xdef\test@{y} \else \xdef\test@{n} \fi
\ifdim\temp@@length<\arrow@height\temp@@length=\arrow@height\fi
\else
\ifdim\temp@@length>-\arrow@height\temp@@length=\arrow@height\fi
\fi
\ifdim\temp@@length<100pt\arrow@width=100\arrow@width\arrow@height=100\arrow@height\else
\ifdim\temp@@length<10pt\arrow@width=1000\arrow@width\arrow@height=1000\arrow@height\else
\ifdim\temp@@length<1pt\arrow@width=10000\arrow@width\arrow@height=10000\arrow@height\else
\ifdim\temp@@length<0.1pt\arrow@width=100000\arrow@width\arrow@height=100000\arrow@height\else
\ifdim\temp@@length<0.01pt\arrow@width=1000000\arrow@width \arrow@height=1000000\arrow@height\else
\ifdim\temp@@length<0.001pt\arrow@width=10000000\arrow@width \arrow@height=10000000\arrow@height\else
\ifdim\temp@@length<0.0001pt\arrow@width=100000000\arrow@width \arrow@height=100000000\arrow@height\else
\ifdim\temp@@length<0.00001pt\arrow@width=1000000000\arrow@width \arrow@height=1000000000\arrow@height
\fi\fi\fi\fi\fi\fi\fi\fi
\ifx\test@\y@
\xdef\pm@{0}
\else
\xdef\test@{-\the\arrow@height @}
\expandafter\rm@measure\test@
\divide\arrow@width by \third@
\xdef\pm@{\the\arrow@width @}
\expandafter\rm@measure\pm@
\xdef\pm@{\first@}
\fi
}
\def\read@graph{%
\bgroup
\immediate\openin\structurefile = \fill@char\relax
\ifeof\structurefile
\PackageError{TeXshade}
{File `\fill@char' not found}
{\MessageBreak
The file you specified is missing or you have \MessageBreak
misspelled it. \MessageBreak\MessageBreak
No feature graph will be displayed. \MessageBreak
Type <return> to proceed. \MessageBreak
Type X <return> to quit. \MessageBreak
}
\immediate\closein\structurefile\egroup
\else
\ifx\g@min\comm@
\def\par@{}
\xdef\g@min{,} \xdef\g@max{,}
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\second@{\test@ @}
\expandafter\check@letter\second@
\ifletter
\xdef\second@{\expandafter\string\readline}
\xdef\second@{\second@ @}
\expandafter\firstchar@get\second@
\if\first@ - \numbertrue\fi
\fi
\ifnumber
\temp@@length=1pt
\temp@@length=\test@\temp@@length
\innerloopcount=\temp@@length
\ifx\g@min\comm@ \xdef\min@{\test@ pt} \xdef\g@min{\test@}
\else
\ifdim\temp@@length<\min@\relax \xdef\min@{\the\temp@@length} \xdef\g@min{\test@} \fi\fi%
\ifx\g@max\comm@ \xdef\m@x{\test@ pt} \xdef\g@max{\test@}
\else
\ifdim\temp@@length>\m@x\relax \xdef\m@x{\the\temp@@length} \xdef\g@max{\test@} \fi\fi%
\fi
\fi
\ifeof\structurefile\else\repeat
\fi
\immediate\closein\structurefile
\pm@calc
\expandafter\temp@count=\csname seq@start\seq@\endcsname
\advance\temp@count by -1
\xdef\temp@@@{n}
\immediate\openin\structurefile = \fill@char\relax
\loop
\read\structurefile to \readline
\xdef\test@{\expandafter\string\readline}
\ifx\test@\par@
\else
\xdef\second@{\test@ @}
\expandafter\check@letter\second@
\ifletter
\xdef\second@{\expandafter\string\readline}
\xdef\second@{\second@ @}
\expandafter\firstchar@get\second@
\if\first@ - \numbertrue
\else
\if\first@ N
\expandafter\firstchar@get\third@
\if\first@ a
\expandafter\firstchar@get\third@
\if\first@ N
\advance\temp@count by 1
\ifnum\temp@count=0 \temp@count=1 \fi
\ifnum\temp@count<\st@rt
\else
\ifnum\temp@count>\st@p
\else
\ifx\temp@@@\n@
\xdef\temp@@@{N}
\else
\xdef\temp@@@{\temp@@@,N}
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\ifnumber
\advance\temp@count by 1
\ifnum\temp@count=0 \temp@count=1 \fi
\ifnum\temp@count<\st@rt
\else
\ifnum\temp@count>\st@p
\else
\temp@@length=100000sp
\temp@@length=\test@\temp@@length
\innerloopcount=\temp@@length
\advance\innerloopcount by 1
\xdef\test@{\pm@ pt}
\ifdim\test@=0pt
\advance\innerloopcount by -\min@
\else
\ifx\b@r\n@
\advance\innerloopcount by -\min@
\fi
\fi
\divide\innerloopcount by \m@x
\ifx\temp@@@\n@
\xdef\temp@@@{\the\innerloopcount}
\else
\xdef\temp@@@{\temp@@@,\the\innerloopcount}
\fi
\fi
\fi
\fi
\fi
\ifeof\structurefile\else\repeat
\immediate\closein\structurefile
\xdef\temp@@@{\temp@@@,@} \xdef\temp@@{y}
\fi
\egroup
}
\def\sort@gstack{%
\expandafter\get@fromstack\last@
\ifx\first@\ampers@nd
\xdef\tmpstack{\tmpstack\f@text@&;&;&;&;@}
\else
\ifnum\loopcount<\second@
\xdef\tmpstack{\tmpstack\f@text@\first@;\second@;\third@;\fourth@;\last@}
\else
\xdef\tmpstack{\tmpstack\first@;\second@;\third@;\fourth@;}
\sort@gstack
\fi\fi
}
\def\get@gregion#1..#2,#3&{%
\xdef\st@rt{#1} \xdef\st@p{#2} \xdef\list@{#3}
}
\def\do@bargraph{%
\expandafter\get@gregion\list@
\expandafter\ifnum\csname seq@start\seq@\endcsname>\st@rt
\else
\xdef\temp@@{n}
\xdef\b@r{y}
\xdef\pm@{0}
\xdef\temp@@@{\fill@char,@}
\expandafter\check@letter\temp@@@
\ifletter
\read@graph
\else
\ifx\g@min\comm@ \xdef\g@min{0} \fi
\ifx\g@max\comm@ \xdef\g@max{100} \fi
\pm@calc
\xdef\temp@@@{\fill@char,@}
\xdef\temp@@{y}
\fi
\ifx\temp@@\y@
\loopcount=\st@rt
\xdef\tmpstack{}
\loop
\expandafter\get@item\temp@@@
\xdef\temp@@@{\first@}
\xdef\style@{bar[\pm@,0]:\fourth@[\f@color]}
\xdef\tmpstack{\tmpstack\f@text@;\the\loopcount;\the\loopcount;\style@;}
\advance\loopcount by 1
\ifnum\loopcount=0 \loopcount=1 \fi
\ifnum\loopcount>\st@p
\else\repeat
\xdef\f@text@{\tmpstack} \xdef\tmpstack{}
\xdef\last@{\csname stack@\bottop@\seq@\endcsname}
\sort@gstack
\expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
\fi
\fi
\xdef\list@{\list@ &}
\ifx\list@\ampers@nd\else\do@bargraph\fi
}
\def\do@colorgraph{%
\expandafter\get@gregion\list@
\expandafter\ifnum\csname seq@start\seq@\endcsname>\st@rt
\else
\xdef\temp@@{n}
\xdef\b@r{n}
\xdef\pm@{0}
\xdef\temp@@@{\fill@char,@}
\expandafter\check@letter\temp@@@
\ifletter
\read@graph
\else
\ifx\g@min\comm@ \xdef\g@min{0} \fi
\ifx\g@max\comm@ \xdef\g@max{100} \fi
\pm@calc
\xdef\temp@@@{\fill@char,@}
\xdef\temp@@{y}
\fi
\ifx\temp@@\y@
\loopcount=\st@rt
\xdef\tmpstack{}
\loop
\xdef\last@{\csname stack@\bottop@\seq@\endcsname}
\expandafter\get@item\temp@@@
\xdef\temp@@@{\first@}
\ifx\fourth@\N@
\xdef\style@{color:50[White]}
\else
\ifnum\fourth@<1 \xdef\fourth@{1} \fi
\innerloopcount=\fourth@
\advance\innerloopcount by 4
\divide\innerloopcount by 5
\multiply\innerloopcount by 5
\ifnum\innerloopcount>100 \innerloopcount=100 \fi
\xdef\style@{color:50[\f@color\the\innerloopcount]}
\fi
\xdef\tmpstack{\tmpstack\f@text@;\the\loopcount;\the\loopcount;\style@;}
\advance\loopcount by 1
\ifnum\loopcount=0 \loopcount=1 \fi
\ifnum\loopcount>\st@p
\else\repeat
\xdef\f@text@{\tmpstack} \xdef\tmpstack{}
\xdef\last@{\csname stack@\bottop@\seq@\endcsname}
\sort@gstack
\expandafter\xdef\csname stack@\bottop@\seq@\endcsname{\tmpstack}
\fi
\fi
\xdef\list@{\list@ &}
\ifx\list@\ampers@nd\else\do@colorgraph\fi
}
\def\feature#1#2#3#4#5{%
\xdef\bottop@{#1}
\xdef\temp@{top}
\ifx\bottop@\temp@ \topfeaturetrue\fi
\xdef\temp@{ttop}
\ifx\bottop@\temp@ \ttopfeaturetrue\fi
\xdef\temp@{tttop}
\ifx\bottop@\temp@ \tttopfeaturetrue\fi
\xdef\temp@{ttttop}
\ifx\bottop@\temp@ \ttttopfeaturetrue\fi
\xdef\temp@{bottom}
\ifx\bottop@\temp@ \bottomfeaturetrue\fi
\xdef\temp@{bbottom}
\ifx\bottop@\temp@ \bbottomfeaturetrue\fi
\xdef\temp@{bbbottom}
\ifx\bottop@\temp@ \bbbottomfeaturetrue\fi
\xdef\temp@{bbbbottom}
\ifx\bottop@\temp@ \bbbbottomfeaturetrue\fi
\xdef\seq@{#2}
\xdef\temp@{consensus} \ifx\seq@\temp@ \xdef\seq@{0} \fi
\xdef\first@{\seq@ @} \expandafter\check@letter\first@
\xdef\first@{\seq@}
\ifletter \get@name@number \xdef\seq@{\first@} \fi
\ifnum\seq@>\seq@count
\message{<Ignored seq `\seq@' in \noexpand\feature>}
\else
\ifnum\seq@>-1
\xdef\temp@{#4::&}\expandafter\test@fill\temp@
\xdef\last@{bar}
\ifx\second@@\last@
\xdef\last@{hydrophobicity}
\ifx\last@\fourth@
\xdef\second@@{bh}
\else
\xdef\last@{molweight}
\ifx\last@\fourth@
\xdef\second@@{bm}
\else
\xdef\last@{charge}
\ifx\last@\fourth@
\xdef\second@@{bc}
\else
\xdef\last@{conservation}
\ifx\last@\fourth@
\xdef\second@@{bcons}
\fi
\fi
\fi
\fi
\fi
\xdef\last@{color}
\ifx\second@@\last@
\xdef\last@{hydrophobicity}
\ifx\last@\fourth@
\xdef\second@@{ch}
\else
\xdef\last@{molweight}
\ifx\last@\fourth@
\xdef\second@@{cm}
\else
\xdef\last@{charge}
\ifx\last@\fourth@
\xdef\second@@{cc}
\else
\xdef\last@{conservation}
\ifx\last@\fourth@
\xdef\second@@{ccons}
\fi
\fi
\fi
\fi
\fi
\xdef\last@{bar}
\ifx\second@@\last@
\xdef\list@{#3,&}
\xdef\style@{#4}
\def\f@text@{#5}
\do@bargraph
\xdef\temp@{bottom}
\ifx\bottop@\temp@ \xdef\bottom@stretch{y}\fi
\xdef\temp@{bbottom}
\ifx\bottop@\temp@ \xdef\bbottom@stretch{y}\fi
\xdef\temp@{bbbottom}
\ifx\bottop@\temp@ \xdef\bbbottom@stretch{y}\fi
\xdef\temp@{bbbbottom}
\ifx\bottop@\temp@ \xdef\bbbbottom@stretch{y}\fi
\else
\xdef\last@{color}
\ifx\second@@\last@
\xdef\list@{#3,&}
\xdef\style@{#4}
\def\f@text@{#5}
\do@colorgraph
\else
\xdef\f@@color{\f@color}
\def\f@text@{#5}
\xdef\f@color{\f@@color}
\xdef\temp@{#4&}
\ifx\temp@\ampers@nd
\xdef\list@{#3,&}
\xdef\style@{&}
\def\f@text@{#5}
\else
\xdef\last@{restriction}
\ifx\second@@\last@
\xdef\temp@{\bottop@ @}
\expandafter\firstchar@get\temp@
\xdef\temp@{y}
\if\first@ t
\xdef\style@{fill:\kern0.9\box@width$\blacktriangledown$[\f@color]}
\else
\xdef\style@{fill:\kern0.9\box@width$\blacktriangle$[\f@color]}
\fi
\xdef\f@text@{\kern0.9\box@width#5}
\else
\xdef\last@{bh}
\ifx\second@@\last@
\ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi
\xdef\style@{plot[bar]:Hydro[\f@color][-53]}
\else
\xdef\last@{bm}
\ifx\second@@\last@
\ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi
\xdef\style@{plot[bar]:molw[\f@color][0]}
\else
\xdef\last@{bc}
\ifx\second@@\last@
\ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi
\xdef\style@{plot[bar]:charge[\f@color][-50]}
\else
\xdef\last@{bcons}
\ifx\second@@\last@
\ifx\f@color\gr@ydef@ult\xdef\f@color{Gray50}\fi
\xdef\last@{T-Coffee}
\ifx\f@color\last@
\xdef\T@coffee@bcons{y}
\xdef\f@color{Gray50}
\fi
\xdef\style@{cons[bar]:cons[\f@color][0]}
\else
\xdef\last@{ch}
\ifx\second@@\last@
\ifx\f@color\gr@ydef@ult\xdef\f@color{RedGreen}\fi
\xdef\style@{plot[color]:Hydro[\f@color][-53]}
\else
\xdef\last@{cm}
\ifx\second@@\last@
\ifx\f@color\gr@ydef@ult\xdef\f@color{Gray}\fi
\xdef\style@{plot[color]:molw[\f@color][0]}
\else
\xdef\last@{cc}
\ifx\second@@\last@
\ifx\f@color\gr@ydef@ult\xdef\f@color{RedBlue}\fi
\xdef\style@{plot[color]:charge[\f@color][-50]}
\else
\xdef\last@{ccons}
\ifx\second@@\last@
\ifx\f@color\gr@ydef@ult\xdef\f@color{ColdHot}\fi
\xdef\last@{T-Coffee}
\ifx\f@color\last@
\xdef\T@coffee@ccons{y}
\xdef\f@color{TC}
\fi
\xdef\style@{cons[color]:cons[\f@color][0]}
\else
\xdef\style@{#4} \expandafter\getarrow@shape\temp@
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\xdef\list@{#3,&}
\xdef\@ll{\f@text@}
\xdef\temp@@{\bottop@}
\xdef\temp@{#3,,,:,,,,@} \expandafter\test@PDB\temp@
\fi
\loopcount=0
\ifx\list@\ampers@nd
\else
\loop
\advance\loopcount by 1\relax
\xdef\list@{\list@ @}
\expandafter\get@fregions\list@
\ifx\list@\ampers@nd\else\repeat
\fi
\fi\fi\fi
\fi
}
\def\showfeaturename#1#2{\expandafter\xdef\csname featuretextn@me#1\endcsname{#2}}
\def\showfeaturestylename#1#2{\expandafter\xdef\csname featurestylesn@me#1\endcsname{#2}}
\def\hidefeaturename#1{\expandafter\xdef\csname featuretextn@me#1\endcsname{}}
\def\hidefeaturenames{\xdef\featuretextn@mettop{}\xdef\featuretextn@metop{}\xdef\featuretextn@mebottom{}\xdef\featuretextn@mebbottom{}
\xdef\featuretextn@metttop{}\xdef\featuretextn@mettttop{}\xdef\featuretextn@mebbbbottom{}\xdef\featuretextn@mebbbottom{}}
\def\hidefeaturestylename#1{\expandafter\xdef\csname featurestylesn@me#1\endcsname{}}
\def\hidefeaturestylenames{\xdef\featurestylesn@mettop{}\xdef\featurestylesn@metop{}\xdef\featurestylesn@mebottom{}\xdef\featurestylesn@mebbottom{}
\xdef\featurestylesn@metttop{}\xdef\featurestylesn@mettttop{}\xdef\featurestylesn@mebbbbottom{}\xdef\featurestylesn@mebbbottom{}}
\def\seqtype#1{\xdef\seq@type{#1}
\if\seq@type P \xdef\prefix@{pep}
\else \if\seq@type p \xdef\seq@type{P} \xdef\prefix@{pep}
\else \xdef\seq@type{N} \xdef\prefix@{DNA} \fi\fi}
\def\nameseq#1#2{%
\xdef\first@{#1 @} \expandafter\check@letter\first@
\xdef\first@{#1} \ifletter \get@name@number \fi
\expandafter\xdef\csname newseqname\first@\endcsname{#2}
}
\newcommand\threshold[2][n]{%
\xdef\first@{#1}
\ifx\first@\n@
\xdef\thresh@ld{#2}
\else
\all@shadetrue
\ifnum\first@>#2
\xdef\thresh@ld{#2}
\xdef\all@thresh@ld{#1}
\else
\xdef\thresh@ld{#1}
\xdef\all@thresh@ld{#2}
\fi
\fi
}
\def\constosingleseq#1{%
\xdef\first@{#1 @} \expandafter\check@letter\first@
\xdef\first@{#1} \ifletter \get@name@number \fi
\ifnum\first@>\seq@count
\message{<Ignored seq `#1' in \noexpand\constosingleseq>}
\else
\ifnum\first@>0 \xdef\cons@num{\first@} \hideconsensus\fi\fi
}
\def\constoallseqs{\xdef\cons@num{0}}
\def\residuesperline{%
\def\@rplfix*##1{%
\res@perline=##1
\ifnum\res@perline<1 \res@perline=1\fi \rpl@fixtrue}
\def\@rplvar ##1{%
\res@perline=##1
\ifnum\res@perline<5 \res@perline=5\fi \rpl@fixfalse}
\def\decide@{\ifx\l@@k * \let\next\@rplfix \else \let\next\@rplvar \fi \next}
\futurelet\l@@k\decide@}
\def\numberingwidth#1{\def\num@width{#1}}
\def\charstretch#1{%
\def\char@stretch{#1}
\xdef\temp@{\char@stretch .00@} \expandafter\coord@get\temp@ \loopcount=\c@@rd
\multiply \loopcount by 7
\divide \loopcount by 10
\ifnum\loopcount<10
\xdef\temp@{0\the\loopcount @}
\else
\xdef\temp@{\the\loopcount @}
\fi
\expandafter\decimal@B\temp@
\ifnum\loopcount>99
\xdef\char@stretch@W{#1}
\else
\xdef\char@stretch@W{\temp@}
\fi
}
\def\linestretch#1{\def\line@stretch{#1}}
\def\logostretch#1{%
\def\logo@stretch{#1}
\setlength\temp@@length{1000sp}
\setlength\temp@@length{\logo@stretch\temp@@length}
\loopcount=\temp@@length
\xdef\logo@stretch@IOOO{\the\loopcount}
}
\def\noblockskip{\def\block@skip{\vspace{0pt}}}
\def\smallblockskip{\def\block@skip{\vspace{\baselineskip}}}
\def\medblockskip{\def\block@skip{\vspace{1.5\baselineskip}}}
\def\bigblockskip{\def\block@skip{\vspace{2\baselineskip}}}
\def\vblockspace#1{\def\block@skip{\vspace{#1}}}
\def\topspace#1{\def\t@sp@ce{#1}}
\def\ttopspace#1{\def\tt@sp@ce{#1}}
\def\tttopspace#1{\def\ttt@sp@ce{#1}}
\def\ttttopspace#1{\def\tttt@sp@ce{#1}}
\def\bottomspace#1{\def\b@sp@ce{#1}}
\def\bbottomspace#1{\def\bb@sp@ce{#1}}
\def\bbbottomspace#1{\def\bbb@sp@ce{#1}}
\def\bbbbottomspace#1{\def\bbbb@sp@ce{#1}}
\def\rulerspace#1{\def\ruler@sp@ce{#1}}
\def\fixblockspace{\fix@true}
\def\flexblockspace{\fix@false}
\def\nosepline{\def\seq@skip{\relax}}
\def\smallsepline{\def\seq@skip{\vspace{3pt}}\def\sep@space{3pt}}
\def\medsepline{\def\seq@skip{\vspace{6pt}}\def\sep@space{6pt}}
\def\bigsepline{\def\seq@skip{\vspace{12pt}}\def\sep@space{12pt}}
\def\vsepspace#1{\def\seq@skip{\vspace{#1}}\xdef\sep@space{#1}}
\def\separationline#1{%
\xdef\first@@{#1}
\xdef\first@{#1 @} \expandafter\check@letter\first@
\xdef\first@{#1}
\ifletter \get@name@number \xdef\first@@{\first@} \fi
\ifnum\first@@>\seq@count \xdef\first@@{1}
\else
\ifnum\first@@<0 \xdef\first@@{1}
\else
\expandafter\def\csname seq@gap\first@@\endcsname{yes}
\loopcount=\seq@gap@num
\advance\loopcount by 1
\xdef\seq@gap@num{\the\loopcount}
\fi
\fi}
\newcommand{\shadingmode}[2][-1]{%
\T@coffeefalse
\xdef\last@{#2}
\xdef\first@{identical}
\ifx\first@\last@
\simmodefalse \funcmodefalse
\xdef\second@{#1 @} \expandafter\check@letter\second@
\ifnumber \all@shadetrue
\ifnum#1<0 \all@shadefalse
\else
\ifnum#1>100 \xdef\all@thresh@ld{100}
\else
\xdef\all@thresh@ld{#1}
\fi\fi
\else
\xdef\last@{#1}
\xdef\first@{allmatchspecial}
\ifx\last@\first@
\xdef\all@thresh@ld{100} \all@shadetrue
\fi
\fi
\else
\xdef\first@{similar}
\ifx\first@\last@
\simmodetrue \funcmodefalse
\xdef\second@{#1 @} \expandafter\check@letter\second@
\ifnumber \all@shadetrue
\ifnum#1<0 \all@shadefalse
\else
\ifnum#1>100 \xdef\all@thresh@ld{100}
\else
\xdef\all@thresh@ld{#1}
\fi\fi
\else
\xdef\last@{#1}
\xdef\first@{allmatchspecial}
\ifx\last@\first@
\xdef\all@thresh@ld{100} \all@shadetrue
\fi
\fi
\else
\xdef\first@{functional}
\ifx\first@\last@
\if\seq@type N \message{<No functional shading on DNA sequences>}
\else \simmodefalse \funcmodetrue \func@shading{#1}
\xdef\seq@type{P} \xdef\prefix@{pep} \fi
\else
\xdef\first@{T-Coffee}
\ifx\first@\last@
\simmodefalse \funcmodefalse \T@coffeetrue
\xdef\second@{#1 @} \expandafter\check@letter\second@
\ifletter \xdef\TC@first@{#1}\include@T@coffee\fi
\else
\xdef\first@{diverse}
\ifx\first@\last@
\xdef\last@{#1}
\ifnum\last@>\seq@count \xdef\last@{1}\fi
\ifnum\last@<1 \xdef\last@{1}\fi
\simmodetrue \funcmodefalse
\threshold{0}
\xdef\divref@{\last@}
\constosingleseq{\last@}
\nomatchresidues{Black}{White}{lower}{up}
\similarresidues{Black}{White}{lower}{up}
\conservedresidues{Black}{White}{{.}}{up}
\allmatchresidues{Black}{White}{{.}}{up}
\gapchar{-}
\hideconsensus
\else
\message{<Unknown shading mode - using `similar'>}
\simmodetrue \funcmodefalse
\fi\fi\fi\fi\fi}
\def\hideallmatchpositions{\xdef\all@out{y}}
\def\showallmatchpositions{\xdef\all@out{n}}
\newcommand\allmatchspecial[1][100]{%
\ifnum#1<0
\xdef\all@thresh@ld{0}
\else
\ifnum#1>100
\xdef\all@thresh@ld{100}
\else
\xdef\all@thresh@ld{#1}
\fi\fi
\all@shadetrue}
\def\allmatchspecialoff{\all@shadefalse}
\def\stopchar#1{\def\st@p@char{#1}}
\def\gapchar#1{%
\xdef\first@{rule}\xdef\second@{#1}
\ifx\first@\second@\def\gap@char{o}
\else\def\gap@char{#1}\fi}
\def\gaprule#1{\def\gap@rulethick{#1}}
\def\domaingaprule#1{\def\domgap@rulethick{#1}}
\newcommand{\setends}[3][&]{%
\xdef\start@seq{#2}
\xdef\temp@{consensus}
\ifx\start@seq\temp@
%%% \message{<\noexpand\setends does not accept `consensus'>}
\xdef\start@seq{0}
%%%%%%%%%%
\xdef\second@{#3@} \expandafter\get@nums\second@
\xdef\start@num{\first@} \xdef\end@num{\second@}
\ifnum\start@num<1 \xdef\start@num{1}\fi
\ifnum\end@num<\start@num \xdef\end@num{\start@num}\fi
\loopcount=\end@num
\advance\loopcount by 1
\advance\loopcount by -\start@num
\xdef\end@num{\the\loopcount}
\start@false
%%%%%%%%%%
\else
\xdef\first@{\start@seq @} \expandafter\check@letter\first@
\xdef\first@{\start@seq}
\ifletter \get@name@number \xdef\start@seq{\first@} \fi
\ifnum\start@seq>\seq@count
\message{<\noexpand\setends{} error: sequence `#2' not defined>}
\xdef\start@seq{0}
\else
\ifnum\start@seq<1
\message{<\noexpand\setends{} error: sequence `#2' not defined>}
\xdef\start@seq{0}
\else
\xdef\second@{#3@} \expandafter\get@nums\second@
\xdef\start@num{\first@} \xdef\end@num{\second@}
\ifnum\start@num=0 \xdef\allow@zero{y}\fi
\ifnum\end@num=0 \xdef\allow@zero{y}\fi
\start@false
\fi
\fi
\fi
\xdef\first@{#1}\ifx\first@\ampers@nd\else\startnumber{#2}{#1}\fi
}
\newcommand{\startnumber}[3][&]{%
\xdef\first@{#2} \xdef\second@{consensus}
\ifx\first@\second@
\ifnum#3=0 \xdef\allow@zero{y} \fi
\expandafter\xdef\csname seq@start0\endcsname{#2}
\cons@count=#3 \advance\cons@count by -1\relax
\expandafter\xdef\csname res@count0\endcsname{\the\cons@count}
\else
\xdef\first@{#2 @} \expandafter\check@letter\first@
\xdef\first@{#2} \ifletter \get@name@number \fi
\ifnum\first@>\seq@count \message{<Ignored seq `#2' in \noexpand\startnumber>}
\else
\xdef\second@{#3}
\ifnum\second@=0 \xdef\allow@zero{y} \fi
\expandafter\xdef\csname seq@start\first@\endcsname{\second@}
\res@count=\second@
\advance\res@count by -1
\expandafter\xdef\csname res@count\first@\endcsname{\the\res@count}
\fi
\fi
\xdef\first@{#1}\ifx\first@\ampers@nd\else\setends{#2}{#1}\fi
}
\def\seqlength#1#2{%
\xdef\first@{#1 @} \expandafter\check@letter\first@
\xdef\first@{#1} \ifletter \get@name@number \fi
\ifnum\first@>\seq@count \message{<Ignored seq `#1' in \noexpand\seqlength>}
\else
\xdef\second@{#2} \ifnum\second@<0 \xdef\second@{1} \fi
\expandafter\xdef\csname seq@len\first@\endcsname{\second@}
\fi}
\newcommand\shownumbering[2][n]{%
\xdef\first@{#1}\ifx\first@\n@\else\xdef\numbering@fg{#1}\fi
\xdef\first@{#2}
\xdef\second@{left}
\ifx\first@\second@ \numbers@lefttrue \numbers@rightfalse \numbers@true \fi
\xdef\second@{right}
\ifx\first@\second@ \numbers@leftfalse \numbers@righttrue \numbers@true \fi
\xdef\second@{leftright}
\ifx\first@\second@ \numbers@lefttrue \numbers@righttrue \numbers@true \fi
}
\def\hidenumbering{\numbers@false}
\def\hidenumber#1{\xdef\first@{#1,&,@} \hidenumber@}
\newcommand\shownames[2][n]{%
\xdef\first@{#1}\ifx\first@\n@\else\xdef\names@fg{#1}\fi
\xdef\first@{#2} \xdef\second@{left}
\ifx\first@\second@ \names@rightfalse \else \names@righttrue \fi
\names@true}
\def\hidenames{\names@false}
\def\hidename#1{\xdef\first@{#1,&,@} \hidename@}
\def\hideresidues{\hidechartrue}
\def\showresidues{\hidecharfalse}
\def\alignment#1{%
\xdef\first@{#1}
\xdef\temp@{left}
\ifx\first@\temp@ \xdef\c@factor{0}
\else
\xdef\temp@{center}
\ifx\first@\temp@ \xdef\c@factor{0.5}
\else
\xdef\temp@{right}
\ifx\first@\temp@ \xdef\c@factor{1}
\fi\fi\fi}
\def\donotshade#1{%
\xdef\temp@{consensus}
\xdef\first@{#1}
\ifx\first@\temp@
\consensuscolors{Black}{White}{Black}{White}{Black}{White}
\else
\xdef\first@{#1,&,@} \donot@shade
\fi}
\def\hideseqs{\xdef\hide@seqs{y}}
\def\showseqs{\xdef\hide@seqs{n}}
\def\hideseq#1{\xdef\first@{#1,&,@} \hideseq@}
\def\killseq#1{\xdef\first@{#1,&,@} \killseq@}
\def\hidesequencelogo{\show@logofalse}
\def\hidesubfamilylogo{\show@sublogofalse}
\def\logo@group@get#1#2@{%
\xdef\first@{#1}\xdef\third@{#2@}
\ifx\first@\ampers@nd
\else
\ifnum`#1>96 \make@upper\fi
\expandafter\xdef\csname logo@col\first@\endcsname{\second@}
\expandafter\logo@group@get\third@
\fi
}
\def\logocolor#1#2{%
\xdef\logo@colors@set{yes}
\xdef\second@{#2}
\xdef\third@{#1&@}
\expandafter\logo@group@get\third@
}
\newcommand\clearlogocolors[1][Black]{%
\logocolor{ABCDEFGHIJKLMNOPQRSTUVWXYZ}{#1}
}
\def\dofrequencycorrection{\xdef\do@freq@correction{y}}
\def\undofrequencycorrection{\xdef\do@freq@correction{n}}
\newcommand\showlogoscale[2][Black]{\xdef\logo@scalecol{#1}\xdef\show@logoscale{#2}}
\def\hidelogoscale{\xdef\show@logoscale{n}}
\def\hidenegatives{\xdef\hide@negatives{y}\xdef\sublogo@tint{}}
\newcommand\shownegatives[1][medium]{%
\xdef\hide@negatives{n}
\xdef\first@{#1}
\xdef\second@{full}
\ifx\first@\second@
\xdef\sublogo@tint{}
\else
\xdef\second@{strong}
\ifx\first@\second@
\xdef\sublogo@tint{Light}
\else
\xdef\second@{medium}
\ifx\first@\second@
\xdef\sublogo@tint{LightLight}
\else
\xdef\second@{weak}
\ifx\first@\second@
\xdef\sublogo@tint{LightLightLight}
\else
\xdef\sublogo@tint{LightLight}
\fi\fi\fi\fi
}
\def\set@logocolors{%
\xdef\second@{undefined}
\ifx\first@\second@
\if\logo@colors@set\n@
\xdef\first@{standard}
\fi
\fi
\xdef\second@{standard}
\ifx\first@\second@
\if\seq@type A
\xdef\logo@colors@set{n}
\else
\if\seq@type P
\xdef\first@{rasmol}
\else
\xdef\first@{nucleotide}
\fi
\fi
\fi
\xdef\second@{nucleotide}
\ifx\first@\second@
\clearlogocolors
\logocolor{G}{Black}
\logocolor{A}{Green}
\logocolor{TU}{Red}
\logocolor{C}{Blue}
\else
\xdef\second@{rasmol}
\ifx\first@\second@
\clearlogocolors
\logocolor{DE}{Red}
\logocolor{CM}{Yellow}
\logocolor{KR}{Blue}
\logocolor{ST}{Orange}
\logocolor{FY}{MidnightBlue}
\logocolor{NQ}{Cyan}
\logocolor{G}{LightGray}
\logocolor{LVI}{Green}
\logocolor{A}{DarkGray}
\logocolor{W}{CarnationPink}
\logocolor{H}{CornflowerBlue}
\logocolor{P}{Apricot}
\logocolor{BZ}{LightMagenta}
\else
\xdef\second@{chemical}
\ifx\first@\second@
\clearlogocolors
\logocolor{DE}{Red}
\logocolor{VIL}{Black}
\logocolor{AG}{Gray}
\logocolor{NQ}{Green}
\logocolor{FYW}{Brown}
\logocolor{KRH}{Blue}
\logocolor{ST}{Magenta}
\logocolor{P}{Orange}
\logocolor{CM}{Yellow}
\else
\xdef\second@{hydropathy}
\ifx\first@\second@
\clearlogocolors
\logocolor{DE}{Red}
\logocolor{KRH}{Blue}
\logocolor{YSTGNQC}{Yellow}
\logocolor{AFPMWVIL}{Green}
\else
\xdef\second@{structure}
\ifx\first@\second@
\clearlogocolors
\logocolor{DEHKNQR}{Orange}
\logocolor{ACGPSTWY}{Yellow}
\logocolor{FILMV}{Green}
\else
\xdef\second@{standard area}
\ifx\first@\second@
\clearlogocolors
\logocolor{G}{BrickRed}
\logocolor{AS}{Orange}
\logocolor{CP}{Yellow}
\logocolor{TDVN}{YellowGreen}
\logocolor{IE}{PineGreen}
\logocolor{LQHM}{SkyBlue}
\logocolor{FK}{RoyalPurple}
\logocolor{Y}{RedViolet}
\logocolor{RW}{Black}
\else
\xdef\second@{accessible area}
\ifx\first@\second@
\clearlogocolors
\logocolor{C}{BrickRed}
\logocolor{IVG}{Orange}
\logocolor{FLMA}{Yellow}
\logocolor{WSTH}{YellowGreen}
\logocolor{P}{PineGreen}
\logocolor{YDN}{SkyBlue}
\logocolor{EQ}{RoyalPurple}
\logocolor{R}{RedViolet}
\logocolor{K}{Black}
\fi\fi\fi\fi\fi\fi\fi
}
\newcommand\findsubfamily[2][n]{%
\xdef\first@{#1}
\ifx\first@\n@
\else
\xdef\subfamily@threshold{#1}
\fi
\xdef\subfamily@seq{#2}
}
\def\setsubfamily#1{%
\xdef\sub@family@setting{#1}
\loopcount=1
\loop
\expandafter\xdef\csname subfamily@num\the\loopcount\endcsname{1}
\advance\loopcount by 1
\ifnum\loopcount>\seq@count\else\repeat
\xdef\subfamily@count{2}
\res@count=0
\xdef\first@{#1,&,@}
\setsubfamily@
\clear@res@nums{1}
\clear@res@nums{2}
\expandafter\xdef\csname group@num2\endcsname{\the\res@count}
\loopcount=\seq@count
\advance\loopcount by -\res@count
\expandafter\xdef\csname group@num1\endcsname{\the\loopcount}
}
\def\subfamilythreshold#1{\xdef\subfamily@threshold{#1}}
\newcommand\showsubfamilylogo[2][undefined]{%
\xdef\first@{#1} \set@logocolors
\xdef\first@{#2} \xdef\last@{top}
\ifx\first@\last@\xdef\sublogo@top{0}\else\xdef\sublogo@top{1}\fi
\show@sublogotrue
}
\def\relevance#1{%
\def\sig@max{#1}
\setlength\temp@@length{1000sp}
\setlength\temp@@length{\sig@max\temp@@length}
\loopcount=\temp@@length
\xdef\sig@max{\the\loopcount}
}
\newcommand\showrelevance[2][Black]{\def\sig@color{#1}\def\sig@char{#2}\xdef\hide@sig{n}}
\def\hiderelevance{\xdef\hide@sig{y}}
\newcommand\showsequencelogo[2][undefined]{%
\xdef\first@{#1} \set@logocolors
\xdef\first@{#2} \xdef\last@{top}
\ifx\first@\last@\xdef\logo@top{0}\else\xdef\logo@top{1}\fi
\show@logotrue
}
\newcommand\showconsensus[2][n]{%
\xdef\text@scale{n}
\xdef\box@scale{n}
\xdef\first@{#1}
\ifx\first@\n@
\xdef\collect@cons@colors{no}
\else
\xdef\first@{#1,&,@}
\expandafter\get@item\first@
\xdef\c@nsc@l{\fourth@}
\xdef\first@@{Gray}
\ifx\c@nsc@l\first@@\xdef\text@scale{y}\else
\xdef\first@@{RedBlue}
\ifx\c@nsc@l\first@@\xdef\text@scale{y}\else
\xdef\first@@{BlueRed}
\ifx\c@nsc@l\first@@\xdef\text@scale{y}\else
\xdef\first@@{RedGreen}
\ifx\c@nsc@l\first@@\xdef\text@scale{y}\else
\xdef\first@@{GreenRed}
\ifx\c@nsc@l\first@@\xdef\text@scale{y}\else
\xdef\first@@{ColdHot}
\ifx\c@nsc@l\first@@\xdef\text@scale{y}\else
\xdef\first@@{HotCold}
\ifx\c@nsc@l\first@@\xdef\text@scale{y}
\fi\fi\fi\fi\fi\fi\fi
\expandafter\get@item\first@
\ifx\fourth@\ampers@nd
\xdef\c@nssc@le{White}
\else
\xdef\c@nssc@le{\fourth@}
\xdef\first@{Gray}
\ifx\c@nssc@le\first@\xdef\box@scale{y}\else
\xdef\first@{RedBlue}
\ifx\c@nssc@le\first@\xdef\box@scale{y}\else
\xdef\first@{BlueRed}
\ifx\c@nssc@le\first@\xdef\box@scale{y}\else
\xdef\first@{RedGreen}
\ifx\c@nssc@le\first@\xdef\box@scale{y}\else
\xdef\first@{GreenRed}
\ifx\c@nssc@le\first@\xdef\box@scale{y}\else
\xdef\first@{ColdHot}
\ifx\c@nssc@le\first@\xdef\box@scale{y}\else
\xdef\first@{HotCold}
\ifx\c@nssc@le\first@\xdef\box@scale{y}\else
\fi\fi\fi\fi\fi\fi\fi
\fi
\xdef\collect@cons@colors{y}
\fi
\xdef\first@{#2} \xdef\last@{top}
\ifx\first@\last@\xdef\cons@top{0}\else\xdef\cons@top{1}\fi
\show@construe}
\def\consensuscolors#1#2#3#4#5#6{%
\xdef\last@{\ampers@nd}
\xdef\first@{#1&}\xdef\second@{#2&}
\ifx\first@\last@\else\def\ConsTextNomatch{#1}\fi
\ifx\second@\last@\else\def\ConsNomatch{#2}\fi
\xdef\first@{#3&}\xdef\second@{#4&}
\ifx\first@\last@\else\def\ConsTextMatch{#3}\fi
\ifx\second@\last@\else\def\ConsMatch{#4}\fi
\xdef\first@{#5&}\xdef\second@{#6&}
\ifx\first@\last@\else\def\ConsTextAllmatch{#5}\fi
\ifx\second@\last@\else\def\ConsAllmatch{#6}\fi
}
\def\defconsensus#1#2#3{%
\xdef\second@{#1&}
\ifx\second@\ampers@nd \else \def\n@m@tch{#1}\fi
\xdef\second@{#2&}
\ifx\second@\ampers@nd \else \def\m@tch{#2}\fi
\xdef\second@{#3&}
\ifx\second@\ampers@nd \else \def\@llm@tch{#3}\fi}
\def\hideconsensus{\show@consfalse}
\def\nameconsensus#1{\def\cons@name{#1}}
\def\namesequencelogo#1{\def\logo@name@user{#1}}
\newcommand\namesubfamilylogo[2][]{\def\sublogo@name@neg{#1}\def\sublogo@name@user{#2}}
\def\hideleadinggaps{\sh@wg@psfalse}
\def\showleadinggaps{\sh@wg@pstrue}
\newcommand\showruler[3][n]{%
\xdef\first@{#1}
\ifx\first@\n@\else\xdef\ruler@fg{#1}\fi
\xdef\first@{consensus} \xdef\second@{#3}
\xdef\third@{bottom} \xdef\fourth@{#2}
\ifx\third@\fourth@ \xdef\rule@top{1}\else\xdef\rule@top{0}\fi
\ifx\first@\second@ \xdef\rule@num{0}
\else
\xdef\first@{#3 @} \expandafter\check@letter\first@
\xdef\first@{#3} \ifletter \get@name@number \fi
\ifnum\first@>\seq@count
\else
\ifnum\first@>0
\xdef\rule@num{\first@}
\fi
\fi
\fi
\xdef\ruler@{}}
\def\hideruler{\xdef\rule@num{-1}}
\def\allowzero{\xdef\allow@zero{y}}
\def\disallowzero{\xdef\allow@zero{n}}
\def\rulersteps#1{%
\xdef\ruler@step{#1}
\ifnum#1<4 \xdef\ruler@rot{90}\fi
}
\def\rotateruler{\xdef\ruler@rot{90}}
\def\unrotateruler{\xdef\ruler@rot{0}}
\def\namerulerpos#1#2{%
\expandafter\xdef\csname alt@ruler#1\endcsname{#2}
}
\def\featurerule#1{\setlength\rule@thick{#1}}
\def\orderseqs#1{%
\def\order@loop{%
\expandafter\check@letter\first@
\ifletter
\expandafter\get@item\first@
\xdef\first@{\fourth@}
\get@name@number
\xdef\seq@order{\seq@order,\first@}
\xdef\first@{\first@@ @}
\order@loop
\else
\expandafter\get@digit\first@
\ifx\fourth@\ampers@nd
\else
\xdef\seq@order{\seq@order,\fourth@}
\order@loop
\fi
\fi}
\xdef\first@{#1,&,@}
\xdef\seq@order{}
\order@loop
\xdef\seq@order{\seq@order @}
\expandafter\get@item\seq@order
\xdef\seq@order{\first@@,@}
}
\def\setfamily#1#2{%
\xdef\second@{#2&}
\ifx\second@\ampers@nd
\else
\xdef\first@{#1}
\xdef\second@{#2}
\xdef\temp@{rm}
\ifx\second@\temp@
\xdef\third@{\rmdefault}
\else
\xdef\temp@{sf}
\ifx\second@\temp@
\xdef\third@{\sfdefault}
\else
\xdef\temp@{tt}
\ifx\second@\temp@
\xdef\third@{\ttdefault}
\else
\xdef\third@{\second@}
\fi\fi\fi
\xdef\temp@{featurenames}
\ifx\first@\temp@ \xdef\ftext@family{\third@}
\else
\xdef\temp@{featurestylenames}
\ifx\first@\temp@ \xdef\fstyles@family{\third@}
\else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@family{\third@}
\else
\xdef\temp@{featurestyles}
\ifx\first@\temp@ \xdef\featurestyles@family{\third@}
\else
\xdef\temp@{numbering}
\ifx\first@\temp@ \xdef\numbertext@family{\third@}
\else
\xdef\temp@{names}
\ifx\first@\temp@ \xdef\namestext@family{\third@}
\else
\xdef\temp@{residues}
\ifx\first@\temp@ \xdef\residues@family{\third@}
\else
\xdef\temp@{legend}
\ifx\first@\temp@ \xdef\legend@family{\third@}
\else
\xdef\temp@{labels}
\ifx\first@\temp@ \xdef\label@family{\third@}
\else
\xdef\temp@{ruler}
\ifx\first@\temp@ \xdef\ruler@family{\second@}
\else
\xdef\temp@{all}
\ifx\first@\temp@
\xdef\ftext@family{\third@}
\xdef\fstyles@family{\third@}
\xdef\featuretext@family{\third@}
\xdef\featurestyles@family{\third@}
\xdef\numbertext@family{\third@}
\xdef\namestext@family{\third@}
\xdef\residues@family{\third@}
\xdef\legend@family{\third@}
\xdef\label@family{\third@}
\xdef\ruler@family{\second@}
\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setseries#1#2{%
\xdef\second@{#2&}
\ifx\second@\ampers@nd
\else
\xdef\first@{#1}
\xdef\second@{#2}
\xdef\temp@{bf}
\ifx\second@\temp@
\xdef\third@{\bfdefault}
\else
\xdef\temp@{md}
\ifx\second@\temp@
\xdef\third@{\mddefault}
\else
\xdef\third@{\second@}
\fi\fi
\xdef\temp@{featurenames}
\ifx\first@\temp@ \xdef\ftext@series{\third@}
\else
\xdef\temp@{featurestylenames}
\ifx\first@\temp@ \xdef\fstyles@series{\third@}
\else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@series{\third@}
\else
\xdef\temp@{featurestyles}
\ifx\first@\temp@ \xdef\featurestyles@series{\third@}
\else
\xdef\temp@{numbering}
\ifx\first@\temp@ \xdef\numbertext@series{\third@}
\else
\xdef\temp@{names}
\ifx\first@\temp@ \xdef\namestext@series{\third@}
\else
\xdef\temp@{residues}
\ifx\first@\temp@ \xdef\residues@series{\third@}
\else
\xdef\temp@{legend}
\ifx\first@\temp@ \xdef\legend@series{\third@}
\else
\xdef\temp@{labels}
\ifx\first@\temp@ \xdef\label@series{\third@}
\else
\xdef\temp@{all}
\ifx\first@\temp@
\xdef\ftext@series{\third@}
\xdef\fstyles@series{\third@}
\xdef\featuretext@series{\third@}
\xdef\featurestyles@series{\third@}
\xdef\numbertext@series{\third@}
\xdef\namestext@series{\third@}
\xdef\residues@series{\third@}
\xdef\legend@series{\third@}
\xdef\label@series{\third@}
\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setshape#1#2{%
\xdef\second@{#2&}
\ifx\second@\ampers@nd
\else
\xdef\first@{#1}
\xdef\second@{#2}
\xdef\temp@{it}
\ifx\second@\temp@
\xdef\third@{\itdefault}
\else
\xdef\temp@{sl}
\ifx\second@\temp@
\xdef\third@{\sldefault}
\else
\xdef\temp@{sc}
\ifx\second@\temp@
\xdef\third@{\scdefault}
\else
\xdef\temp@{up}
\ifx\second@\temp@
\xdef\third@{\updefault}
\else
\xdef\third@{\second@}
\fi\fi\fi\fi
\xdef\temp@{featurenames}
\ifx\first@\temp@ \xdef\ftext@shape{\third@}
\else
\xdef\temp@{featurestylenames}
\ifx\first@\temp@ \xdef\fstyles@shape{\third@}
\else
\xdef\temp@{features}
\ifx\first@\temp@ \xdef\featuretext@shape{\third@}
\else
\xdef\temp@{featurestyles}
\ifx\first@\temp@ \xdef\featurestyles@shape{\third@}
\else
\xdef\temp@{numbering}
\ifx\first@\temp@ \xdef\numbertext@shape{\third@}
\else
\xdef\temp@{names}
\ifx\first@\temp@ \xdef\namestext@shape{\third@}
\else
\xdef\temp@{residues}
\ifx\first@\temp@ \xdef\residues@shape{\third@}
\else
\xdef\temp@{legend}
\ifx\first@\temp@ \xdef\legend@shape{\third@}
\else
\xdef\temp@{labels}
\ifx\first@\temp@ \xdef\label@shape{\third@}
\else
\xdef\temp@{all}
\ifx\first@\temp@
\xdef\ftext@shape{\third@}
\xdef\fstyles@shape{\third@}
\xdef\featuretext@shape{\third@}
\xdef\featurestyles@shape{\third@}
\xdef\numbertext@shape{\third@}
\xdef\namestext@shape{\third@}
\xdef\residues@shape{\third@}
\xdef\legend@shape{\third@}
\xdef\label@shape{\third@}
\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\fi
}
\def\setsize#1#2{%
\xdef\second@{#2&}
\ifx\second@\ampers@nd
\else
\xdef\first@{#1}
\xdef\temp@{features}
\ifx\first@\temp@
\def\featuretext@size{\csname #2\endcsname}
\else
\xdef\temp@{featurestyles}
\ifx\first@\temp@
\def\featurestyles@size{\csname #2\endcsname}
\else
\xdef\temp@{featurenames}
\ifx\first@\temp@
\def\ftext@size{\csname #2\endcsname}
\else
\xdef\temp@{featurestylenames}
\ifx\first@\temp@
\def\fstyles@size{\csname #2\endcsname}
\else
\xdef\temp@{numbering}
\ifx\first@\temp@
\def\numbertext@size{\csname #2\endcsname}
\else
\xdef\temp@{names}
\ifx\first@\temp@
\def\namestext@size{\csname #2\endcsname}
\else
\xdef\temp@{legend}
\ifx\first@\temp@
\def\legend@size{\csname #2\endcsname}
\else
\xdef\temp@{labels}
\ifx\first@\temp@
\def\label@size{\csname #2\endcsname}
\else
\xdef\temp@{residues}
\ifx\first@\temp@
\def\residues@size{\csname #2\endcsname}
\xdef\res@size{#2}
\else
\xdef\temp@{all}
\ifx\first@\temp@
\def\featuretext@size{\csname #2\endcsname}
\def\featurestyles@size{\csname #2\endcsname}
\def\ftext@size{\csname #2\endcsname}
\def\fstyles@size{\csname #2\endcsname}
\def\numbertext@size{\csname #2\endcsname}
\def\namestext@size{\csname #2\endcsname}
\def\legend@size{\csname #2\endcsname}
\def\label@size{\csname #2\endcsname}
\def\residues@size{\csname #2\endcsname}
\xdef\res@size{#2}
\fi\fi\fi\fi\fi\fi\fi\fi\fi\fi
\xdef\temp@{Huge}
\ifx\temp@\res@size
\def\bottomruler@size{\csname Large\endcsname}
\else
\xdef\temp@{huge}
\ifx\temp@\res@size
\def\bottomruler@size{\csname large\endcsname}
\else
\xdef\temp@{LARGE}
\ifx\temp@\res@size
\def\bottomruler@size{\csname normalsize\endcsname}
\else
\xdef\temp@{Large}
\ifx\temp@\res@size
\def\bottomruler@size{\csname small\endcsname}
\else
\xdef\temp@{large}
\ifx\temp@\res@size
\def\bottomruler@size{\csname footnotesize\endcsname}
\else
\xdef\temp@{normalsize}
\ifx\temp@\res@size
\def\bottomruler@size{\csname scriptsize\endcsname}
\else
\def\bottomruler@size{\csname tiny\endcsname}
\fi\fi\fi\fi\fi\fi
\fi
\xdef\temp@{ruler}
\ifx\first@\temp@
\def\bottomruler@size{\csname #2\endcsname}
\fi
}
\def\setfont#1#2#3#4#5{%
\setfamily{#1}{#2}\setseries{#1}{#3}
\setshape{#1}{#4}\setsize{#1}{#5}}
\def\featurenamesrm{\setfamily{featurenames}{rm}}
\def\featurenamessf{\setfamily{featurenames}{sf}}
\def\featurenamestt{\setfamily{featurenames}{tt}}
\def\featurenamesmd{\setseries{featurenames}{md}}
\def\featurenamesbf{\setseries{featurenames}{bf}}
\def\featurenamesup{\setshape {featurenames}{up}}
\def\featurenamesit{\setshape {featurenames}{it}}
\def\featurenamessl{\setshape {featurenames}{sl}}
\def\featurenamessc{\setshape {featurenames}{sc}}
\def\featurenamestiny {\setsize{featurenames}{tiny}}
\def\featurenamesscriptsize {\setsize{featurenames}{scriptsize}}
\def\featurenamesfootnotesize{\setsize{featurenames}{footnotesize}}
\def\featurenamessmall {\setsize{featurenames}{small}}
\def\featurenamesnormalsize {\setsize{featurenames}{normalsize}}
\def\featurenameslarge {\setsize{featurenames}{large}}
\def\featurenamesLarge {\setsize{featurenames}{Large}}
\def\featurenamesLARGE {\setsize{featurenames}{LARGE}}
\def\featurenameshuge {\setsize{featurenames}{huge}}
\def\featurenamesHuge {\setsize{featurenames}{Huge}}
\def\featurestylenamesrm{\setfamily{featurestylenames}{rm}}
\def\featurestylenamessf{\setfamily{featurestylenames}{sf}}
\def\featurestylenamestt{\setfamily{featurestylenames}{tt}}
\def\featurestylenamesmd{\setseries{featurestylenames}{md}}
\def\featurestylenamesbf{\setseries{featurestylenames}{bf}}
\def\featurestylenamesup{\setshape {featurestylenames}{up}}
\def\featurestylenamesit{\setshape {featurestylenames}{it}}
\def\featurestylenamessl{\setshape {featurestylenames}{sl}}
\def\featurestylenamessc{\setshape {featurestylenames}{sc}}
\def\featurestylenamestiny {\setsize{featurestylenames}{tiny}}
\def\featurestylenamesscriptsize {\setsize{featurestylenames}{scriptsize}}
\def\featurestylenamesfootnotesize{\setsize{featurestylenames}{footnotesize}}
\def\featurestylenamessmall {\setsize{featurestylenames}{small}}
\def\featurestylenamesnormalsize {\setsize{featurestylenames}{normalsize}}
\def\featurestylenameslarge {\setsize{featurestylenames}{large}}
\def\featurestylenamesLarge {\setsize{featurestylenames}{Large}}
\def\featurestylenamesLARGE {\setsize{featurestylenames}{LARGE}}
\def\featurestylenameshuge {\setsize{featurestylenames}{huge}}
\def\featurestylenamesHuge {\setsize{featurestylenames}{Huge}}
\def\featuresrm{\setfamily{features}{rm}}
\def\featuressf{\setfamily{features}{sf}}
\def\featurestt{\setfamily{features}{tt}}
\def\featuresmd{\setseries{features}{md}}
\def\featuresbf{\setseries{features}{bf}}
\def\featuresup{\setshape {features}{up}}
\def\featuresit{\setshape {features}{it}}
\def\featuressl{\setshape {features}{sl}}
\def\featuressc{\setshape {features}{sc}}
\def\featurestiny {\setsize{features}{tiny}}
\def\featuresscriptsize {\setsize{features}{scriptsize}}
\def\featuresfootnotesize{\setsize{features}{footnotesize}}
\def\featuressmall {\setsize{features}{small}}
\def\featuresnormalsize {\setsize{features}{normalsize}}
\def\featureslarge {\setsize{features}{large}}
\def\featuresLarge {\setsize{features}{Large}}
\def\featuresLARGE {\setsize{features}{LARGE}}
\def\featureshuge {\setsize{features}{huge}}
\def\featuresHuge {\setsize{features}{Huge}}
\def\featurestylesrm{\setfamily{featurestyles}{rm}}
\def\featurestylessf{\setfamily{featurestyles}{sf}}
\def\featurestylestt{\setfamily{featurestyles}{tt}}
\def\featurestylesmd{\setseries{featurestyles}{md}}
\def\featurestylesbf{\setseries{featurestyles}{bf}}
\def\featurestylesup{\setshape {featurestyles}{up}}
\def\featurestylesit{\setshape {featurestyles}{it}}
\def\featurestylessl{\setshape {featurestyles}{sl}}
\def\featurestylessc{\setshape {featurestyles}{sc}}
\def\featurestylestiny {\setsize{featurestyles}{tiny}}
\def\featurestylesscriptsize {\setsize{featurestyles}{scriptsize}}
\def\featurestylesfootnotesize{\setsize{featurestyles}{footnotesize}}
\def\featurestylessmall {\setsize{featurestyles}{small}}
\def\featurestylesnormalsize {\setsize{featurestyles}{normalsize}}
\def\featurestyleslarge {\setsize{featurestyles}{large}}
\def\featurestylesLarge {\setsize{featurestyles}{Large}}
\def\featurestylesLARGE {\setsize{featurestyles}{LARGE}}
\def\featurestyleshuge {\setsize{featurestyles}{huge}}
\def\featurestylesHuge {\setsize{featurestyles}{Huge}}
\def\numberingrm{\setfamily{numbering}{rm}}
\def\numberingsf{\setfamily{numbering}{sf}}
\def\numberingtt{\setfamily{numbering}{tt}}
\def\numberingmd{\setseries{numbering}{md}}
\def\numberingbf{\setseries{numbering}{bf}}
\def\numberingup{\setshape {numbering}{up}}
\def\numberingit{\setshape {numbering}{it}}
\def\numberingsl{\setshape {numbering}{sl}}
\def\numberingsc{\setshape {numbering}{sc}}
\def\numberingtiny {\setsize{numbering}{tiny}}
\def\numberingscriptsize {\setsize{numbering}{scriptsize}}
\def\numberingfootnotesize{\setsize{numbering}{footnotesize}}
\def\numberingsmall {\setsize{numbering}{small}}
\def\numberingnormalsize {\setsize{numbering}{normalsize}}
\def\numberinglarge {\setsize{numbering}{large}}
\def\numberingLarge {\setsize{numbering}{Large}}
\def\numberingLARGE {\setsize{numbering}{LARGE}}
\def\numberinghuge {\setsize{numbering}{huge}}
\def\numberingHuge {\setsize{numbering}{Huge}}
\def\namesrm{\setfamily{names}{rm}}
\def\namessf{\setfamily{names}{sf}}
\def\namestt{\setfamily{names}{tt}}
\def\namesmd{\setseries{names}{md}}
\def\namesbf{\setseries{names}{bf}}
\def\namesup{\setshape {names}{up}}
\def\namesit{\setshape {names}{it}}
\def\namessl{\setshape {names}{sl}}
\def\namessc{\setshape {names}{sc}}
\def\namestiny {\setsize{names}{tiny}}
\def\namesscriptsize {\setsize{names}{scriptsize}}
\def\namesfootnotesize{\setsize{names}{footnotesize}}
\def\namessmall {\setsize{names}{small}}
\def\namesnormalsize {\setsize{names}{normalsize}}
\def\nameslarge {\setsize{names}{large}}
\def\namesLarge {\setsize{names}{Large}}
\def\namesLARGE {\setsize{names}{LARGE}}
\def\nameshuge {\setsize{names}{huge}}
\def\namesHuge {\setsize{names}{Huge}}
\def\residuesrm{\setfamily{residues}{rm}}
\def\residuessf{\setfamily{residues}{sf}}
\def\residuestt{\setfamily{residues}{tt}}
\def\residuesmd{\setseries{residues}{md}}
\def\residuesbf{\setseries{residues}{bf}}
\def\residuesup{\setshape {residues}{up}}
\def\residuesit{\setshape {residues}{it}}
\def\residuessl{\setshape {residues}{sl}}
\def\residuessc{\setshape {residues}{sc}}
\def\residuestiny {\setsize{residues}{tiny}}
\def\residuesscriptsize {\setsize{residues}{scriptsize}}
\def\residuesfootnotesize{\setsize{residues}{footnotesize}}
\def\residuessmall {\setsize{residues}{small}}
\def\residuesnormalsize {\setsize{residues}{normalsize}}
\def\residueslarge {\setsize{residues}{large}}
\def\residuesLarge {\setsize{residues}{Large}}
\def\residuesLARGE {\setsize{residues}{LARGE}}
\def\residueshuge {\setsize{residues}{huge}}
\def\residuesHuge {\setsize{residues}{Huge}}
\def\legendrm{\setfamily{legend}{rm}}
\def\legendsf{\setfamily{legend}{sf}}
\def\legendtt{\setfamily{legend}{tt}}
\def\legendmd{\setseries{legend}{md}}
\def\legendbf{\setseries{legend}{bf}}
\def\legendup{\setshape {legend}{up}}
\def\legendit{\setshape {legend}{it}}
\def\legendsl{\setshape {legend}{sl}}
\def\legendsc{\setshape {legend}{sc}}
\def\legendtiny {\setsize{legend}{tiny}}
\def\legendscriptsize {\setsize{legend}{scriptsize}}
\def\legendfootnotesize{\setsize{legend}{footnotesize}}
\def\legendsmall {\setsize{legend}{small}}
\def\legendnormalsize {\setsize{legend}{normalsize}}
\def\legendlarge {\setsize{legend}{large}}
\def\legendLarge {\setsize{legend}{Large}}
\def\legendLARGE {\setsize{legend}{LARGE}}
\def\legendhuge {\setsize{legend}{huge}}
\def\legendHuge {\setsize{legend}{Huge}}
\def\rulerrm{\setfamily{ruler}{rm}}
\def\rulersf{\setfamily{ruler}{sf}}
\def\rulertt{\setfamily{ruler}{tt}}
\def\rulertiny {\setsize{ruler}{tiny}}
\def\rulerscriptsize {\setsize{ruler}{scriptsize}}
\def\rulerfootnotesize{\setsize{ruler}{footnotesize}}
\def\rulersmall {\setsize{ruler}{small}}
\def\rulernormalsize {\setsize{ruler}{normalsize}}
\def\rulerlarge {\setsize{ruler}{large}}
\def\rulerLarge {\setsize{ruler}{Large}}
\def\rulerLARGE {\setsize{ruler}{LARGE}}
\def\rulerhuge {\setsize{ruler}{huge}}
\def\rulerHuge {\setsize{ruler}{Huge}}
\def\funcshadingstyle#1#2#3#4#5{%
\xdef\temp@{nomatch} \xdef\first@{#1}
\ifx\temp@\first@
\xdef\first@{0}
\else
\xdef\first@{\csname funcgrp#1\endcsname}
\fi
\ifnum\first@>-1
\expandafter\xdef\csname fg@textcolor\first@\endcsname{#2}
\expandafter\xdef\csname fg@color\first@\endcsname{#3}
\expandafter\xdef\csname funcm@tch\first@\endcsname{#4}
\expandafter\def\csname func@style\first@\endcsname{\csname text#5\endcsname}
\fi}
\def\defshadingcolors#1{%
\expandafter\xdef\csname TextNomatch@#1\endcsname{\TextNomatch}
\expandafter\xdef\csname Nomatch@#1\endcsname{\Nomatch}
\expandafter\xdef\csname resn@m@tch@#1\endcsname{\resn@m@tch}
\expandafter\xdef\csname TextSimilar@#1\endcsname{\TextSimilar}
\expandafter\xdef\csname Similar@#1\endcsname{\Similar}
\expandafter\xdef\csname ressimm@tch@#1\endcsname{\ressimm@tch}
\expandafter\xdef\csname TextIdentical@#1\endcsname{\TextIdentical}
\expandafter\xdef\csname Identical@#1\endcsname{\Identical}
\expandafter\xdef\csname resm@tch@#1\endcsname{\resm@tch}
\expandafter\xdef\csname TextAllmatch@#1\endcsname{\TextAllmatch}
\expandafter\xdef\csname Allmatch@#1\endcsname{\Allmatch}
\expandafter\xdef\csname res@llm@tch@#1\endcsname{\res@llm@tch}
\expandafter\xdef\csname gap@fg@#1\endcsname{\gap@fg}
\expandafter\xdef\csname gap@bg@#1\endcsname{\gap@bg}
}
\def\shadingcolors#1{%
\gapcolors{Black}{White}
\nomatchresidues{Black}{White}{upper}{up}
\xdef\first@{#1} \xdef\second@{blues}
\ifx\first@\second@
\similarresidues{Black}{Magenta}{upper}{up}
\conservedresidues{White}{RoyalBlue}{upper}{up}
\allmatchresidues{Goldenrod}{RoyalPurple}{upper}{up}
\else \xdef\second@{greens}
\ifx\first@\second@
\similarresidues{Black}{GreenYellow}{upper}{up}
\conservedresidues{White}{PineGreen}{upper}{up}
\allmatchresidues{YellowOrange}{OliveGreen}{upper}{up}
\else \xdef\second@{reds}
\ifx\first@\second@
\similarresidues{Black}{YellowOrange}{upper}{up}
\conservedresidues{White}{BrickRed}{upper}{up}
\allmatchresidues{YellowGreen}{Mahagony}{upper}{up}
\else \xdef\second@{black}
\ifx\first@\second@
\similarresidues{Black}{White}{upper}{sl}
\conservedresidues{White}{Black}{upper}{up}
\allmatchresidues{White}{Black}{upper}{sl}
\else \xdef\second@{grays}
\ifx\first@\second@
\similarresidues{Black}{LightGray}{upper}{up}
\conservedresidues{White}{DarkGray}{upper}{up}
\allmatchresidues{White}{Black}{upper}{up}
\else
\xdef\TextNomatch{\csname TextNomatch@#1\endcsname}
\xdef\Nomatch {\csname Nomatch@#1\endcsname}
\xdef\resn@m@tch {\csname resn@m@tch@#1\endcsname}
\xdef\TextSimilar{\csname TextSimilar@#1\endcsname}
\xdef\Similar {\csname Similar@#1\endcsname}
\xdef\ressimm@tch{\csname ressimm@tch@#1\endcsname}
\xdef\TextIdentical{\csname TextIdentical@#1\endcsname}
\xdef\Identical {\csname Identical@#1\endcsname}
\xdef\resm@tch {\csname resm@tch@#1\endcsname}
\xdef\TextAllmatch{\csname TextAllmatch@#1\endcsname}
\xdef\Allmatch {\csname Allmatch@#1\endcsname}
\xdef\res@llm@tch {\csname res@llm@tch@#1\endcsname}
\xdef\gap@fg {\csname gap@fg@#1\endcsname}
\xdef\gap@bg {\csname gap@bg@#1\endcsname}
\xdef\domgap@fg {\csname domgap@fg@#1\endcsname}
\xdef\domgap@bg {\csname domgap@bg@#1\endcsname}
\fi\fi\fi\fi\fi
\xdef\first@{#1}
\expandafter\defshadingcolors{\first@}
}
\def\nomatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&}
\xdef\last@{\ampers@nd}
\ifx\first@\last@\else\def\TextNomatch{#1}
\expandafter\def\csname fg@textcolor0\endcsname{#1}
\fi
\ifx\second@\last@\else\gdef\Nomatch{#2}
\expandafter\def\csname fg@color0\endcsname{#2}
\fi
\ifx\third@\last@\else\def\resn@m@tch{#3}
\fi
\xdef\first@{#4&}
\ifx\first@\last@\else
\def\no@style{\csname text#4\endcsname}
\expandafter\def\csname func@style0\endcsname%
{\csname text#4\endcsname}\fi}
\def\similarresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&}
\xdef\last@{\ampers@nd}
\ifx\first@\last@\else\def\TextSimilar{#1}\fi
\ifx\second@\last@\else\gdef\Similar{#2}\fi
\ifx\third@\last@\else\def\ressimm@tch{#3}\fi
\xdef\first@{#4&}
\ifx\first@\last@\else
\def\sim@style{\csname text#4\endcsname}\fi}
\def\conservedresidues#1#2#3#4{\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&}
\xdef\last@{\ampers@nd}
\ifx\first@\last@\else\def\TextIdentical{#1}\fi
\ifx\second@\last@\else\gdef\Identical{#2}\fi
\ifx\third@\last@\else\def\resm@tch{#3}\fi
\xdef\first@{#4&}
\ifx\first@\last@\else
\def\id@style{\csname text#4\endcsname}\fi}
\def\allmatchresidues#1#2#3#4 {\xdef\first@{#1&}\xdef\second@{#2&}\xdef\third@{#3&}
\xdef\last@{\ampers@nd}
\ifx\first@\last@\else\def\TextAllmatch{#1}\fi
\ifx\second@\last@\else\gdef\Allmatch{#2}\fi
\ifx\third@\last@\else\def\res@llm@tch{#3}\fi
\xdef\first@{#4&}
\ifx\first@\last@\else
\def\all@style{\csname text#4\endcsname}\fi}
\def\gapcolors#1#2 {\xdef\first@{#1&}\xdef\second@{#2&}
\xdef\last@{\ampers@nd}
\ifx\first@\last@\else\def\gap@fg{#1}
\expandafter\def\csname fg@textcolor*\endcsname{#1}\fi
\ifx\second@\last@\else\def\gap@bg{#2}
\expandafter\def\csname fg@color*\endcsname{#2}\fi}
\def\domaingapcolors#1#2 {\xdef\first@{#1&}\xdef\second@{#2&}
\xdef\last@{\ampers@nd}
\ifx\first@\last@\else\def\domgap@fg{#1}
\expandafter\def\csname fg@textcolor!\endcsname{#1}\fi
\ifx\second@\last@\else\def\domgap@bg{#2}
\expandafter\def\csname fg@color!\endcsname{#2}\fi}
\def\shadebox#1{%
\xdef\first@{White}%
\xdef\third@{#1}%
\xdef\second@{nomatch}%
\ifx\second@\third@
\ifx\Nomatch\first@\white@box\else\textcolor{\Nomatch}{\box@rule}\fi%
\else
\xdef\second@{similar}%
\ifx\second@\third@
\ifx\Similar\first@\white@box\else\textcolor{\Similar}{\box@rule}\fi%
\else
\xdef\second@{conserved}%
\ifx\second@\third@
\ifx\Identical\first@\white@box\else\textcolor{\Identical}{\box@rule}\fi%
\else
\xdef\second@{allmatch}%
\ifx\second@\third@
\ifx\Allmatch\first@\white@box\else\textcolor{\Allmatch}{\box@rule}\fi%
\else
\ifx\third@\first@\white@box\else\textcolor{\third@}{\box@rule}\fi
\fi\fi\fi\fi}
\def\featurenamescolor#1{%
\expandafter\xdef\csname ftext@fg@ttttop\endcsname{#1}
\expandafter\xdef\csname ftext@fg@tttop\endcsname{#1}
\expandafter\xdef\csname ftext@fg@ttop\endcsname{#1}
\expandafter\xdef\csname ftext@fg@top\endcsname{#1}
\expandafter\xdef\csname ftext@fg@bottom\endcsname{#1}
\expandafter\xdef\csname ftext@fg@bbottom\endcsname{#1}
\expandafter\xdef\csname ftext@fg@bbbottom\endcsname{#1}
\expandafter\xdef\csname ftext@fg@bbbbottom\endcsname{#1}
}
\def\featurestylenamescolor#1{%
\expandafter\xdef\csname fstyles@fg@ttttop\endcsname{#1}
\expandafter\xdef\csname fstyles@fg@tttop\endcsname{#1}
\expandafter\xdef\csname fstyles@fg@ttop\endcsname{#1}
\expandafter\xdef\csname fstyles@fg@top\endcsname{#1}
\expandafter\xdef\csname fstyles@fg@bottom\endcsname{#1}
\expandafter\xdef\csname fstyles@fg@bbottom\endcsname{#1}
\expandafter\xdef\csname fstyles@fg@bbbottom\endcsname{#1}
\expandafter\xdef\csname fstyles@fg@bbbbottom\endcsname{#1}
}
\def\featurenamecolor#1#2{\expandafter\xdef\csname ftext@fg@#1\endcsname{#2}}
\def\featurestylenamecolor#1#2{\expandafter\xdef\csname fstyles@fg@#1\endcsname{#2}}
\def\namescolor#1{\xdef\names@fg{#1}}
\def\namecolor#1#2{%
\xdef\first@{consensus} \xdef\second@{#1}
\ifx\first@\second@
\expandafter\xdef\csname name@col0\endcsname{#2}
\else
\xdef\first@{featurenames} \xdef\second@{#1}
\ifx\first@\second@
\xdef\ftext@fg{#2}
\else
\xdef\first@{featurestylenames} \xdef\second@{#1}
\ifx\first@\second@
\xdef\fstyles@fg{#2}
\else
\xdef\first@{#1,&,@} \xdef\third@{#2} \namecolor@
\fi\fi\fi
}
\def\numberingcolor#1{\xdef\numbering@fg{#1}}
\def\numbercolor#1#2{%
\xdef\first@{consensus} \xdef\second@{#1}
\ifx\first@\second@
\expandafter\xdef\csname number@col0\endcsname{#2}
\else
\xdef\first@{#1,&,@} \xdef\third@{#2} \numbercolor@
\fi
}
\def\legendcolor#1{\xdef\legend@fg{#1}}
\def\rulercolor#1{\xdef\ruler@fg{#1}}
\def\molweight#1#2{%
\xdef\temp@{Da}%
\xdef\second@{#2}%
\ifx\second@\temp@\xdef\third@{Da}\else\xdef\third@{kDa}\fi%
\xdef\first@{#1 @} \expandafter\check@letter\first@
\xdef\first@{#1} \ifletter \get@name@number \fi
\xdef\first@{\csname @rd\first@\endcsname}%
\loopcount=\csname mol@weight\first@\endcsname%
\divide\loopcount by 10\relax%
\innerloopcount=\loopcount%
\hbox{%
\ifnum\loopcount>1000%
\divide\loopcount by 1000\relax%
\pos@count=\loopcount%
\multiply\loopcount by 1000\relax%
\advance\innerloopcount by -\loopcount%
\loopcount=\innerloopcount%
\ifnum\loopcount>949\advance\pos@count by 1\relax\fi%
\the\pos@count%
\ifx\temp@\second@\ifgerm@n .\else {,}\fi\fi%
\else%
\ifx\second@\temp@ \else 0\fi%
\fi%
\ifx\second@\temp@%
\the\loopcount%
\loopcount=\csname mol@weight\first@\endcsname%
\innerloopcount=\loopcount%
\divide\loopcount by 10\relax%
\multiply\loopcount by 10\relax%
\advance\innerloopcount by -\loopcount\relax%
\else%
\divide\innerloopcount by 10\relax%
\advance\innerloopcount by 5\relax%
\divide\innerloopcount by 10\relax%
\fi%
\ifnum\innerloopcount>9\relax\innerloopcount=0\relax\fi%
\ifgerm@n {,}\else .\fi%
\the\innerloopcount~\third@}}
\newcommand\charge[2][o]{%
\xdef\temp@{pep}%
\ifx\prefix@\temp@%
\xdef\first@{#2 @} \expandafter\check@letter\first@
\xdef\first@{#2} \ifletter \get@name@number \fi
\xdef\second@{\csname @rd\first@\endcsname}%
\loopcount=\csname ch@rge\second@\endcsname%
\xdef\first@{#1}\make@lower%
\if\first@ i\fi%
\if\first@ o\advance\loopcount by \chargeNterm%
\advance\loopcount by \chargeCterm\fi%
\if\first@ n\advance\loopcount by \chargeNterm\fi%
\if\first@ c\advance\loopcount by \chargeCterm\fi%
\hbox{\ensuremath{%
\ifnum\loopcount>0 +%
\else\ifnum\loopcount=0 \pm%
\else -\multiply\loopcount by -1\relax%
\fi\fi%
\innerloopcount=\loopcount%
\divide\loopcount by 1000\relax%
\the\loopcount%
\multiply\loopcount by 1000\relax%
\advance\innerloopcount by -\loopcount\relax%
\divide\innerloopcount by 10\relax%
\ifnum\innerloopcount=0%
\else%
\ifgerm@n {,}\else .\fi%
\ifnum\innerloopcount<10 0\fi%
\the\innerloopcount%
\fi}}%
\fi}
\def\TeXshade{%
\setbox1=\hbox{\texttt{H}}%
\def\logo@rule{\vrule depth0.25\ht1 height1.25\ht1 width\wd1}%
\TeX%
\logo@rule\kern-\wd1\textcolor{White}{\texttt{s}}%
\logo@rule\kern-\wd1\textcolor{White}{\texttt{h}}%
\texttt{a}%
\logo@rule\kern-\wd1\textcolor{White}{\texttt{d}}%
\texttt{e}}
\def\includeTCoffee#1{%
\xdef\TC@first@{#1}\include@T@coffee}
\def\firstcolumnDSSP{\xdef\fc@DSSP{y}}
\def\secondcolumnDSSP{\xdef\fc@DSSP{n}}
\newcommand{\includeDSSP}[3][existing]{%
\temp@count=\dssp@num
\advance\temp@count by 1
\xdef\dssp@num{\the\temp@count}
\xdef\first@{#1} \xdef\temp@{existing}
\ifx\first@\temp@ \else\xdef\first@{make new}\fi
\expandafter\xdef\csname optiondssp\the\temp@count\endcsname{\first@}
\xdef\first@{#2 @} \expandafter\check@letter\first@
\xdef\first@{#2} \ifletter \get@name@number \fi
\expandafter\xdef\csname doseqdssp\the\temp@count\endcsname{\first@}
\expandafter\xdef\csname filenamedssp\the\temp@count\endcsname{#3}
\expandafter\ifnum\csname doseqdssp\the\temp@count\endcsname>\seq@count
\message{<Ignoring `#2' in \noexpand\includeDSSP>}
\advance\temp@count by -1
\xdef\dssp@num{\the\temp@count}
\fi
}
\newcommand{\includeHMMTOP}[3][existing]{%
\temp@count=\HMMTOP@num
\advance\temp@count by 1
\xdef\HMMTOP@num{\the\temp@count}
\xdef\first@{#1} \xdef\temp@{existing}
\ifx\first@\temp@ \else\xdef\first@{make new}\fi
\expandafter\xdef\csname optionHMMTOP\the\temp@count\endcsname{\first@}
\xdef\first@{#2[,]&}\expandafter\opt@color\first@
\ifx\f@color\comm@
\expandafter\xdef\csname fileseqHMMTOP\the\temp@count\endcsname{0}
\else
\expandafter\xdef\csname fileseqHMMTOP\the\temp@count\endcsname{\f@color}
\fi
\xdef\first@{\fourth@ @} \expandafter\check@letter\first@
\xdef\first@{\fourth@} \ifletter \get@name@number \fi
\expandafter\xdef\csname doseqHMMTOP\the\temp@count\endcsname{\first@}
\expandafter\xdef\csname filenameHMMTOP\the\temp@count\endcsname{#3}
\expandafter\ifnum\csname doseqHMMTOP\the\temp@count\endcsname>\seq@count
\message{<Ignoring `#2' in \noexpand\includeHMMTOP>}
\advance\temp@count by -1
\xdef\HMMTOP@num{\the\temp@count}
\fi
}
\newcommand{\includeSTRIDE}[3][existing]{%
\temp@count=\stride@num
\advance\temp@count by 1
\xdef\stride@num{\the\temp@count}
\xdef\first@{#1} \xdef\temp@{existing}
\ifx\first@\temp@ \else\xdef\first@{make new}\fi
\expandafter\xdef\csname optionstride\the\temp@count\endcsname{\first@}
\xdef\first@{#2 @} \expandafter\check@letter\first@
\xdef\first@{#2} \ifletter \get@name@number \fi
\expandafter\xdef\csname doseqstride\the\temp@count\endcsname{\first@}
\expandafter\xdef\csname filenamestride\the\temp@count\endcsname{#3}
\expandafter\ifnum\csname doseqstride\the\temp@count\endcsname>\seq@count
\message{<Ignoring `#2' in \noexpand\includeSTRIDE>}
\advance\temp@count by -1
\xdef\stride@num{\the\temp@count}
\fi
}
\newcommand{\includePHDsec}[3][existing]{%
\temp@count=\PHD@num
\advance\temp@count by 1
\xdef\PHD@num{\the\temp@count}
\xdef\first@{#1} \xdef\temp@{existing}
\ifx\first@\temp@ \else\xdef\first@{make new}\fi
\expandafter\xdef\csname optionphd\the\temp@count\endcsname{\first@}
\xdef\first@{#2 @} \expandafter\check@letter\first@
\xdef\first@{#2} \ifletter \get@name@number \fi
\expandafter\xdef\csname doseqphd\the\temp@count\endcsname{\first@}
\expandafter\xdef\csname modephd\the\temp@count\endcsname{structure}
\expandafter\xdef\csname filenamephd\the\temp@count\endcsname{#3}
\expandafter\ifnum\csname doseqphd\the\temp@count\endcsname>\seq@count
\message{<Ignoring `#2' in \noexpand\includePHDsec>}
\advance\temp@count by -1
\xdef\PHD@num{\the\temp@count}
\fi
}
\newcommand{\includePHDtopo}[3][existing]{%
\temp@count=\PHD@num
\advance\temp@count by 1
\xdef\PHD@num{\the\temp@count}
\xdef\first@{#1} \xdef\temp@{existing}
\ifx\first@\temp@ \else\xdef\first@{make new}\fi
\expandafter\xdef\csname optionphd\the\temp@count\endcsname{\first@}
\xdef\first@{#2 @} \expandafter\check@letter\first@
\xdef\first@{#2} \ifletter \get@name@number \fi
\expandafter\xdef\csname doseqphd\the\temp@count\endcsname{\first@}
\expandafter\xdef\csname modephd\the\temp@count\endcsname{topology}
\expandafter\xdef\csname filenamephd\the\temp@count\endcsname{#3}
\expandafter\ifnum\csname doseqphd\the\temp@count\endcsname>\seq@count
\message{<Ignoring `#2' in \noexpand\includePHDtopo>}
\advance\temp@count by -1
\xdef\PHD@num{\the\temp@count}
\fi
}
\def\appearance#1#2#3#4#5{%
\xdef\first@{#1} \xdef\second@{#2}
\xdef\temp@{PHDsec}
\ifx\temp@\first@
\xdef\temp@{alpha}
\ifx\second@\temp@
\def\bottop@Hsec{#3}
\def\label@Hsec{#4}
\def\text@Hsec{#5}
\else
\xdef\temp@{beta}
\ifx\second@\temp@
\def\bottop@Esec{#3}
\def\label@Esec{#4}
\def\text@Esec{#5}
\fi\fi
\else
\xdef\temp@{PHDtopo}
\ifx\temp@\first@
\xdef\temp@{internal}
\ifx\second@\temp@
\def\bottop@itop{#3}
\def\label@itop{#4}
\def\text@itop{#5}
\else
\xdef\temp@{external}
\ifx\second@\temp@
\def\bottop@etop{#3}
\def\label@etop{#4}
\def\text@etop{#5}
\else
\xdef\temp@{TM}
\ifx\second@\temp@
\def\bottop@TMtop{#3}
\def\label@TMtop{#4}
\def\text@TMtop{#5}
\fi\fi\fi
\else
\xdef\temp@{STRIDE}
\ifx\temp@\first@
\xdef\temp@{alpha}
\ifx\second@\temp@
\def\bottop@Hstride{#3}
\def\label@Hstride{#4}
\def\text@Hstride{#5}
\else
\xdef\temp@{3-10}
\ifx\second@\temp@
\def\bottop@Gstride{#3}
\def\label@Gstride{#4}
\def\text@Gstride{#5}
\else
\xdef\temp@{pi}
\ifx\second@\temp@
\def\bottop@Istride{#3}
\def\label@Istride{#4}
\def\text@Istride{#5}
\else
\xdef\temp@{beta}
\ifx\second@\temp@
\def\bottop@Estride{#3}
\def\label@Estride{#4}
\def\text@Estride{#5}
\else
\xdef\temp@{bridge}
\ifx\second@\temp@
\def\bottop@Bstride{#3}
\def\label@Bstride{#4}
\def\text@Bstride{#5}
\else
\xdef\temp@{turn}
\ifx\second@\temp@
\def\bottop@Tstride{#3}
\def\label@Tstride{#4}
\def\text@Tstride{#5}
\fi\fi\fi\fi\fi\fi
\else
\xdef\temp@{DSSP}
\ifx\temp@\first@
\xdef\temp@{alpha}
\ifx\second@\temp@
\def\bottop@Hdssp{#3}
\def\label@Hdssp{#4}
\def\text@Hdssp{#5}
\else
\xdef\temp@{3-10}
\ifx\second@\temp@
\def\bottop@Gdssp{#3}
\def\label@Gdssp{#4}
\def\text@Gdssp{#5}
\else
\xdef\temp@{pi}
\ifx\second@\temp@
\def\bottop@Idssp{#3}
\def\label@Idssp{#4}
\def\text@Idssp{#5}
\else
\xdef\temp@{beta}
\ifx\second@\temp@
\def\bottop@Edssp{#3}
\def\label@Edssp{#4}
\def\text@Edssp{#5}
\else
\xdef\temp@{bridge}
\ifx\second@\temp@
\def\bottop@Bdssp{#3}
\def\label@Bdssp{#4}
\def\text@Bdssp{#5}
\else
\xdef\temp@{turn}
\ifx\second@\temp@
\def\bottop@Tdssp{#3}
\def\label@Tdssp{#4}
\def\text@Tdssp{#5}
\else
\xdef\temp@{bend}
\ifx\second@\temp@
\def\bottop@Sdssp{#3}
\def\label@Sdssp{#4}
\def\text@Sdssp{#5}
\fi\fi\fi\fi\fi\fi\fi
\else
\xdef\temp@{HMMTOP}
\ifx\temp@\first@
\xdef\temp@{internal}
\ifx\second@\temp@
\def\bottop@i@HMMTOP{#3}
\def\label@i@HMMTOP{#4}
\def\text@i@HMMTOP{#5}
\else
\xdef\temp@{external}
\ifx\second@\temp@
\def\bottop@e@HMMTOP{#3}
\def\label@e@HMMTOP{#4}
\def\text@e@HMMTOP{#5}
\else
\xdef\temp@{TM}
\ifx\second@\temp@
\def\bottop@TM@HMMTOP{#3}
\def\label@TM@HMMTOP{#4}
\def\text@TM@HMMTOP{#5}
\fi\fi\fi
\fi\fi\fi\fi\fi
}
\def\showonDSSP#1{%
\xdef\first@{#1,&,@} \xdef\second@{yes} \show@DSSP}
\def\hideonDSSP#1{%
\xdef\first@{#1,&,@} \xdef\second@{no} \show@DSSP}
\def\showonSTRIDE#1{%
\xdef\first@{#1,&,@} \xdef\second@{yes} \show@STRIDE}
\def\hideonSTRIDE#1{%
\xdef\first@{#1,&,@} \xdef\second@{no} \show@STRIDE}
\def\showonPHDtopo#1{%
\xdef\first@{#1,&,@} \xdef\second@{yes} \show@PHDtopo}
\def\hideonPHDtopo#1{%
\xdef\first@{#1,&,@} \xdef\second@{no} \show@PHDtopo}
\def\showonPHDsec#1{%
\xdef\first@{#1,&,@} \xdef\second@{yes} \show@PHDsec}
\def\hideonPHDsec#1{%
\xdef\first@{#1,&,@} \xdef\second@{no} \show@PHDsec}
\def\showonHMMTOP#1{%
\xdef\first@{#1,&,@} \xdef\second@{yes} \show@HMMTOP}
\def\hideonHMMTOP#1{%
\xdef\first@{#1,&,@} \xdef\second@{no} \show@HMMTOP}
\def\codon#1#2{%
\xdef\first@{#1}
\xdef\second@{#2,&,@}
\expandafter\get@triplet\second@}
\def\geneticcode#1{%
\xdef\first@{#1}
\xdef\temp@{standard}
\ifx\first@\temp@
\c@d@ns
\else
\input{#1.cod}
\fi}
\newcommand{\backtranslabel}[2][tiny]{%
\def\trans@size{\csname #1\endcsname}
\xdef\first@{#2}
\xdef\temp@{horizontal}
\ifx\temp@\first@ \xdef\tr@nsstyle{0}\fi
\xdef\temp@{zigzag}
\ifx\temp@\first@ \xdef\tr@nsstyle{1}\fi
\xdef\temp@{alternating}
\ifx\temp@\first@ \xdef\tr@nsstyle{2}\fi
\xdef\temp@{oblique}
\ifx\temp@\first@ \xdef\tr@nsstyle{3}\fi
\xdef\temp@{vertical}
\ifx\temp@\first@ \xdef\tr@nsstyle{4}\fi
}
\newcommand{\backtranstext}[2][tiny]{%
\def\transtext@size{\csname #1\endcsname}
\xdef\first@{#2}
\xdef\temp@{horizontal}
\ifx\temp@\first@ \xdef\tr@nstextstyle{0}\fi
\xdef\temp@{zigzag}
\ifx\temp@\first@ \xdef\tr@nstextstyle{1}\fi
\xdef\temp@{alternating}
\ifx\temp@\first@ \xdef\tr@nstextstyle{2}\fi
\xdef\temp@{oblique}
\ifx\temp@\first@ \xdef\tr@nstextstyle{3}\fi
\xdef\temp@{vertical}
\ifx\temp@\first@ \xdef\tr@nstextstyle{4}\fi
}
\newcommand\exportconsensus[2][export.txt]{%
\ifx\exp@rt\n@
\xdef\first@{#2 @} \expandafter\check@letter\first@
\xdef\first@{#2} \ifletter \get@name@number \fi
\xdef\exp@rt@num{\first@}
\xdef\exp@rt{y}
\immediate\openout\exp@rtfile = #1
\fi
}
\def\setdomain#1#2{%
\xdef\first@{#1}
\xdef\temp@{consensus}
\ifx\first@\temp@ \xdef\domain@seq{0}
\else
\xdef\first@{#1 @} \expandafter\check@letter\first@
\xdef\first@{#1} \ifletter \get@name@number \fi
\xdef\domain@seq{\csname @rd\first@\endcsname}%
\fi
\xdef\list@{#2,&}
\xdef\temp@{#2,,,:,,,,@} \expandafter\test@PDB\temp@
\loop
\xdef\list@{\list@ @}
\expandafter\get@domainregions\list@
\ifx\list@\ampers@nd\else\repeat
\xdef\dom@in{y}
}
\def\decimal@IOO#1#2#3{#1#2\temp@#3}
\def\decimal@IO#1#2{#1\temp@#2}
\def\decimal@I#1{0\temp@#1}
\def\percentsimilarity#1#2{%
\xdef\first@{#2@}\expandafter\check@letter\first@%
\xdef\first@{#2}\xdef\second@@{#2}%
\ifletter\get@name@number@table\xdef\second@@{\first@}\fi%
\xdef\first@{#1@}\expandafter\check@letter\first@%
\xdef\first@{#1}\xdef\first@@{#1}%
\ifletter\get@name@number@table\xdef\first@@{\first@}\fi%
\ifnum\first@@<\second@@%
\loopcount=\csname simcount\first@@ @\second@@\endcsname%
\temp@count=\csname poscount\first@@ @\second@@\endcsname%
\else%
\ifnum\first@@=\second@@ \loopcount=1 \temp@count=1%
\else%
\loopcount=\csname simcount\second@@ @\first@@\endcsname%
\temp@count=\csname poscount\second@@ @\first@@\endcsname%
\fi%
\fi%
\multiply\loopcount by 1000%
\divide\loopcount by \temp@count%
\xdef\first@{\the\loopcount}%
\ifgerm@n\xdef\temp@{,}\else\xdef\temp@{.}\fi%
\ifnum\first@=1000 100\temp@0%
\else%
\ifnum\first@>99 \expandafter\decimal@IOO\first@%
\else%
\ifnum\first@>9 \expandafter\decimal@IO\first@%
\else%
\ifnum\first@>0 \expandafter\decimal@I\first@%
\else 0\temp@0%
\fi%
\fi%
\fi%
\fi%
}
\def\percentidentity#1#2{%
\xdef\first@{#2@}\expandafter\check@letter\first@%
\xdef\first@{#2}\xdef\second@@{#2}%
\ifletter\get@name@number@table\xdef\second@@{\first@}\fi%
\xdef\first@{#1@}\expandafter\check@letter\first@%
\xdef\first@{#1}\xdef\first@@{#1}%
\ifletter\get@name@number@table\xdef\first@@{\first@}\fi%
\ifnum\first@@<\second@@%
\loopcount=\csname identcount\first@@ @\second@@\endcsname%
\temp@count=\csname poscount\first@@ @\second@@\endcsname%
\else%
\ifnum\first@@=\second@@ \loopcount=1 \temp@count=1%
\else%
\loopcount=\csname identcount\second@@ @\first@@\endcsname%
\temp@count=\csname poscount\second@@ @\first@@\endcsname%
\fi%
\fi%
\multiply\loopcount by 1000%
\divide\loopcount by \temp@count%
\xdef\first@{\the\loopcount}%
\ifgerm@n\xdef\temp@{,}\else\xdef\temp@{.}\fi%
\ifnum\first@=1000 100\temp@0%
\else%
\ifnum\first@>99 \expandafter\decimal@IOO\first@%
\else%
\ifnum\first@>9 \expandafter\decimal@IO\first@%
\else%
\ifnum\first@>0 \expandafter\decimal@I\first@%
\else 0\temp@0%
\fi%
\fi%
\fi%
\fi%
}
\def\similaritytable{%
\def\name@loop{%
\advance\outerloopcount by 1
\ifnum\outerloopcount>\seq@num\relax
\else
\immediate\write\exp@rtfile{&\string\multicolumn{1}{c}{\string\kern1ex\string\begin{rotopo}{90}\csname newseqname\the\outerloopcount\endcsname\string\end{rotopo}}}
\name@loop\fi
}
\def\inner@loop{%
\advance\innerloopcount by 1
\ifnum\innerloopcount>\seq@num\relax
\else
\ifnum\innerloopcount=\outerloopcount\relax \immediate\write\exp@rtfile{& {---\hss}}\fi
\ifnum\innerloopcount>\outerloopcount\relax \immediate\write\exp@rtfile{& \string\percentsimilarity{\the\outerloopcount}{\the\innerloopcount}}\fi
\ifnum\innerloopcount<\outerloopcount\relax \immediate\write\exp@rtfile{& \string\percentidentity{\the\outerloopcount}{\the\innerloopcount}}\fi
\inner@loop\fi
}
\def\outer@loop{%
\advance\outerloopcount by 1
\ifnum\outerloopcount>\seq@num\relax
\else
\immediate\write\exp@rtfile{\csname newseqname\the\outerloopcount\endcsname}
\innerloopcount=0 \inner@loop \immediate\write\exp@rtfile{&\string\\}
\outer@loop\fi
}
\xdef\temp@{l|}
\outerloopcount=0
\loop
\advance\outerloopcount by 1
\xdef\temp@{\temp@ r}
\ifnum\outerloopcount<\seq@num\repeat
\advance\outerloopcount by 1 \xdef\seq@num@plus{\the\outerloopcount}
\advance\outerloopcount by 1 \xdef\seq@num@plus@plus{\the\outerloopcount}
\ifnum\seq@num<3 \xdef\temp@@{$\approx$} \else
\ifnum\seq@num<5 \xdef\temp@@{simil.}\ifgerm@n\def\temp@@{\string\"{A}hnl.}\fi\ifsp@nish\xdef\temp@@{simil.}\fi\else
\xdef\temp@@{similarity}
\ifgerm@n\ifnum\seq@num=5\def\temp@@{\string\"{A}hnlichk.}\else\def\temp@@{\string\"{A}hnlichkeit}\fi\fi\ifsp@nish\xdef\temp@@{similitud}\fi\fi
\fi
\xdef\temp@@@{identity}\ifgerm@n\def\temp@@@{Identit\string\"{a}t}\fi\ifsp@nish\xdef\temp@@@{identidad}\fi
\immediate\openout\exp@rtfile = simtable.tmp
\immediate\write\exp@rtfile{\string\begin{tabular}{\temp@ |r}}
\immediate\write\exp@rtfile{\string\multicolumn{\seq@num@plus@plus}{c}{}\string\\[\name@@width]}
\immediate\write\exp@rtfile{\string\multicolumn{1}{c}{}}
\outerloopcount=0 \name@loop \immediate\write\exp@rtfile{&\string\\ \string\cline{2-\seq@num@plus}}
\immediate\write\exp@rtfile{&\string\multicolumn{\seq@num}{|c|}{}&\string\\[-2ex]}
\outerloopcount=0 \outer@loop
\immediate\write\exp@rtfile{\string\cline{2-\seq@num@plus}}
\immediate\write\exp@rtfile{\string\multicolumn{\seq@num@plus}{c}{}&}
\immediate\write\exp@rtfile{\string\multicolumn{1}{r}{\string\kern1.5ex\string\begin{rotopo}{90}\kern1em\% \temp@@\string\end{rotopo}}\string\\[-2ex]}
\immediate\write\exp@rtfile{\string\multicolumn{1}{c}{}&\string\multicolumn{\seq@num}{l}{\% \temp@@@}&\string\\}
\immediate\write\exp@rtfile{\string\end{tabular}}
\immediate\closeout\exp@rtfile
\input{simtable.tmp}
}
\def\identitytable{\similaritytable}
%%%%% Calculate consensus
\def\check@sim{%
\xdef\first@{\csname res\the\loopcount\endcsname}
\xdef\first@{\csname \prefix@ grp\first@\endcsname}
\newrestrue
\ifnum\first@<0 \newresfalse
\else
\innerloopcount=\loopcount
\ifnum\loopcount=\cons@num \innerloopcount=\seq@count \fi
\ifnum\innerloopcount<\seq@count
\loop
\advance\innerloopcount by 1
\xdef\second@{\csname res\the\innerloopcount\endcsname}
\expandafter\ifx\csname \prefix@ grp\second@\endcsname\first@
\newresfalse \innerloopcount=\seq@count \fi
\ifnum\innerloopcount<\seq@count \repeat
\fi
\fi
\ifnewres
\pos@sum=0
\innerloopcount=0
\loop
\advance\innerloopcount by 1
\xdef\second@{\csname res\the\innerloopcount\endcsname}
\expandafter\ifx\csname \prefix@ grp\second@\endcsname\first@
\advance\pos@sum by 1 \fi
\ifnum\innerloopcount<\seq@count \repeat
\multiply\pos@sum by \seq@percent
\expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
\expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
\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
\multiply\pos@sum by \seq@percent
\expandafter\xdef\csname pos\the\loopcount\endcsname{\the\pos@sum}
\expandafter\ifnum\csname pos\the\loopcount\endcsname<\thresh@ld
\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{<No subfamilies found (check threshold) - hiding subfamily logo>}
\show@sublogofalse
\immediate\write\featurefile{<No subfamilies found (check threshold) - hiding subfamily logo>}
\fi
\loopcount=\seq@count
\advance\loopcount by -\temp@count
\ifnum\loopcount>0
\expandafter\xdef\csname group@num1\endcsname{\the\loopcount}
\else
\message{<No subfamilies found (check threshold) - hiding subfamily logo>}
\immediate\write\featurefile{<No subfamilies found (check threshold) - hiding subfamily logo>}
\show@sublogofalse
\fi
\else
\immediate\write\featurefile{TeXshade subfamily logo data file for \alignfilename}
\immediate\write\featurefile{--}
\immediate\write\featurefile{Average information content [1000*bits per position]: \bit@mean}
\immediate\write\featurefile{Subfamily threshold setting [percent]: \subfamily@threshold}
\immediate\write\featurefile{=> \bit@mean\space * 0.\subfamily@threshold\space = \sub@threshold\space [1000*bits per position]}
\immediate\write\featurefile{}
\immediate\write\featurefile{User defined subfamily: \sub@family@setting}
\immediate\write\featurefile{}
\immediate\write\featurefile{//}
\fi
}
\def\prep@sublogo{%
\message{<Calculating subfamily logo...>}
\immediate\openout\featurefile = sublogo.txt
\if\seq@type P
\ifx\do@freq@correction\y@
\xdef\do@freq@correction{n}
\loopcount=1
\loop
\xdef\first@{\csname @rd\the\loopcount\endcsname} %%%
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\first@\endcsname &@}
\advance\loopcount by 1
\ifnum\loopcount>\seq@count\else\repeat
\xdef\corr@max{0}
\loopcount=1
\calc@total@frequency
\total@frequency@correction
\fi
\fi
\loopcount=1
\loop
\xdef\first@{\csname @rd\the\loopcount\endcsname} %%%
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\first@\endcsname &@}
\advance\loopcount by 1
\ifnum\loopcount>\seq@count\else\repeat
\loopcount=1
\do@grouping
\define@subfamilies
\ifshow@sublogo
\loopcount=1
\loop
\xdef\first@{\csname @rd\the\loopcount\endcsname} %%%
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\first@\endcsname &@}
\advance\loopcount by 1
\ifnum\loopcount>\seq@count\else\repeat
\xdef\first@{\csname group@num1\endcsname}
\xdef\first@@{\csname log2@\first@\endcsname}
\xdef\second@{\csname group@num2\endcsname}
\xdef\second@@{\csname log2@\second@\endcsname}
\loopcount=\first@
\advance\loopcount by \second@
\xdef\third@{\the\loopcount}
\xdef\third@@{\csname log2@\third@\endcsname}
\loopcount=\first@@
\advance\loopcount by -\third@@
\multiply\loopcount by \first@
\divide\loopcount by \third@
\xdef\first@@@{\the\loopcount}
\loopcount=\second@@
\advance\loopcount by -\third@@
\multiply\loopcount by \second@
\divide\loopcount by \third@
\xdef\second@@@{\the\loopcount}
\loopcount=\bit@max
\advance\loopcount by \first@@@
\advance\loopcount by \second@@@
\xdef\group@correction{\the\loopcount}
\loopcount=1 \total@count=0
\do@sublogo
\immediate\closeout\featurefile
\openin\sublogofile = sublogo.txt\relax
\read@header
\else
\immediate\closeout\featurefile
\fi
}
\def\read@header{%
\read\sublogofile to \first@\relax
\xdef\first@{\expandafter\string\first@}
\ifx\first@\par@ \read@header
\else
\xdef\first@{\first@ @}
\expandafter\seq@get\first@
\ifx\first@\he@derend
\else\read@header
\fi
\fi
}
\def\read@sublogo{%
\xdef\stack@sublogo{}%
\loopcount=1 %
\loop%
\ifeof\sublogofile%
\advance\loopcount by \res@perline%
\else%
\read\sublogofile to \first@\relax%
\xdef\first@{\expandafter\string\first@}%
\ifx\first@\par@%
\advance\loopcount by \res@perline%
\else
\xdef\first@{\first@ @}%
\expandafter\sublogo@get\first@%
\xdef\stack@sublogo{\stack@sublogo\first@}%
\advance\loopcount by 1%
\fi%
\fi%
\ifnum\loopcount=\res@perline\else\repeat%
}
\def\calc@sublogo{%
\xdef\seventh@{\csname res@num.2\endcsname}
\xdef\first@{\csname group@num2\endcsname}
\innerloopcount=\first@
\advance\innerloopcount by -\seventh@
\xdef\seventh@{\the\innerloopcount}
\xdef\eighth@{\csname res@num.1\endcsname}
\xdef\first@{\csname group@num1\endcsname}
\innerloopcount=\first@
\advance\innerloopcount by -\eighth@
\xdef\eighth@{\the\innerloopcount}
\xdef\nineth@{n}
\xdef\pos@max{0}
\xdef\pos@min{0}
\outerloopcount=65
\loop
\xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname}
\xdef\first@{\csname res@num\first@@ 1\endcsname} \xdef\temp@{\first@}
\temp@count=\first@
\ifnum\seventh@>0 \multiply\temp@count by \seventh@ \fi
\xdef\first@{\the\temp@count}
\xdef\second@{\csname res@num\first@@ 2\endcsname}
\temp@count=\temp@
\advance\temp@count by \second@\relax
\ifnum\temp@count>0
\temp@count=\second@
\ifnum\eighth@>0 \multiply\temp@count by \eighth@ \fi
\advance\temp@count by -\first@
\xdef\last@{\csname bit@pos\the\loopcount\endcsname}
\multiply\temp@count by \last@
\ifnum\seventh@>0 \divide\temp@count by \seventh@ \fi
\ifnum\eighth@>0 \divide\temp@count by \eighth@ \fi
\multiply\temp@count by \bit@max
\divide\temp@count by \group@correction
\ifx\hide@negatives\y@
\ifnum\temp@count>0 \else \temp@count=1 \fi%
\else
\ifnum\temp@count=0 \temp@count=1 \fi%
\fi
\expandafter\xdef\csname res@val\first@@\endcsname{\the\temp@count}
\expandafter\xdef\csname res@num\first@@ 1\endcsname{0}
\expandafter\xdef\csname res@num\first@@ 2\endcsname{0}
\xdef\nineth@{y}
\else
\expandafter\xdef\csname res@val\first@@\endcsname{0}
\expandafter\xdef\csname res@num\first@@ 1\endcsname{0}
\expandafter\xdef\csname res@num\first@@ 2\endcsname{0}
\fi
\ifnum\temp@count>\pos@max \xdef\pos@max{\the\temp@count}\fi
\ifnum\temp@count<\pos@min \xdef\pos@min{\the\temp@count}\fi
\advance\outerloopcount by 1
\ifnum\outerloopcount>90\else\repeat
\expandafter\xdef\csname res@val\d@t\endcsname{0}
\expandafter\xdef\csname res@num\d@t 1\endcsname{0}
\expandafter\xdef\csname res@num\d@t 2\endcsname{0}
\temp@count=\pos@min\relax
\multiply\temp@count by -1\relax
\xdef\pos@min{\the\temp@count}
\ifnum\pos@min>\pos@max \xdef\pos@max{\pos@min}\fi
\temp@count=\pos@max
\multiply\temp@count by 100 \relax
\divide\temp@count by \bit@max \relax
\xdef\sublogo@num{\sublogo@num\the\temp@count,}
\ifnum\pos@max<\sig@max \xdef\sublogo@sig{\sublogo@sig n} \else \xdef\sublogo@sig{\sublogo@sig y} \fi
\ifx\nineth@\y@
\xdef\tmpstack{&:&,}
\outerloopcount=65
\loop
\xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname}
\xdef\second@@{\csname res@val\first@@\endcsname}
\ifnum\second@@=0
\else
\xdef\third@{\tmpstack @} \xdef\tmpstack{}
\sort@logostack
\fi
\advance\outerloopcount by 1
\ifnum\outerloopcount>90
\immediate\write\featurefile{\expandafter\string\tmpstack&:&,}
\else\repeat
\else
\immediate\write\featurefile{\expandafter\string O:0,&:&,}
\fi
}
\def\do@sublogo{%
\ifnum\loopcount>\total@pos
\xdef\sublogo@sig{\sublogo@sig &@}
\else
\triple@count=1
\loop
\xdef\first@{\csname seq\the\triple@count\endcsname}
\expandafter\dis@get\first@
\ifnum\triple@count=\start@seq
\ifx\first@\d@t\else \advance\total@count by 1\relax\fi
\fi
\ifnum\loopcount<\start@number
\else
\ifnum\total@count>\end@num
\else
\ifx\first@\ampers@nd
\else
\xdef\second@{\csname subfamily@num\the\triple@count\endcsname}
\innerloopcount=\csname res@num\first@\second@\endcsname
\advance\innerloopcount by 1
\expandafter\xdef\csname res@num\first@\second@\endcsname{\the\innerloopcount}
\fi
\fi
\fi
\advance\triple@count by 1\relax
\ifnum\triple@count>\seq@count
\ifnum\loopcount<\start@number
\else
\ifnum\total@count>\end@num
\else
\calc@sublogo
\fi
\fi
\advance\loopcount by 1
\do@sublogo
\else
\repeat
\fi
}
\def\calc@logo{%
\xdef\second@{\csname res@num\d@t\endcsname}
\innerloopcount=\seq@count
\advance\innerloopcount by -\second@
\xdef\second@{\the\innerloopcount}
\xdef\seventh@{0}
\innerloopcount=0
\outerloopcount=65
\loop
\xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname}
\xdef\first@{\csname res@num\first@@\endcsname}
\ifnum\first@>0
\temp@count=\csname log2@\first@\endcsname
\advance\temp@count by -\csname log2@\second@\endcsname
\advance\temp@count by \csname res@corr\first@@\endcsname %%%% correct for background freq.
\multiply\temp@count by -\first@
\divide\temp@count by \second@
\advance\innerloopcount by \temp@count\relax
\fi
\advance\outerloopcount by 1
\ifnum\outerloopcount>90\else\repeat
\if\seq@type P
\temp@count=\csname log2@20\endcsname
\else
\temp@count=\csname log2@4\endcsname
\fi
\advance\temp@count by -\innerloopcount
\multiply\temp@count by \second@
\divide\temp@count by \seq@count
\xdef\last@{\the\temp@count}
\xdef\nineth@{n}
\outerloopcount=65
\loop
\xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname}
\xdef\first@{\csname res@num\first@@\endcsname}
\ifnum\first@>0
\temp@count=\last@
\multiply\temp@count by \first@\relax
\divide\temp@count by \second@\relax
\ifnum\temp@count=0 %
\temp@count=1 %
\fi%
\expandafter\xdef\csname res@val\first@@\endcsname{\the\temp@count}
\expandafter\xdef\csname res@num\first@@\endcsname{0}
\xdef\nineth@{y}
\else
\expandafter\xdef\csname res@val\first@@\endcsname{0}
\fi
\advance\outerloopcount by 1
\ifnum\outerloopcount>90\else\repeat
\expandafter\xdef\csname res@val\d@t\endcsname{0}
\expandafter\xdef\csname res@num\d@t\endcsname{0}
\ifx\nineth@\y@
\xdef\tmpstack{&:&,}
\outerloopcount=65
\loop
\xdef\first@@{\csname ch@r@\the\outerloopcount\endcsname}
\xdef\second@@{\csname res@val\first@@\endcsname}
\ifnum\second@@>0
\xdef\third@{\tmpstack @} \xdef\tmpstack{}
\sort@logostack
\fi
\advance\outerloopcount by 1
\ifnum\outerloopcount>90
\xdef\stack@sequencelogo{\stack@sequencelogo\tmpstack&:&,}
\else\repeat
\else
\xdef\stack@sequencelogo{\stack@sequencelogo O:0,&:&,}
\fi
}
\def\get@fromlogostack#1:#2,#3@{%
\xdef\first@{#1} \xdef\second@{#2} \xdef\third@{#3}
}
\def\sort@logostack{%
\expandafter\get@fromlogostack\third@
\ifx\first@\ampers@nd
\xdef\tmpstack{\tmpstack\first@@:\second@@,}
\else
\ifnum\second@@<0
\ifnum\second@>0
\xdef\tmpstack{\tmpstack\first@@:\second@@,\first@:\second@,\third@}
\else
\temp@count=\second@@\relax \multiply\temp@count by -1\relax
\triple@count=\second@\relax \multiply\triple@count by -1\relax
\ifnum\temp@count<\triple@count
\xdef\tmpstack{\tmpstack\first@@:\second@@,\first@:\second@,\third@}
\else
\xdef\tmpstack{\tmpstack\first@:\second@,}
\xdef\third@@{\third@ .}
\ifx\third@@\d@t
\xdef\third@{&:&,@}
\else
\xdef\third@{\third@ @}
\fi
\sort@logostack
\fi
\fi
\else
\ifnum\second@@<\second@
\xdef\tmpstack{\tmpstack\first@@:\second@@,\first@:\second@,\third@}
\else
\xdef\tmpstack{\tmpstack\first@:\second@,}
\xdef\third@@{\third@ .}
\ifx\third@@\d@t
\xdef\third@{&:&,@}
\else
\xdef\third@{\third@ @}
\fi
\sort@logostack
\fi
\fi
\fi
}
\def\calc@feature{%
\loopcount=-1 \innerloopcount=0
\loop
\advance\loopcount by 1
\ifnum\loopcount=0 \xdef\first@@{\the\cons@count}
\else \xdef\first@@{\csname res@count\the\loopcount\endcsname} \fi
\expandafter\ifx\csname start\bottop@\the\loopcount\endcsname\ampers@nd
\else
\expandafter\ifnum\csname start\bottop@\the\loopcount\endcsname>\first@@
\else
\expandafter\ifnum\csname stop\bottop@\the\loopcount\endcsname<\first@@
\expandafter\getregion@fromfstack{\the\loopcount}
\else
\innerloopcount=\loopcount
\expandafter\ifnum\csname featureon\bottop@\endcsname=0
\expandafter\xdef\csname featureon\bottop@\endcsname{1}
\expandafter\xdef\csname feature@\bottop@\endcsname{1}
\expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{%
\csname text\bottop@\the\loopcount\endcsname}
\expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{%
\csname style\bottop@\the\loopcount\endcsname}
\innerloopcount=\pos@count
\advance\innerloopcount by -\csname featurepos\bottop@\endcsname
\expandafter\xdef\csname textfeature\bottop@\endcsname{%
\csname textfeature\bottop@\endcsname%
&\the\innerloopcount;{};}
\expandafter\xdef\csname stylefeature\bottop@\endcsname{%
\csname stylefeature\bottop@\endcsname%
&\the\innerloopcount;&;}
\expandafter\xdef\csname featurepos\bottop@\endcsname{\the\pos@count}
\xdef\temp@@@{n}
\xdef\fourth@{}
\xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname}
\xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@
\ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi
\xdef\fourth@{}
\xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname}
\xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@
\ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi
\ifx\temp@@@\y@
\ifnum\loopcount=0
\message{<No translations of the consensus sequence>}
\expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{%
No consensus translations!}
\expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{%
///}
\else
\if\seq@type P
\expandafter\xdef\csname collect@res\bottop@\endcsname{yes}
\expandafter\xdef\csname tr@nsseq\bottop@\endcsname{\the\loopcount}
\expandafter\xdef\csname tr@nslate\bottop@\endcsname{%
\csname res\the\loopcount\endcsname}
\else
\expandafter\xdef\csname collect@res\bottop@\endcsname{yes}
\expandafter\xdef\csname tr@nsseq\bottop@\endcsname{\the\loopcount}
\expandafter\ifx\csname res\the\loopcount\endcsname\gap@char
\expandafter\xdef\csname triple@count\bottop@\endcsname{0}
\expandafter\xdef\csname tr@nslate\bottop@\endcsname{-}
\else
\expandafter\xdef\csname triple@count\bottop@\endcsname{1}
\expandafter\xdef\csname tr@nslate\bottop@\endcsname{%
\csname res\the\loopcount\endcsname}
\expandafter\xdef\csname last@@res\bottop@\endcsname{%
\csname res\the\loopcount\endcsname}
\fi
\fi
\fi
\fi
\xdef\temp@{plot}
\ifx\temp@\fourth@
\ifnum\loopcount=0
\message{<No bar graphs/scales with the consensus sequence>}
\expandafter\xdef\csname ftext\bottop@\the\loopcount\endcsname{}
\expandafter\xdef\csname fstyle\bottop@\the\loopcount\endcsname{%
///}
\else
\expandafter\xdef\csname collect@val\bottop@\endcsname{yes}
\expandafter\xdef\csname v@lseq\bottop@\endcsname{\the\loopcount}
\expandafter\xdef\csname ffourth@\bottop@\endcsname{\ffourth@}
\xdef\temp@{\ffourth@\csname res\the\loopcount\endcsname}
\expandafter\xdef\csname v@l\bottop@\endcsname{\csname \temp@\endcsname}
\fi
\fi
\xdef\temp@{cons}
\ifx\temp@\fourth@
\expandafter\xdef\csname collect@cons@graph\bottop@\endcsname{yes}
\expandafter\xdef\csname v@lseq\bottop@\endcsname{\the\loopcount}
\expandafter\xdef\csname ffourth@\bottop@\endcsname{\ffourth@}
\innerloopcount=1
\collect@cons@res
\expandafter\xdef\csname v@l\bottop@\endcsname{\cons@val}
\fi
\else
\ifnum\pos@count=1\relax
\xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname @}
\expandafter\getstyle@right\temp@
\xdef\temp@@@{n}
\xdef\fourth@{}
\xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname}
\xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@
\ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi
\xdef\fourth@{}
\xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname}
\xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@
\ifx\fourth@\tr@ns \xdef\temp@@@{y} \fi
\ifx\temp@@@\y@
\if\seq@type P
\expandafter\xdef\csname tr@nslate\bottop@\endcsname{%
\csname res\the\loopcount\endcsname}
\else
\expandafter\ifnum\csname triple@count\bottop@\endcsname=2
\expandafter\ifx\csname res\the\loopcount\endcsname\gap@char
\else
\expandafter\xdef\csname tr@nslate\bottop@\endcsname{%
+\csname last@res\bottop@\endcsname%
\csname tr@nslate\bottop@\endcsname}
\fi
\fi
\expandafter\ifnum\csname triple@count\bottop@\endcsname=1
\expandafter\xdef\csname last@res\bottop@\endcsname{%
\csname last@@res\bottop@\endcsname}
\expandafter\ifx\csname res\the\loopcount\endcsname\gap@char
\expandafter\xdef\csname tr@nslate\bottop@\endcsname{%
+\csname last@res\bottop@\endcsname%
\csname tr@nslate\bottop@\endcsname}
\fi
\fi
\fi
\fi
\xdef\temp@{plot}
\ifx\temp@\fourth@
\expandafter\ifx\csname res\the\loopcount\endcsname\gap@char
\expandafter\xdef\csname v@l\bottop@\endcsname{N}
\else
\xdef\temp@{\ffourth@\csname res\the\loopcount\endcsname}
\expandafter\xdef\csname v@l\bottop@\endcsname{%
\csname \temp@\endcsname}
\fi
\fi
\xdef\temp@{cons}
\ifx\temp@\fourth@
\innerloopcount=1
\collect@cons@res
\expandafter\xdef\csname v@l\bottop@\endcsname{\cons@val}
\fi
\fi
\fi
\expandafter\ifnum\csname stop\bottop@\the\loopcount\endcsname=\first@@
\expandafter\getregion@fromfstack{\the\loopcount}
\xdef\temp@@@{n}
\xdef\fourth@{}
\xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname}
\xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@
\ifx\fourth@\tr@ns
\ifx\f@color\comm@
\xdef\f@color{} \else \xdef\f@color{[\f@color]}
\fi
\xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname}
\if\seq@type N \do@translation \else \rev@translation \fi
\xdef\temp@{translate:\tr@nsl@ted\f@color}
\xdef\temp@@@{y}
\else
\xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname}
\fi
\xdef\fourth@{}
\xdef\temp@@{\csname fstyle\bottop@\the\loopcount\endcsname}
\xdef\temp@@{\temp@@[,]:[,][]&}\expandafter\graph@opt@color\temp@@
\ifx\fourth@\tr@ns
\ifx\f@color\comm@
\xdef\f@color{} \else \xdef\f@color{[\f@color]}
\fi
\xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname}
\if\seq@type N \do@translation \else \rev@translation \fi
\xdef\temp@@{translate:\tr@nsl@ted\f@color}
\xdef\temp@@@{y}
\else
\xdef\temp@@{plot}
\ifx\temp@@\fourth@
\xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]}
\expandafter\xdef\csname collect@val\bottop@\endcsname{no}
\expandafter\xdef\csname v@l\bottop@\endcsname{}
\else
\xdef\temp@@{cons}
\ifx\temp@@\fourth@
\xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]}
\expandafter\xdef\csname collect@cons@graph\bottop@\endcsname{no}
\expandafter\xdef\csname v@l\bottop@\endcsname{}
\else
\xdef\temp@@{\csname fstyle\bottop@\the\loopcount\endcsname}
\fi
\fi
\fi
\ifx\temp@@@\y@
\expandafter\xdef\csname collect@res\bottop@\endcsname{no}
\expandafter\xdef\csname tr@nslate\bottop@\endcsname{}
\fi
\expandafter\ifnum\csname featureon\bottop@\endcsname=1
\expandafter\xdef\csname featureon\bottop@\endcsname{0}
\innerloopcount=\pos@count \advance\innerloopcount by 1
\advance\innerloopcount by -\csname featurepos\bottop@\endcsname
\expandafter\xdef\csname textfeature\bottop@\endcsname{%
\csname textfeature\bottop@\endcsname%
&\the\innerloopcount;\temp@;}
\expandafter\xdef\csname stylefeature\bottop@\endcsname{%
\csname stylefeature\bottop@\endcsname%
&\the\innerloopcount;\temp@@;}
\innerloopcount=\pos@count \advance\innerloopcount by 1
\expandafter\xdef\csname %
featurepos\bottop@\endcsname{\the\innerloopcount}
\fi
\fi
\ifnum\pos@count=\res@perline
\expandafter\ifnum\csname featureon\bottop@\endcsname=1
\innerloopcount=\pos@count
\advance\innerloopcount by 1
\advance\innerloopcount by -\csname featurepos\bottop@\endcsname
\xdef\temp@{\csname fstyle\bottop@\the\loopcount\endcsname @}
\expandafter\getstyle@left\temp@
\xdef\temp@@@{n}
\xdef\fourth@{}
\xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname}
\xdef\temp@{\temp@[,]:[,][]&}\expandafter\graph@opt@color\temp@
\ifx\fourth@\tr@ns
\ifx\f@color\comm@
\xdef\f@color{} \else \xdef\f@color{[\f@color]}
\fi
\expandafter\ifnum\csname triple@count\bottop@\endcsname=2
\if\seq@type N
\xdef\temp@{\csname sequence\the\loopcount\endcsname:}
\expandafter\get@nextres\temp@
\xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname\temp@}
\do@translation
\xdef\temp@@@{2}
\else
\xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname}
\rev@translation
\xdef\temp@@@{}
\fi
\xdef\temp@{translate:\tr@nsl@ted\f@color}
\else
\xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname}
\if\seq@type N \do@translation \else \rev@translation \fi
\xdef\temp@{translate:\tr@nsl@ted\f@color}
\xdef\temp@@@{}
\fi
\else \xdef\temp@{\csname ftext\bottop@\the\loopcount\endcsname}
\fi
\xdef\fourth@{}
\xdef\temp@@{\csname fstyle\bottop@\the\loopcount\endcsname}
\xdef\temp@@{\temp@@[,]:[,][]&}\expandafter\graph@opt@color\temp@@
\ifx\fourth@\tr@ns
\ifx\f@color\comm@
\xdef\f@color{} \else \xdef\f@color{[\f@color]}
\fi
\expandafter\ifnum\csname triple@count\bottop@\endcsname=2
\if\seq@type N
\xdef\temp@@{\csname sequence\the\loopcount\endcsname:}
\expandafter\get@@nextres\temp@@
\xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname\temp@@}
\do@translation
\xdef\temp@@@{2}
\else
\xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname}
\rev@translation
\xdef\temp@@@{}
\fi
\xdef\temp@@{translate:\tr@nsl@ted\f@color}
\else
\xdef\tr@nsl@ted{\csname tr@nslate\bottop@\endcsname}
\if\seq@type N \do@translation \else \rev@translation \fi
\xdef\temp@@{translate:\tr@nsl@ted\f@color}
\xdef\temp@@@{}
\fi
\else
\xdef\temp@@{plot}
\ifx\temp@@\fourth@
\xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]}
\else
\xdef\temp@@{cons}
\ifx\temp@@\fourth@
\xdef\temp@@{plot\f@color[\fffourth@]:\csname v@l\bottop@\endcsname[\ff@color]}
\else
\xdef\temp@@{\style@@}
\fi
\fi
\fi
\ifx\temp@@@\n@
\else
\expandafter\xdef\csname tr@nslate\bottop@\endcsname{\temp@@@}
\fi
\expandafter\xdef\csname textfeature\bottop@\endcsname{%
\csname textfeature\bottop@\endcsname%
&\the\innerloopcount;\temp@;}
\expandafter\xdef\csname stylefeature\bottop@\endcsname{%
\csname stylefeature\bottop@\endcsname%
&\the\innerloopcount;\temp@@;}
\innerloopcount=\pos@count \advance\innerloopcount by 1
\expandafter\xdef\csname %
featurepos\bottop@\endcsname{\the\innerloopcount}
\fi
\fi
\fi
\fi
\fi
\ifnum\loopcount<\seq@count \repeat
}
\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%
\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@@ ,%
\rule{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
\else%
\if\first@@ |%
\rule{0.1\arrow@height}{2\arrow@height}\kern-0.35\arrow@height%
\else%
\if\first@@ `\xdef\first@@{'}\fi%
\if\first@@ '%
\rule[\arrow@height]%
{0.1\arrow@height}{\arrow@height}\kern-0.35\arrow@height%
\else%
\if\first@@ -%
\rule{0pt}{0pt}\kern-0.35\arrow@height%
\fi%
\fi%
\fi%
\fi%
\if\third@@ v%
\if\first@@ v%
\ensuremath{\overleftarrow{\hbox to %
\second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}%
\kern-\arrow@width%
\ensuremath{\overrightarrow{\hbox%
{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}%
\else%
\ensuremath{\overrightarrow{\hbox to %
\second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}%
\fi%
\else%
\if\first@@ v%
\ensuremath{\overleftarrow{\hbox to %
\second@\box@width{\rule[0.4\arrow@height]{0pt}{0pt}\hss}}}%
\else
\kern0.35\arrow@height%
\rule[0.9\arrow@height]{\second@\box@width}{0.1\arrow@height}%
\kern0.35\arrow@height%
\fi
\if\third@@ ,%
\kern-0.4\arrow@height\rule{0.1\arrow@height}{\arrow@height}%
\else%
\if\third@@ |%
\kern-0.4\arrow@height\rule{0.1\arrow@height}{2\arrow@height}%
\else%
\if\third@@ `\xdef\third@@{'}\fi%
\if\third@@ '%
\kern-0.4\arrow@height%
\rule[\arrow@height]{0.1\arrow@height}{\arrow@height}%
\fi%
\fi%
\fi%
\fi}}%
\else%
\xdef\last@{doublearrow}%
\ifx\second@@\last@%
\setbox1=\hbox{\ensuremath{\Rightarrow}}%
\arrow@height=\ht1%
\arrow@width=\wd1%
\setbox1=\hbox to \second@\box@width{}%
\width@tmp=\wd1%
\kern-0.75\box@width%
\xdef\temp@{top}%
\ifx\bottop@\temp@ \xdef\last@{0.25}%
\else%
\xdef\temp@{ttop}%
\ifx\bottop@\temp@ \xdef\last@{0.25}%
\else%
\xdef\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@@ ,%
\rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
\kern-0.1\arrow@height%
\else%
\if\first@@ |%
\rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
\kern-0.1\arrow@height%
\else%
\if\first@@ `\xdef\first@@{'}\fi%
\if\first@@ '%
\rule[0.4\arrow@height]%
{0.1\arrow@height}{1.5\arrow@height}%
\kern-0.1\arrow@height%
\else%
\if\first@@ <%
\ensuremath{\Leftarrow}\kern-0.5\arrow@width%
\advance\width@tmp by -0.5\arrow@width
\else
\rule{0pt}{0pt}%
\fi%
\fi%
\fi%
\fi%
\if\third@@ >%
\advance\width@tmp by -0.5\arrow@width%
\rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}%
\kern-\width@tmp%
\rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}%
\kern-0.5\arrow@width\ensuremath{\Rightarrow}%
\else%
\rule[0.37\arrow@height]{\width@tmp}{0.1\arrow@height}%
\kern-\width@tmp%
\rule[0.9\arrow@height]{\width@tmp}{0.1\arrow@height}%
\if\third@@ ,%
\kern-0.05\arrow@height%
\rule[-0.5\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
\else%
\if\third@@ |%
\kern-0.05\arrow@height%
\rule[-0.5\arrow@height]{0.1\arrow@height}{2.25\arrow@height}%
\else%
\if\third@@ `\xdef\third@@{'}\fi%
\if\third@@ '%
\kern-0.05\arrow@height%
\rule[0.4\arrow@height]{0.1\arrow@height}{1.5\arrow@height}%
\fi%
\fi%
\fi%
\fi}}%
\else
\loopcount=0\relax%
\width@tmp=\arrow@height%
\temp@@length=\rule@@thick%
\advance\width@tmp by -0.5\temp@@length%
\if\first@@ o\xdef\first@@{O}\fi%
\if\third@@ o\xdef\third@@{O}\fi%
\textcolor{\f@color}{%
\if\first@@ ,%
\rule{\temp@@length}{\arrow@height}\kern-\temp@@length%
\else%
\if\first@@ |%
\rule{\temp@@length}{2\arrow@height}\kern-\temp@@length%
\else%
\if\first@@ O%
\raisebox{0.06ex}{\ensuremath{\bullet}}\kern-0.55ex%
\rule[\width@tmp]{0.65ex}{\temp@@length}%
\else%
\if\first@@ <%
\raisebox{0.06ex}{\ensuremath{\blacktriangleleft}}\kern-0.35ex%
\else
\if\first@@ `\xdef\first@@{'}\fi%
\if\first@@ '%
\advance\width@tmp by 0.5\temp@@length%
\rule[\width@tmp]{\temp@@length}{\arrow@height}\kern-\temp@@length%
\advance\width@tmp by -0.5\temp@@length%
\fi%
\fi%
\fi%
\fi%
\fi%
\loopcount=\second@%
\if\first@@ <\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
\if\third@@ >\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
\if\first@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
\if\third@@ O\advance\loopcount by -1\relax\ifnum\loopcount<0 \loopcount=0\fi\fi%
\xdef\second@{\the\loopcount}%
\rule[\width@tmp]{\second@\box@width}{\temp@@length}%
\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@@ |%
\kern-\temp@@length\rule{\temp@@length}{2\arrow@height}%
\else%
\if\third@@ O%
\rule[\width@tmp]{0.65ex}{\temp@@length}%
\kern-0.55ex\raisebox{0.06ex}{\ensuremath{\bullet}}%
\else%
\if\third@@ >%
\kern-0.35ex\raisebox{0.06ex}{\ensuremath{\blacktriangleright}}%
\else
\if\third@@ `\xdef\third@@{'}\fi%
\if\third@@ '%
\advance\width@tmp by 0.5\temp@@length%
\kern-\temp@@length\rule[\width@tmp]{\temp@@length}{\arrow@height}%
\fi%
\fi%
\fi%
\fi
\fi}%
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
\fi
}
\def\next@featuretext#2;#3@{%
\xdef\first@{#3@}%
\xdef\last@{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%
\ifnum\feature@ttttop=1
\ifnum\featureonttttop=0 \xdef\feature@ttttop{0} \fi
\xdef\bottop@{ttttop}%
\put@feature%
\vspace{\tttt@sp@ce}%
\vspace{-\baselineskip}%
\newline\hbox{}%
\else
\iffix@\ifttttopfeature \vspace{\tttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
\fi
\ifnum\feature@tttop=1
\ifnum\featureontttop=0 \xdef\feature@tttop{0} \fi
\xdef\bottop@{tttop}%
\put@feature%
\vspace{\ttt@sp@ce}%
\vspace{-\baselineskip}%
\newline\hbox{}%
\else
\iffix@\iftttopfeature \vspace{\ttt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
\fi
\ifnum\feature@ttop=1
\ifnum\featureonttop=0 \xdef\feature@ttop{0} \fi
\xdef\bottop@{ttop}%
\put@feature%
\vspace{\tt@sp@ce}%
\vspace{-\baselineskip}%
\newline\hbox{}%
\else
\iffix@\ifttopfeature \vspace{\tt@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
\fi
\ifnum\feature@top=1
\ifnum\featureontop=0 \xdef\feature@top{0} \fi
\xdef\bottop@{top}%
\put@feature%
\vspace{\t@sp@ce}%
\vspace{-\baselineskip}%
\newline\hbox{}%
\else
\iffix@\iftopfeature \vspace{\t@sp@ce}\newline\hbox{}\newline\hbox{}\fi\fi
\fi
\ifnum\rule@num<0 \else \ifnum\rule@top=0 \loopcount=0 \put@ruler \fi\fi
\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%
\ifnum\feature@bottom=1 %
\ifnum\featureonbottom=0 \xdef\feature@bottom{0}\fi%
\xdef\bottop@{bottom}%
\vspace{\b@sp@ce}%
\if\bottom@stretch y%
\vspace{-\box@height}%
\vspace{\b@r@stretch\box@height}%
\fi%
\put@feature%
\else
\iffix@
\if\bottom@stretch y%
\vspace{-\box@height}%
\vspace{\b@r@stretch\box@height}%
\fi%
\ifbottomfeature%
\vspace{\b@sp@ce}\newline\hbox{}\newline\hbox{}%
\fi%
\fi%
\fi%
\ifnum\feature@bbottom=1 %
\ifnum\featureonbbottom=0 \xdef\feature@bbottom{0}\fi%
\xdef\bottop@{bbottom}%
\vspace{\bb@sp@ce}%
\if\bbottom@stretch y%
\vspace{-\box@height}%
\vspace{\b@r@stretch\box@height}%
\fi%
\put@feature%
\else
\iffix@
\if\bbottom@stretch y%
\vspace{-\box@height}%
\vspace{\b@r@stretch\box@height}%
\fi%
\ifbbottomfeature
\vspace{\bb@sp@ce}\newline\hbox{}\newline\hbox{}%
\fi
\fi
\fi
\ifnum\feature@bbbottom=1 %
\ifnum\featureonbbbottom=0 \xdef\feature@bbbottom{0}\fi%
\xdef\bottop@{bbbottom}%
\vspace{\bbb@sp@ce}%
\if\bbbottom@stretch y%
\vspace{-\box@height}%
\vspace{\b@r@stretch\box@height}%
\fi%
\put@feature%
\else
\iffix@
\if\bbbottom@stretch y%
\vspace{-\box@height}%
\vspace{\b@r@stretch\box@height}%
\fi%
\ifbbbottomfeature
\vspace{\bbb@sp@ce}\newline\hbox{}\newline\hbox{}%
\fi
\fi
\fi
\ifnum\feature@bbbbottom=1 %
\ifnum\featureonbbbbottom=0 \xdef\feature@bbbbottom{0}\fi%
\xdef\bottop@{bbbbottom}%
\vspace{\bbbb@sp@ce}%
\if\bbbbottom@stretch y%
\vspace{-\box@height}%
\vspace{\b@r@stretch\box@height}%
\fi%
\put@feature%
\else
\iffix@
\if\bbbbottom@stretch y%
\vspace{-\box@height}%
\vspace{\b@r@stretch\box@height}%
\fi%
\ifbbbbottomfeature
\vspace{\bbbb@sp@ce}\newline\hbox{}\newline\hbox{}%
\fi
\fi
\fi
\xdef\consensus{} \xdef\ruler@{}
\xdef\styleframe{}
\xdef\textfeaturetop{} \xdef\textfeaturebottom{}
\xdef\textfeaturettop{} \xdef\textfeaturebbottom{}
\xdef\textfeaturetttop{} \xdef\textfeaturebbbottom{}
\xdef\textfeaturettttop{} \xdef\textfeaturebbbbottom{}
\xdef\stylefeaturetop{} \xdef\stylefeaturebottom{}
\xdef\stylefeaturettop{} \xdef\stylefeaturebbottom{}
\xdef\stylefeaturetttop{} \xdef\stylefeaturebbbottom{}
\xdef\stylefeaturettttop{} \xdef\stylefeaturebbbbottom{}
\loopcount=0
\loop
\advance\loopcount by 1
\xdef\seq@line{\csname sequence\the\loopcount\endcsname}
\expandafter\remove@fromseq\seq@line
\ifnum\loopcount<\seq@count \repeat}
\def\block@output{%
\expandafter\ifnum\csname res@count\start@seq\endcsname<\end@num\relax
\message{.}
\ifx\out@put\y@
\vbox{\set@lines}\par
\block@skip
\else
\pos@count=1
\findc@nsensus
\loopcount=0
\loop
\advance\loopcount by 1\relax
\xdef\seq@line{\csname sequence\the\loopcount\endcsname}
\expandafter\remove@fromseq\seq@line
\ifT@coffee
\xdef\TC@cons{\csname TC0\endcsname}
\expandafter\remove@fromTC\TC@cons
\fi
\ifnum\loopcount<\seq@count \repeat
\fi
\ifstop@
\else
\advance\seq@pointer by -\res@perline
\ifnum\seq@pointer>\res@perline \block@output \fi
\fi
\fi}
%%%%% Basic input routines
\def\savedseqlength#1#2#3{%
\expandafter\xdef\csname savelength#1seq#2\endcsname{#3}}
\def\set@savedseqlength{%
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\ifx%
\csname savelength\@lign@count seq\the\loopcount\endcsname\relax
\else
\expandafter\xdef\csname seq@len\the\loopcount\endcsname{%
\csname savelength\@lign@count seq\the\loopcount\endcsname}
\fi
\ifnum\loopcount<\seq@count\repeat
}
\def\save@lengths{%
\loopcount=0
\loop
\advance\loopcount by 1\relax
\immediate\write\@auxout{%
\string\savedseqlength{\@lign@count}{\the\loopcount}%
{\csname res@count\the\loopcount\endcsname}}
\ifnum\loopcount<\seq@count \repeat
}
\def\do@cleanup{%
\expandafter\firstchar@get\third@
\expandafter\check@char\first@
\ifletter
\xdef\second@{\second@\first@}
\else
\ifnumber
\ifx\first@\gre@ter
\xdef\second@{\second@{$>$}}
\else
\ifx\first@\sm@ller
\xdef\second@{\second@{$<$}}
\else
\xdef\second@{\second@\first@}
\fi\fi
\else
\ifnum\code@num=6
\xdef\second@{\second@\#}
\else
\ifnum\code@num=14
\xdef\second@{\second@\%}
\else
\xdef\second@{\second@\noexpand\string\first@}
\fi\fi
\fi
\fi
\ifx\third@\@t \else \do@cleanup \fi
}
\def\cleanup@name{%
\xdef\third@{\csname seqname\the\loopcount\endcsname @}
\xdef\second@{}
\do@cleanup
\expandafter\xdef\csname newseqname\the\loopcount\endcsname{\second@}
}
\def\clear@seq{%
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\def\csname sequence\the\loopcount\endcsname{}
\ifnum\loopcount<\seq@count \repeat
\xdef\consensus{}
\xdef\constopo{}
\xdef\frame@on{0}
\xdef\textfeaturetop{} \xdef\featureontop{0}
\xdef\textfeaturettop{} \xdef\featureonttop{0}
\xdef\textfeaturetttop{} \xdef\featureontttop{0}
\xdef\textfeaturettttop{} \xdef\featureonttttop{0}
\xdef\textfeaturebottom{} \xdef\featureonbottom{0}
\xdef\textfeaturebbottom{} \xdef\featureonbbottom{0}
\xdef\textfeaturebbbottom{} \xdef\featureonbbbottom{0}
\xdef\textfeaturebbbbottom{} \xdef\featureonbbbbottom{0}
\xdef\styleframe{}
\xdef\stylefeaturetop{}
\xdef\stylefeaturettop{}
\xdef\stylefeaturetttop{}
\xdef\stylefeaturettttop{}
\xdef\stylefeaturebottom{}
\xdef\stylefeaturebbottom{}
\xdef\stylefeaturebbbottom{}
\xdef\stylefeaturebbbbottom{}}
\def\guess@protein{\seqtype{P}\message{<Seqtype guess: protein>}}
\def\guess@DNA{\seqtype{N}\message{<Seqtype guess: nucleotide>}}
\def\allmatch@out{%
\xdef\leave@in{n}
\loopcount=1
\xdef\seq@line{\csname seq\the\loopcount\endcsname}
\expandafter\res@get\seq@line
\expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line}
\ifnum\loopcount=\start@seq\relax
\expandafter\check@char\first@
\ifletter
\advance\temp@@count by 1
\ifnum\temp@@count=\end@num\relax
\advance\temp@count by 1
\xdef\second@{\the\temp@count}
\advance\temp@count by -1
\fi
\fi
\fi
\ifx\first@\ampers@nd
\ifx\domain@active\y@
\xdef\stack@dom{\stack@dom\the\temp@count;}
\fi
\xdef\stack@dom{\stack@dom &;&;@}
\else
\xdef\first@@{\first@}
\advance\temp@count by 1
\loop
\advance\loopcount by 1
\xdef\seq@line{\csname seq\the\loopcount\endcsname}
\expandafter\res@get\seq@line
\expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line}
\ifx\first@@\first@\else\xdef\leave@in{y}\fi
\ifnum\loopcount=\start@seq\relax
\expandafter\check@char\first@
\ifletter
\advance\temp@@count by 1
\ifnum\temp@@count=\end@num\relax \xdef\second@{\the\temp@count}\fi
\fi
\fi
\ifnum\loopcount<\seq@count\repeat
\ifx\leave@in\y@
\ifx\domain@active\n@
\ifnum\start@seq=0
\xdef\domain@active{y}
\xdef\stack@dom{\stack@dom\the\temp@count;}
\else
\ifnum\temp@@count<\start@num\relax
\else
\ifnum\temp@@count>\end@num\relax
\else
\xdef\domain@active{y}
\xdef\stack@dom{\stack@dom\the\temp@count;}
\fi
\fi
\fi
\else
\ifnum\start@seq>0
\ifnum\temp@@count<\end@num\relax
\else
\xdef\domain@active{n}
\xdef\stack@dom{\stack@dom\second@;}
\fi
\fi
\fi
\else
\ifx\domain@active\y@
\xdef\domain@active{n}
\advance\temp@count by -1
\xdef\stack@dom{\stack@dom\the\temp@count;}
\advance\temp@count by 1
\fi
\fi
\allmatch@out
\fi
}
\def\domain@count{%
\xdef\@ddg@p{n}
\loopcount=0
\ifT@coffee
\xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
\expandafter\res@get\seq@line
\expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
\fi
\loop
\advance\loopcount by 1
\xdef\seq@line{\csname seq\the\loopcount\endcsname}
\expandafter\res@get\seq@line
\expandafter\xdef\csname res\the\loopcount\endcsname{\first@}
\expandafter\xdef\csname seq\the\loopcount\endcsname{\seq@line}
\ifT@coffee
\xdef\seq@line{\csname T@cof\the\loopcount\endcsname}
\expandafter\res@get\seq@line
\expandafter\xdef\csname TC@num\the\loopcount\endcsname{\first@}
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\seq@line}
\fi
\ifnum\loopcount<\seq@count\repeat
\ifx\first@\ampers@nd
\else
\ifnum\next@domain@num>-99999\relax
\ifnum\domain@seq=0
\temp@count=\csname dom@count0\endcsname
\advance\temp@count by 1
\expandafter\xdef\csname dom@count0\endcsname{\the\temp@count}
\fi
\loopcount=0
\loop
\advance\loopcount by 1
\xdef\first@{\csname res\the\loopcount\endcsname}
\expandafter\check@char\first@
\ifletter
\temp@count=\csname dom@count\the\loopcount\endcsname
\advance\temp@count by 1
\expandafter\xdef\csname dom@count\the\loopcount\endcsname{\the\temp@count}
\if\seq@type A \relax
\temp@count=\char@num
\ifnum\temp@count>96 \advance\temp@count by -32 \fi
\ifnum\temp@count=69 \guess@protein
\else
\ifnum\temp@count=70 \guess@protein
\else
\ifnum\temp@count=73 \guess@protein
\else
\ifnum\temp@count=76 \guess@protein
\else
\ifnum\temp@count=80 \guess@protein
\else
\ifnum\temp@count=81 \guess@protein
\fi\fi\fi\fi\fi\fi
\fi
\else
\ifx\d@m@in\y@
\ifnum\loopcount=\domain@seq \xdef\@ddg@p{y} \fi
\fi
\fi
\ifnum\loopcount<\seq@count\repeat
\ifx\@ddg@p\y@
\ifx\g@p\n@
\loopcount=0
\loop
\advance\loopcount by 1
\ifT@coffee
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
\csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
\fi
\expandafter\xdef\csname sequence\the\loopcount\endcsname{%
\csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname}
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
\csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
\ifnum\loopcount<\seq@count\repeat
\advance\total@count by 1
\advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi
\fi
\fi
\expandafter\ifnum\csname dom@count\domain@seq\endcsname=\next@domain@num
\xdef\d@m@in{y}
\advance\total@count by 1
\advance\outerloopcount by 1 \ifnum\outerloopcount=\res@perline \outerloopcount=0 \fi
\loopcount=0
\ifx\g@p\y@
\ifT@coffee
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
\csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
\fi
\fi
\ifT@coffee
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
\csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
\fi
\loop
\advance\loopcount by 1
\ifx\g@p\y@
\ifT@coffee
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
\csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
\fi
\expandafter\xdef\csname sequence\the\loopcount\endcsname{%
\csname sequence\the\loopcount\endcsname\equ@l}
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
\csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
\ifnum\outerloopcount=0
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
\csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
\fi
\fi
\ifT@coffee
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{%
\csname T@coffee\the\loopcount\endcsname \csname TC@num\the\loopcount\endcsname}
\fi
\expandafter\xdef\csname sequence\the\loopcount\endcsname{%
\csname sequence\the\loopcount\endcsname \csname res\the\loopcount\endcsname}
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{%
\csname dom@num\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
\ifnum\outerloopcount=0
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
\csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
\fi
\ifnum\loopcount<\seq@count\repeat
\ifx\@ddg@p\n@
\expandafter\get@item\domain@num@list
\xdef\domain@num@list{\first@}
\fi
\ifx\fourth@\ampers@nd \xdef\next@domain@num{-99999}
\else
\loopcount=\next@domain@num
\advance\loopcount by 1
\ifnum\loopcount=\fourth@
\xdef\g@p{n}
\else
\xdef\g@p{y}
\advance\total@count by 1
\advance\outerloopcount by 1
\ifnum\outerloopcount=\res@perline
\outerloopcount=0
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
\csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,}
\ifnum\loopcount<\seq@count\repeat
\fi
\fi
\xdef\next@domain@num{\fourth@} \xdef\end@num{\fourth@}
\fi
\fi
\domain@count
\fi
\fi
}
\def\residue@count{%
\expandafter\res@get\seq@line
\if\first@\ampers@nd
\else
\advance\total@count by 1
\advance\innerloopcount by 1
\ifstart@ \advance\res@count by 1 \fi
\ifnum\start@seq=0
\advance\end@count by 1
%%%%%%%%%%
\ifnum\end@count=\start@num\relax
\xdef\start@number{\the\innerloopcount}
\start@true \res@count=1
\fi
%%%%%%%%%%
\else
\expandafter\check@char\first@
\ifletter
\advance\end@count by 1
\if\seq@type A \relax
\temp@count=\char@num
\ifnum\temp@count>96 \advance\temp@count by -32 \fi
\ifnum\temp@count=69 \guess@protein
\else
\ifnum\temp@count=70 \guess@protein
\else
\ifnum\temp@count=73 \guess@protein
\else
\ifnum\temp@count=76 \guess@protein
\else
\ifnum\temp@count=80 \guess@protein
\else
\ifnum\temp@count=81 \guess@protein
\fi\fi\fi\fi\fi\fi
\fi
\fi
\ifnum\end@count=\start@num\relax
\xdef\start@number{\the\innerloopcount}
\start@true \res@count=1
\fi
\fi
\residue@count
\fi}
\def\clean@seq{%
\expandafter\res@get\seq@line
\if\first@\ampers@nd \xdef\seq@line{\seq@@line}
\else
\expandafter\check@char\first@
\ifnum\char@num>64
\ifnum\char@num>96 \make@upper \fi
\xdef\seq@@line{\seq@@line\first@}
\else
\ifnum\char@num=46
\xdef\seq@@line{\seq@@line\d@t}
\else
\ifnum\char@num=45
\xdef\seq@@line{\seq@@line\d@t}
\else
\ifnum\char@num=42
\xdef\seq@@line{\seq@@line\questi@n}
\fi
\fi
\fi
\fi
\clean@seq
\fi}
\def\read@loop{%
\read\alignfile to \inline
\xdef\last@{\expandafter\string\inline}
\ifx\last@\par@
\else
\xdef\inline{\inline @}
\expandafter\seq@get\inline
\ifstop@
\else
\innerloopcount=\csname @rd\the\loopcount\endcsname\relax
\expandafter\ifx\csname seq@name\the\loopcount\endcsname\first@
\xdef\seq@@line{} \xdef\seq@line{\seq@line &@} \clean@seq
\expandafter\xdef\csname sequence\the\innerloopcount\endcsname{%
\csname sequence\the\innerloopcount\endcsname\seq@line}
\advance\loopcount by 1
\ifnum\loopcount>\seq@count
\loopcount=1
\fi
\fi
\fi
\fi
\ifeof\alignfile
\ifx\all@out\y@
\xdef\domain@seq{0}
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
\ifnum\loopcount<\seq@count\repeat
\xdef\domain@active{n}
\xdef\stack@dom{}
\temp@count=0
\temp@@count=0
\allmatch@out
\xdef\dom@in{y}
\fi
\ifx\dom@in\y@
\loopcount=0
\ifT@coffee
\xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
\expandafter\get@temp\temp@
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
\fi
\expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
\loop
\advance\loopcount by 1
\ifT@coffee
\xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
\expandafter\get@temp\temp@
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
\fi
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname}
\ifnum\loopcount<\seq@count\repeat
\xdef\domain@num@list{}
\xdef\last@{\stack@dom}
\get@domain
\xdef\domain@num@list{\domain@num@list &,@}
\expandafter\get@item\domain@num@list
\xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
\xdef\d@m@in{n}
\domain@count
\loopcount=0
\ifT@coffee
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
\fi
\loop
\advance\loopcount by 1
\ifT@coffee
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
\fi
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
\csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
\ifnum\loopcount<\seq@count\repeat
\if\seq@type A \guess@DNA \fi
\advance\seq@pointer by \total@count\relax
\xdef\total@pos{\the\total@count}
\else
\ifnum\start@seq=0
\xdef\seq@line{\csname sequence1\endcsname &@}
\else
\xdef\seq@line{\csname sequence\start@seq\endcsname &@}
\fi
\res@count=0
\innerloopcount=0
\residue@count
\if\seq@type A \guess@DNA \fi
\advance\seq@pointer by \res@count\relax
\xdef\total@pos{\the\total@count}
\ifx\end@num\n@\xdef\end@num{\the\end@count}\fi
\total@count=\end@count\relax
\xdef\first@{\csname res@count\start@seq\endcsname}
\advance\total@count by \first@\relax
\xdef\first@{\the\total@count}
\ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi
\fi
\ifshow@sublogo \prep@sublogo \fi
\ifshow@logo \prep@logo \fi
\ifx\label@motif\y@ \prep@motif \fi
\ifnum\seq@pointer>\res@perline \block@output \fi
\else \read@loop
\fi}
\def\read@fasta{%
\read\alignfile to \inline
\xdef\last@{\expandafter\string\inline}
\ifx\last@\par@
\else
\xdef\seq@line{\inline}
\xdef\inline{\inline @}
\expandafter\firstchar@get\inline
\ifstop@
\else
\ifx\first@\gre@ter
\advance\loopcount by 1\relax
\expandafter\seq@get\third@
\xdef\seq@name{\first@}
\xdef\second@{\first@ &}
\ifx\second@\ampers@nd \xdef\seq@name{seq\the\loopcount}\fi
\innerloopcount=\csname @rd\the\loopcount\endcsname\relax
\else
\expandafter\ifx\csname seq@name\the\loopcount\endcsname\seq@name
\xdef\seq@@line{} \xdef\seq@line{\seq@line &@} \clean@seq
\expandafter\xdef\csname sequence\the\innerloopcount\endcsname{%
\csname sequence\the\innerloopcount\endcsname\seq@line}
\fi
\fi
\fi
\fi
\ifeof\alignfile
\ifx\all@out\y@
\xdef\domain@seq{0}
\loopcount=0
\loop
\advance\loopcount by 1
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
\ifnum\loopcount<\seq@count\repeat
\xdef\domain@active{n}
\xdef\stack@dom{}
\temp@count=0
\temp@@count=0
\allmatch@out
\xdef\dom@in{y}
\fi
\ifx\dom@in\y@
\loopcount=0
\ifT@coffee
\xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
\expandafter\get@temp\temp@
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
\fi
\expandafter\xdef\csname dom@count\the\loopcount\endcsname{0}
\loop
\advance\loopcount by 1
\ifT@coffee
\xdef\temp@{\csname T@coffee\the\loopcount\endcsname}
\expandafter\get@temp\temp@
\expandafter\xdef\csname T@cof\the\loopcount\endcsname{\temp@ &@}
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{}
\fi
\expandafter\xdef\csname seq\the\loopcount\endcsname{\csname sequence\the\loopcount\endcsname &@}
\expandafter\xdef\csname sequence\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{}
\expandafter\xdef\csname dom@count\the\loopcount\endcsname{\csname res@count\the\loopcount\endcsname}
\ifnum\loopcount<\seq@count\repeat
\xdef\domain@num@list{}
\xdef\last@{\stack@dom}
\get@domain
\xdef\domain@num@list{\domain@num@list &,@}
\expandafter\get@item\domain@num@list
\xdef\next@domain@num{\fourth@} \xdef\domain@num@list{\first@}
\xdef\d@m@in{n}
\domain@count
\loopcount=0
\ifT@coffee
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
\fi
\loop
\advance\loopcount by 1
\ifT@coffee
\expandafter\xdef\csname T@coffee\the\loopcount\endcsname{\csname T@coffee\the\loopcount\endcsname @}
\fi
\expandafter\xdef\csname dom@num\the\loopcount\endcsname{\csname dom@num\the\loopcount\endcsname @}
\expandafter\xdef\csname dom@num@break\the\loopcount\endcsname{%
\csname dom@num@break\the\loopcount\endcsname \csname dom@count\the\loopcount\endcsname,@}
\ifnum\loopcount<\seq@count\repeat
\if\seq@type A \guess@DNA \fi
\advance\seq@pointer by \total@count\relax
\xdef\total@pos{\the\total@count}
\else
\ifnum\start@seq=0
\xdef\seq@line{\csname sequence1\endcsname &@}
\else
\xdef\seq@line{\csname sequence\start@seq\endcsname &@}
\fi
\res@count=0
\innerloopcount=0
\residue@count
\if\seq@type A \guess@DNA \fi
\advance\seq@pointer by \res@count
\xdef\total@pos{\the\total@count}
\ifx\end@num\n@\xdef\end@num{\the\end@count}\fi
\total@count=\end@count\relax
\xdef\first@{\csname res@count\start@seq\endcsname}
\advance\total@count by \first@\relax
\xdef\first@{\the\total@count}
\ifnum\end@num>\total@count\xdef\end@num{\the\total@count}\fi
\fi
\ifshow@sublogo \prep@sublogo \fi
\ifshow@logo \prep@logo \fi
\ifx\label@motif\y@ \prep@motif \fi
\ifnum\seq@pointer>\res@perline \block@output \fi
\else
\read@fasta
\fi}
\def\read@lines{%
\openin\alignfile = \alignfilename
\clear@seq
\ifnum\start@seq>0
\xdef\start@seq{\csname @rd\start@seq\endcsname} \fi
\loopcount=\start@num
\advance\loopcount by -\csname res@count\start@seq\endcsname\relax
\expandafter\ifnum\csname res@count\start@seq\endcsname<\start@num\relax
\xdef\start@num{\the\loopcount}
\else \start@true \fi
\res@count=0 \seq@pointer=0 \end@count=0 \total@count=0
\xdef\start@number{0}
\ifx\exp@rt\y@ \prep@reexp@rtfile \fi
\ifx\f@st@\y@
\loopcount=0
\read@fasta
\else
\loopcount=1
\read@loop
\fi
\ifnum\seq@pointer>0
\ifstop@
\else
\res@count=\res@perline
\res@perline=\seq@pointer
\block@output
\fi
\fi
\ifshow@sublogo \closein\sublogofile \fi
\ifx\exp@rt\y@ \closeout\exp@rtfile \fi
\closein\alignfile
\message{)}
}
%%%%% Read alignment, decide whether MSF or ALN, interpret
\def\readalignfile#1{%
\def\alignfilename{#1}
\xdef\first@{byhand}
\ifx\alignfilename\first@
\else
\openin\alignfile = #1
\ifeof\alignfile
\PackageError{TeXshade}
{File `#1' not found}
{\MessageBreak
The alignment file you specified is missing or you have \MessageBreak
misspelled it. \MessageBreak\MessageBreak
Stop here, otherwise you're likely getting in trouble. \MessageBreak
Type X <return> to quit. \MessageBreak
}
\else
\message{(\alignfilename :}
\xdef\seq@type{A} \xdef\he@der{no} \xdef\f@st@{no}
\xdef\first@line{y}
\seq@count=0 \loopcount=0 \innerloopcount=0 \temp@count=0
\loop
\read\alignfile to \inline
\xdef\test@{\expandafter\string\inline}
\ifx\test@\par@ \innerloopcount=0
\else
\xdef\msfline{\inline & & & & @}
\expandafter\inf@@get\msfline
\ifx\first@\@msf \expandafter\type@get\msfline \fi
\ifx\second@\@msf \expandafter\type@get\msfline \fi
\ifx\third@\@msf \expandafter\type@get\msfline \fi
\ifx\first@\n@me \advance\loopcount by 1\relax
\expandafter\xdef\csname seqname\the\loopcount\endcsname{\second@}
\expandafter\xdef\csname seq@len\the\loopcount\endcsname{\fourth@}
\fi
\ifx\first@\he@derend
\ifnum\loopcount>0 \xdef\he@der{yes} \fi
\fi
\xdef\alnline{\inline @}
\expandafter\check@letter\alnline
\ifletter
\expandafter\seq@get\alnline
\advance\innerloopcount by 1\relax
\seq@count=\innerloopcount
\expandafter\xdef\csname newseqname\the\seq@count\endcsname{\first@}
\else
\expandafter\firstchar@get\alnline
\ifx\first@\gre@ter
\ifx\first@line\y@ \xdef\f@st@{y}\fi
\expandafter\seq@get\third@
\advance\temp@count by 1\relax
\xdef\second@{\first@ &}
\ifx\second@\ampers@nd \xdef\first@{seq\the\temp@count}\fi
\expandafter\xdef\csname seq@name\the\temp@count\endcsname{\first@}
\fi
\fi
\fi
\xdef\first@line{n}
\ifeof\alignfile \else\repeat
\closein\alignfile
\xdef\first@{no}
\ifx\he@der\first@
\loopcount=0
\ifx\f@st@\y@
\seq@count=\temp@count \loopcount=0
\loop
\advance\loopcount by 1
\expandafter\xdef\csname seqname\the\loopcount\endcsname{%
\csname seq@name\the\loopcount\endcsname}
\expandafter\xdef\csname newseqname\the\loopcount\endcsname{%
\csname seq@name\the\loopcount\endcsname}
\expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999}
\ifnum\loopcount<\seq@count \repeat
\else
\loop
\advance\loopcount by 1
\expandafter\xdef\csname seqname\the\loopcount\endcsname{%
\csname newseqname\the\loopcount\endcsname}
\expandafter\xdef\csname seq@len\the\loopcount\endcsname{99999999}
\ifnum\loopcount<\seq@count \repeat
\fi
\else
\seq@count=\loopcount \loopcount=0 \box@width=0pt
\loop
\advance\loopcount by 1
\expandafter\xdef\csname newseqname\the\loopcount\endcsname{%
\csname seqname\the\loopcount\endcsname}
\ifnum\loopcount<\seq@count \repeat
\fi
\set@savedseqlength
\loopcount=0 \xdef\seq@order{}
\expandafter\xdef\csname stack@dom\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname seq@start\the\loopcount\endcsname{1}
\expandafter\xdef\csname name@col\the\loopcount\endcsname{yes}
\expandafter\xdef\csname number@col\the\loopcount\endcsname{yes}
\loop
\advance\loopcount by 1
\expandafter\xdef\csname @rd\the\loopcount\endcsname{\the\loopcount}
\expandafter\xdef\csname res@count\the\loopcount\endcsname{0}
\cleanup@name
\expandafter\xdef\csname tint@seq\the\loopcount\endcsname{n}
\expandafter\xdef\csname emph@seq\the\loopcount\endcsname{n}
\expandafter\xdef\csname lower@seq\the\loopcount\endcsname{n}
\expandafter\xdef\csname hide@seq\the\loopcount\endcsname{false}
\expandafter\xdef\csname hide@@@seq\the\loopcount\endcsname{false}
\expandafter\xdef\csname hide@name\the\loopcount\endcsname{no}
\expandafter\xdef\csname name@col\the\loopcount\endcsname{yes}
\expandafter\xdef\csname hide@number\the\loopcount\endcsname{no}
\expandafter\xdef\csname number@col\the\loopcount\endcsname{yes}
\expandafter\xdef\csname stack@reg\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tintreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@emphreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@lowerreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@framereg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@shadingreg\the\loopcount\endcsname{&;&;&;@}
\expandafter\xdef\csname stack@top\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@tttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@ttttop\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@bottom\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@bbottom\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@bbbottom\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname stack@bbbbottom\the\loopcount\endcsname{&;&;&;&;@}
\expandafter\xdef\csname seq@gap\the\loopcount\endcsname{no}
\expandafter\xdef\csname seq@start\the\loopcount\endcsname{1}
\expandafter\xdef\csname mol@weight\the\loopcount\endcsname{0}
\expandafter\xdef\csname ch@rge\the\loopcount\endcsname{0}
\ifnum\loopcount=1 \xdef\seq@order{\the\loopcount}
\else \xdef\seq@order{\seq@order,\the\loopcount}\fi
\ifnum\loopcount<\seq@count \repeat
\xdef\seq@order{\seq@order,@}
\killseq@count=\seq@count
\seq@percent=100
\ifnum\seq@count>0 \divide\seq@percent by \seq@count \fi
\fi
\fi
}
%%%%% TeXshade
\def\calc@widths{%
\fontfamily{cmss}\fontseries{m}\fontshape{n}
\selectfont
\setbox1=\hbox{\residues@size{A}}\logo@height=\ht1
\setlength\logo@height{\logo@stretch\logo@height}
\fontfamily{\residues@family}
\fontseries{\residues@series}
\fontshape{\residues@shape}
\selectfont
\setbox1=\hbox{\residues@size{W}}\box@width=1.15\wd1
\global\setlength\box@width{\char@stretch\box@width}
\box@height=1.2\ht1
\setbox1=\hbox{\residues@size{g}}\box@depth=1.1\dp1
\global\setlength\box@height{\line@stretch\box@height}
\global\setlength\box@depth{\line@stretch\box@depth}
\baselineskip=\box@height \advance\baselineskip by \box@depth
\lineskip=0pt
\ifshow@cons\setbox1=\hbox{\cons@name}\name@width=\wd1\else\name@width=0pt\fi
\loopcount=0
\expandafter\getregion@fromstack{\the\loopcount}
\expandafter\getregion@fromtintstack{\the\loopcount}
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
\expandafter\getregion@fromshadingstack{\the\loopcount}
\xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
\fontfamily{\namestext@family}
\fontseries{\namestext@series}
\fontshape{\namestext@shape}
\selectfont
\ifshow@logo
\ifx\logo@name@user\ampers@nd
\setbox1=\hbox{\namestext@size logo\kern1em}
\else
\setbox1=\hbox{\namestext@size\logo@name@user\kern1em}
\fi
\ifnum\wd1>\name@width \name@width=\wd1 \fi
\fi
\ifshow@sublogo
\ifx\sublogo@name@user\ampers@nd
\setbox1=\hbox{\namestext@size family\kern1em}
\else
\setbox1=\hbox{\namestext@size\sublogo@name@user\kern1em}
\fi
\ifnum\wd1>\name@width \name@width=\wd1 \fi
\ifx\hide@negatives\n@
\setbox1=\hbox{\namestext@size\sublogo@name@neg\kern1em}
\fi
\ifnum\wd1>\name@width \name@width=\wd1 \fi
\fi
\loopcount=1
\loop
\setbox1=\hbox{\namestext@size\csname newseqname\the\loopcount\endcsname}
\ifnum\wd1>\name@width \name@width=\wd1 \fi
\ifnum\ht1>\box@height
\box@height=1.1\ht1
\global\setlength\box@height{\line@stretch\box@height}
\baselineskip=\box@height \advance\baselineskip by \box@depth
\fi
\ifnum\dp1>\box@depth
\box@depth=1.1\dp1
\global\setlength\box@depth{\line@stretch\box@depth}
\baselineskip=\box@height \advance\baselineskip by \box@depth
\fi
\expandafter\getregion@fromstack{\the\loopcount}
\expandafter\getregion@fromtintstack{\the\loopcount}
\expandafter\getregion@fromemphstack{\the\loopcount}
\expandafter\getregion@fromlowerstack{\the\loopcount}
\expandafter\getregion@fromframestack{\the\loopcount}
\expandafter\getregion@fromshadingstack{\the\loopcount}
\xdef\bottop@{top} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttop} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{tttop} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{ttttop} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bottom} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bbottom} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
\xdef\bottop@{bbbbottom} \expandafter\getregion@fromfstack{\the\loopcount}
\innerloopcount = \csname seq@len\the\loopcount\endcsname
\advance\innerloopcount by \csname seq@start\the\loopcount\endcsname
\advance\innerloopcount by -1
\expandafter\xdef\csname seq@len\the\loopcount\endcsname{\the\innerloopcount}
\advance\loopcount by 1
\ifnum\loopcount>\seq@count \else \repeat
\advance\name@width by -2em
\global\xdef\name@@width{\the\name@width}
\advance\name@width by 3em
\fontfamily{\numbertext@family}
\fontseries{\numbertext@series}
\fontshape{\numbertext@shape}
\selectfont
\setbox1=\hbox{\bottomruler@size\num@width\,-}
\xdef\ruler@width{\the\wd1}
\setbox1=\hbox{\numbertext@size\num@width}
\number@width=\wd1
\advance\number@width by 1em
\loopcount=\linewidth
\ifnames@ \advance\loopcount by -\name@width \fi
\width@tmp=1.6\box@width
\ifnumbers@
\ifnumbers@left
\advance\loopcount by -\number@width
\else
\xdef\first@{left}
\ifx\show@logoscale\first@
\advance\loopcount by -\width@tmp
\fi
\fi
\ifnumbers@right
\advance\loopcount by -\number@width
\else
\xdef\first@{right}
\ifx\show@logoscale\first@
\advance\loopcount by -\width@tmp
\fi
\fi
\else
\xdef\first@{left}
\ifx\show@logoscale\first@
\advance\loopcount by -\width@tmp
\fi
\xdef\first@{right}
\ifx\show@logoscale\first@
\advance\loopcount by -\width@tmp
\fi
\xdef\first@{leftright}
\ifx\show@logoscale\first@
\advance\loopcount by -\width@tmp
\advance\loopcount by -\width@tmp
\fi
\fi
\divide\loopcount by \box@width
\divide\loopcount by 5 \multiply\loopcount by 5
\ifrpl@fix\else
\ifnum\res@perline>\loopcount \res@perline=\loopcount\fi\fi
\ifnum\finger@linenum>0
\width@tmp=\linewidth
\ifnames@ \advance\width@tmp by -\name@width \fi
\ifnumbers@ \advance\width@tmp by -\number@width \fi
\divide\width@tmp by \finger@linenum
\global\setlength\box@width{\width@tmp}
\fi
\center@fill=\linewidth
\ifnames@ \advance\center@fill by -\name@width \fi
\ifnumbers@ \advance\center@fill by -\number@width \fi
\width@tmp=\box@width \multiply\width@tmp by \res@perline
\advance\center@fill by -\width@tmp
\ifx\out@put\y@\leftskip\c@factor\center@fill\fi
\ifx\logo@colors@set\n@
\if\seq@type N
\clearlogocolors[Yellow]
\logocolor{G}{Black}
\logocolor{A}{Green}
\logocolor{TU}{Red}
\logocolor{C}{Blue}
\else
\clearlogocolors
\logocolor{DE}{Red}
\logocolor{CM}{Yellow}
\logocolor{KR}{Blue}
\logocolor{ST}{Orange}
\logocolor{FY}{MidnightBlue}
\logocolor{NQ}{Cyan}
\logocolor{G}{LightGray}
\logocolor{LVI}{Green}
\logocolor{A}{DarkGray}
\logocolor{W}{CarnationPink}
\logocolor{H}{CornflowerBlue}
\logocolor{P}{Apricot}
\logocolor{BZ}{LightMagenta}
\fi
\fi
}
\def\multiple@dssp{%
\advance\loopcount by 1
\include@DSSP
\ifnum\loopcount<\dssp@num\multiple@dssp\fi}
\def\multiple@stride{%
\advance\loopcount by 1
\include@stride
\ifnum\loopcount<\stride@num\multiple@stride\fi}
\def\multiple@PHD{%
\advance\loopcount by 1
\include@PHD
\ifnum\loopcount<\PHD@num\multiple@PHD\fi}
\def\multiple@HMMTOP{%
\advance\loopcount by 1
\include@HMMTOP
\ifnum\loopcount<\HMMTOP@num\multiple@HMMTOP\fi}
\newenvironment{texshade}[2][&]%
{\standarddefinitions
\c@d@ns
\xdef\first@{#1}\ifx\first@\ampers@nd\else\input{#1}\fi
\readalignfile{#2}
}%
{\ifnum\seq@count>0
\loopcount=0
\ifnum\loopcount<\dssp@num \multiple@dssp\fi
\loopcount=0
\ifnum\loopcount<\stride@num \multiple@stride\fi
\loopcount=0
\ifnum\loopcount<\PHD@num \multiple@PHD\fi
\loopcount=0
\ifnum\loopcount<\HMMTOP@num \multiple@HMMTOP\fi
\loopcount=1 \kill@seqnow
\reorder@seqs\seq@order \seq@count=\killseq@count
\global\xdef\seq@num{\the\seq@count}
\clear@sim@count
\ifnum\csname res@count\start@seq\endcsname<0
\ifnum\start@num>0
\loopcount=\start@num
\advance\loopcount by -1
\xdef\start@num{\the\loopcount}
\fi
\fi
\ifnum\rule@num>0
\loopcount=\csname res@count\rule@num\endcsname
\divide\loopcount by \ruler@step
\multiply\loopcount by \ruler@step
\ifnum\loopcount<0
\ifnum\ruler@step<3
\advance\loopcount by \ruler@step
\fi
\else
\advance\loopcount by \ruler@step
\fi
\xdef\rule@tens{\the\loopcount}
\else
\loopcount=\cons@count
\divide\loopcount by \ruler@step
\multiply\loopcount by \ruler@step
\ifnum\loopcount<0
\ifnum\ruler@step<3
\advance\loopcount by \ruler@step
\fi
\else
\advance\loopcount by \ruler@step
\fi
\xdef\rule@tens{\the\loopcount}
\fi
\xdef\first@{top}
\ifx\cap@pos\first@
\xdef\@captype{figure}
\ifx\c@pshort\n@
\caption{\c@p}
\else
\caption[\c@pshort]{\c@p}
\fi
\fi
\bgroup
\ifx\out@put\y@\bigskip\fi
\iffuncmode \show@consfalse \fi
\ifall@fshade \iffuncmode \else \all@fshadefalse \fi\fi
\ifnum\finger@linenum>0
\show@consfalse
\hidechartrue
\message{<Fingerprinting---please wait>}
\fi
\calc@widths
\read@lines
\save@lengths
\iflegend@
\vspace{\vspace@legend}
\setbox1=\vbox{\do@legend}
\vbox{\do@legend}\par
\ifnum\ht1<-\vspace@legend
\vspace{-\ht1}\vspace{-\vspace@legend}
\fi
\fi
\egroup
\xdef\first@{bottom}
\ifx\cap@pos\first@
\vspace{-\baselineskip}
\xdef\@captype{figure}
\ifx\c@pshort\n@
\caption{\c@p}
\else
\caption[\c@pshort]{\c@p}
\fi
\fi
\fi}
\def\standarddefinitions{%
\xdef\prfx{pep}\clear@groups\clear@sims
\xdef\prfx{DNA}\clear@groups\clear@sims
\clearfuncgroups
\clear@simpairs
\shadingcolors{blues}
\shadingcolors{reds}
\shadingcolors{greens}
\shadingcolors{grays}
\shadingcolors{black}
\loopcount=\@lign@count
\advance\loopcount by 1\relax
\xdef\@lign@count{\the\loopcount}
\start@true \xdef\start@num{1} \xdef\start@seq{0}
\stop@false \xdef\end@num{n} \xdef\seq@regions{0}
\cons@count=0
\expandafter\xdef\csname res@count0\endcsname{0}
\xdef\allow@zero{n} \xdef\c@ns@shift{0}
\regionalshadefalse\regionalemphfalse\regionallowerfalse\regionaltintfalse
\frame@false\shading@false
\xdef\ruler@rot{0}
\topfeaturefalse \bottomfeaturefalse
\ttopfeaturefalse \bbottomfeaturefalse
\tttopfeaturefalse \bbbottomfeaturefalse
\ttttopfeaturefalse \bbbbottomfeaturefalse
\all@fshadefalse\hidecharfalse
\xdef\finger@linenum{0}
\xdef\hide@seqs{n}
\xdef\dssp@num{0} \xdef\stride@num{0} \xdef\PHD@num{0} \xdef\HMMTOP@num{0}
\xdef\bottop@{top} \expandafter\xdef\csname feature@\bottop@\endcsname{0}
\xdef\bottop@{ttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0}
\xdef\bottop@{tttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0}
\xdef\bottop@{ttttop} \expandafter\xdef\csname feature@\bottop@\endcsname{0}
\xdef\bottop@{bottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0}
\xdef\bottop@{bbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0}
\xdef\bottop@{bbbottom} \expandafter\xdef\csname feature@\bottop@\endcsname{0}
\xdef\bottop@{bbbbottom}\expandafter\xdef\csname feature@\bottop@\endcsname{0}
\xdef\frame@{0}
\xdef\show@Hdssp{no} \xdef\show@Gdssp{no} \xdef\show@Idssp{no}
\xdef\show@Edssp{no} \xdef\show@Bdssp{no} \xdef\show@Tdssp{no}
\xdef\show@Sdssp{no}
\xdef\show@Hstride{no} \xdef\show@Gstride{no} \xdef\show@Istride{no}
\xdef\show@Estride{no} \xdef\show@Bstride{no} \xdef\show@Tstride{no}
\xdef\show@itop{no} \xdef\show@etop{no} \xdef\show@TMtop{no}
\xdef\show@i@HMMTOP{no} \xdef\show@e@HMMTOP{no} \xdef\show@TM@HMMTOP{no}
\xdef\show@Hsec{no} \xdef\show@Esec{no}
\xdef\collect@restop{no} \xdef\collect@resttop{no}
\xdef\collect@restttop{no} \xdef\collect@resttttop{no}
\xdef\collect@resbottom{no} \xdef\collect@resbbottom{no}
\xdef\collect@resbbbottom{no}\xdef\collect@resbbbbottom{no}
\xdef\tr@nslatetop{} \xdef\tr@nslatettop{}
\xdef\tr@nslatetttop{} \xdef\tr@nslatettttop{}
\xdef\tr@nslatebottom{} \xdef\tr@nslatebbottom{}
\xdef\tr@nslatebbbottom{} \xdef\tr@nslatebbbbottom{}
\xdef\tr@nsseqtop{0} \xdef\tr@nsseqttop{0}
\xdef\tr@nsseqtttop{0} \xdef\tr@nsseqttttop{0}
\xdef\tr@nsseqbottom{0} \xdef\tr@nsseqbbottom{0}
\xdef\tr@nsseqbbbottom{0} \xdef\tr@nsseqbbbbottom{0}
\xdef\triple@counttop{0} \xdef\triple@countttop{0}
\xdef\triple@counttttop{0} \xdef\triple@countttttop{0}
\xdef\triple@countbottom{0} \xdef\triple@countbbottom{0}
\xdef\triple@countbbbottom{0}\xdef\triple@countbbbbottom{0}
\xdef\last@@restop{} \xdef\last@@resttop{}
\xdef\last@@restttop{} \xdef\last@@resttttop{}
\xdef\last@@resbottom{} \xdef\last@@resbbottom{}
\xdef\last@@resbbbottom{} \xdef\last@@resbbbbottom{}
\xdef\out@put{y} \xdef\m@p{no}
\xdef\t@sp@ce{0mm} \xdef\tt@sp@ce{0mm}
\xdef\ttt@sp@ce{0mm} \xdef\tttt@sp@ce{0mm}
\xdef\b@sp@ce{0mm} \xdef\bb@sp@ce{0mm}
\xdef\bbb@sp@ce{0mm} \xdef\bbbb@sp@ce{0mm}
\xdef\ruler@sp@ce{0mm}
\xdef\seq@gap@num{0}
\xdef\h@ndalign{no} \xdef\sep@space{0pt}
\xdef\c@pshort{n}
\xdef\bottom@stretch{n} \xdef\bbottom@stretch{n}
\xdef\bbbottom@stretch{n} \xdef\bbbbottom@stretch{n}
\xdef\c@nscol{} \xdef\c@nssc@le{ColdHot}
\xdef\collect@cons@colors{no} \xdef\cons@now{no}
\xdef\res@numA{0} \xdef\res@numB{0}
\xdef\res@numC{0} \xdef\res@numD{0}
\xdef\res@numE{0} \xdef\res@numF{0}
\xdef\res@numG{0} \xdef\res@numH{0}
\xdef\res@numI{0} \xdef\res@numJ{0}
\xdef\res@numK{0} \xdef\res@numL{0}
\xdef\res@numM{0} \xdef\res@numN{0}
\xdef\res@numO{0} \xdef\res@numP{0}
\xdef\res@numQ{0} \xdef\res@numR{0}
\xdef\res@numS{0} \xdef\res@numT{0}
\xdef\res@numU{0} \xdef\res@numV{0}
\xdef\res@numW{0} \xdef\res@numX{0}
\xdef\res@numY{0} \xdef\res@numZ{0}
\expandafter\xdef\csname res@num\questi@n\endcsname{0}
\expandafter\xdef\csname res@num\d@t\endcsname{0}
\expandafter\xdef\csname res@num\equ@l\endcsname{0}
\xdef\res@corrA{0} \xdef\res@corrB{0}
\xdef\res@corrC{0} \xdef\res@corrD{0}
\xdef\res@corrE{0} \xdef\res@corrF{0}
\xdef\res@corrG{0} \xdef\res@corrH{0}
\xdef\res@corrI{0} \xdef\res@corrJ{0}
\xdef\res@corrK{0} \xdef\res@corrL{0}
\xdef\res@corrM{0} \xdef\res@corrN{0}
\xdef\res@corrO{0} \xdef\res@corrP{0}
\xdef\res@corrQ{0} \xdef\res@corrR{0}
\xdef\res@corrS{0} \xdef\res@corrT{0}
\xdef\res@corrU{0} \xdef\res@corrV{0}
\xdef\res@corrW{0} \xdef\res@corrX{0}
\xdef\res@corrY{0} \xdef\res@corrZ{0}
\expandafter\xdef\csname res@corr\questi@n\endcsname{0}
\expandafter\xdef\csname res@corr\d@t\endcsname{0}
\expandafter\xdef\csname res@corr\equ@l\endcsname{0}
\xdef\corr@max{0} \xdef\do@freq@correction{n}
\xdef\res@total{0}
\xdef\stack@sequencelogo{} \xdef\bit@total{0}
\clearlogocolors \xdef\logo@colors@set{n}
\show@sublogofalse \xdef\stack@sublogo{}
\xdef\clear@logo{n} \xdef\subfamily@threshold{50}
\xdef\subfamily@seq{1} \xdef\sig@max{100000}
\xdef\sublogo@num{} \xdef\sublogo@sig{}
\xdef\subfamily@count{0} \xdef\sublogo@name@neg{}
\xdef\logo@name@user{&} \xdef\sublogo@name@user{&}
\expandafter\xdef\csname group@num1\endcsname{0}
\expandafter\xdef\csname group@num2\endcsname{0}
\xdef\exp@rt@num{0} \xdef\exp@rt{n}
\xdef\divref@{0}
\xdef\all@thresh@ld{100} \all@shadefalse
\hidefeaturenames \hidefeaturestylenames
\xdef\T@coffee@ccons{n} \xdef\T@coffee@bcons{n}
\xdef\dom@in{no} \xdef\label@motif{no}
\xdef\motif@num{0} \xdef\all@out{n}
\hfuzz9999pt
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
%%%%% Default parameter settings for the LaTeX ``TeXshade'' package %%%%%
%%%%% %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%% %%%%%
%%%%% Under any circumstances: %%%%%
%%%%% %%%%%
%%%%% DO NOT CHANGE ANY SETTINGS HERE !!! %%%%%
%%%%% %%%%%
%%%%% Please define your personal parameter file! Store your new file %%%%%
%%%%% together with this style-file in the same directory and load the %%%%%
%%%%% file by naming it as an optional parameter in the `texshade' en- %%%%%
%%%%% vironment. The file `texshade.def' can be used as a template for %%%%%
%%%%% the new creation. See the manual for further help. %%%%%
%%%%% %%%%%
%%%%% THANK YOU !!! %%%%%
%%%%% %%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\shadingmode{identical} % Shade identical residues only
\shadingcolors{blues} % Select the blue color scheme for shading
\constoallseqs % Calculate consensus considering all seqs
\threshold{50} % Consensus threshold percentage is 50
\residuesperline{999} % As many residues as possible per line
\numberingwidth{9999} % Assign space for 4 digit numbering
\charstretch{1} % Do not stretch character width
\linestretch{1} % Do not stretch lines vertically
\gapchar{.} % . is printed in sequence gaps
\gaprule{0.3pt} % If a rule is printed in gaps use 0.3 pt
\gapcolors{Black}{White} % Gap symbols appear `Black on White'
\domaingaprule{1pt} % If a rule is set between domains use 1 pt
\domaingapcolors{Red}{White} % Domain separation line appears `Red on White'
\numberingcolor{Black} % Numbering color is `Black'
\shownumbering{right} % Show sequence numbering on the left
\namescolor{Black} % Names' color is `Black'
\featurenamescolor{Black} % Feature names' color is `Black'
\featurestylenamescolor{Black} % Feature names' color is `Black'
\shownames{left} % Show sequence names on the right
\consensuscolors{Black}{White} % All consensus symbols/letters
{Black}{White} % appear `Black on White'
{Black}{White} %
\showconsensus{bottom} % Show consensus line at bottom with
\hidesequencelogo % Do not show a sequence logo as consensus
\showlogoscale{leftright} % Show vertical scale bar if logo is on
\logostretch{1} % Do not stretch sequence logo vertically
\hidesubfamilylogo % Do not show a subfamily logo
\subfamilythreshold{50} % Set subfamily threshold to 50%
\shownegatives % Show negative values in subfamily logo
\showrelevance[Black]{*} % Label relevant subfamily deviations
\defconsensus{{}}{*}{!} % Blank =no match; * =match; ! =all match
\showleadinggaps % Show gap symbols before sequence start
\rulercolor{Black} % Ruler's color is `Black'
\hideruler % Do not show the ruler
\rulersteps{10} % Ruler ticks every 10 residues
\legendcolor{Black} % Legend text color is `Black'
\hidelegend % Do not show the legend
\alignment{center} % Center alignment on page
\medsepline % Medium height if separation line is on
\medblockskip % Medium skip between sequence blocks
\flexblockspace % Use optimized space between blocks
\featurerule{0.5ex} % Set feature rule thickness to 1/2 ex
\bargraphstretch{1} % Do not stretch bars in feature graphs
\colorscalestretch{1} % Do not stretch color scales in features
\backtranstext{horizontal} % Horizontal triplets in feature texts
\backtranslabel{alternating} % Alternating triplets in feature styles
\setfamily{residues}{tt} % Use typewriter family for residues
\setseries{residues}{md} % Use normal series for residues
\setshape {residues}{up} % Use upright shape for residues
\setsize {residues}{normalsize} % Use normal size for residues
\setfamily{numbering}{tt} % Use typewriter family for numbering
\setseries{numbering}{md} % Use normal series for numbering
\setshape {numbering}{up} % Use upright shape for numbering
\setsize {numbering}{normalsize} % Use normal size for numbering
\setfamily{names}{tt} % Use typewriter family for names
\setseries{names}{md} % Use normal series for names
\setshape {names}{up} % Use upright shape for names
\setsize {names}{normalsize} % Use normal size for names
\setfamily{featurenames}{tt} % Use typewriter family for feature names
\setseries{featurenames}{md} % Use normal series for feature names
\setshape {featurenames}{up} % Use upright shape for feature names
\setsize {featurenames}{normalsize}% Use normal size for feature names
\setfamily{featurestylenames}{tt} % Use typewriter family for feature style names
\setseries{featurestylenames}{md} % Use normal series for feature style names
\setshape {featurestylenames}{up} % Use upright shape for feature style names
\setsize {featurestylenames}{normalsize}% Use normal size for feature style names
\setfamily{features}{rm} % Use roman family for feature texts
\setseries{features}{md} % Use normal series for feature texts
\setshape {features}{it} % Use italics shape for feature texts
\setsize {features}{normalsize} % Use normal size for feature texts
\setfamily{featurestyles}{tt} % Use typewriter family for feature styles
\setseries{featurestyles}{md} % Use normal series for feature styles
\setshape {featurestyles}{up} % Use upright shape for feature styles
\setsize {featurestyles}{normalsize}% Use normal size for feature styles
\setfamily{legend}{tt} % Use typewriter family for legend texts
\setseries{legend}{md} % Use normal series for legend texts
\setshape {legend}{up} % Use upright shape for legend texts
\setsize {legend}{normalsize} % Use normal size for legend texts
\setfamily{ruler}{sf} % Use sans serif font for ruler numbers
\tintdefault{medium} % Use medium tint intensity
\emphdefault{it} % Use italics to emphasize regions
\showonPHDsec{alpha,beta} % Show helices and strands (PHD input)
\showonPHDtopo{internal,external,TM}% Show int., ext. and TM's (PHD input)
\showonHMMTOP{TM} % Show TM's (not int/ext on HMMTOP input)
\showonSTRIDE{alpha,3-10,pi,beta} % Show helices and strands (STRIDE input)
\showonDSSP{alpha,3-10,pi,beta} % Show helices and strands (DSSP input)
\secondcolumnDSSP % Use numbering from 2. column in DSSP
\appearance{PHDtopo}{internal} % \
{bottom}{'-'} % \
{int.\ \Alphacount} % |
\appearance{PHDtopo}{external} % |
{top}{,-,} % |
{ext.\ \Alphacount} % |
\appearance{PHDtopo}{TM}{top} % |
{box[LightGray]:TM\numcount}{} % |
\appearance{HMMTOP}{internal} % |
{bottom}{'-'} % |
{int.\ \Alphacount} % |
\appearance{HMMTOP}{external} % |
{top}{,-,} % |
{ext.\ \Alphacount} % |
\appearance{HMMTOP}{TM}{top} % |
{helix}{TM\numcount} % |
\appearance{PHDsec}{alpha}{top} % |
{box:$\alpha$\numcount}{} % |
\appearance{PHDsec}{beta}{top} % |
{-->}{$\beta$\numcount} % |
\appearance{STRIDE}{alpha}{top} % |
{box:$\alpha$\numcount}{} % | Definitions for the appearance of
\appearance{STRIDE}{3-10}{top} % \
{fill:$\circ$}{3$_{10}$} % > secondary structures included from|
\appearance{STRIDE}{pi} % /
{top}{---}{$\pi$} % | PHD-, STRIDE-, or DSSP-files.
\appearance{STRIDE}{beta}{top} % |
{-->}{$\beta$\numcount} % |
\appearance{STRIDE}{bridge} % |
{top}{fill:$\uparrow$}{} % |
\appearance{STRIDE}{turn} % |
{top}{,-,}{turn} % |
\appearance{DSSP}{alpha}{top} % |
{box:$\alpha$\numcount}{} % |
\appearance{DSSP}{3-10}{top} % |
{fill:$\circ$}{3$_{10}$} % |
\appearance{DSSP}{pi} % |
{top}{---}{$\pi$} % |
\appearance{DSSP}{beta}{top} % |
{-->}{$\beta$\numcount} % |
\appearance{DSSP}{bridge} % |
{top}{fill:$\uparrow$}{} % |
\appearance{DSSP}{turn} % |
{top}{,-,}{turn} % |
\appearance{DSSP}{bend}{top} % /
{fill:$\diamond$}{} % /
\pepgroups{FYW,ILVM,RK,DE,GA,ST,NQ} % Amino acid grouping due to similarity
\pepsims{F}{YW} % Y and W are similar to F
\pepsims{Y}{WF} % W and F are similar to Y
\pepsims{W}{YF} % Y and F are similar to W
\pepsims{I}{LVM} % L, V and M are similar to I
\pepsims{L}{VMI} % V, M and I are similar to L
\pepsims{V}{MIL} % M, I and L are similar to V
\pepsims{R}{KH} % K and H are similar to R
\pepsims{K}{HR} % H and R are similar to K
\pepsims{H}{RK} % R and K are similar to H
\pepsims{A}{GS} % G and S are similar to A
\pepsims{G}{A} % A (but not S) is similar to G
\pepsims{S}{TA} % T and A are similar to S
\pepsims{T}{S} % S (but not A) is similar to T
\pepsims{D}{EN} % E and N (but not Q) are similar to D
\pepsims{E}{DQ} % D and Q (but not N) are similar to E
\pepsims{N}{QD} % Q and D (but not E) are similar to N
\pepsims{Q}{NE} % N and E (but not D) are similar to Q
\DNAgroups{GAR,CTY} % Nucleotide grouping due to similarity
\DNAsims{A}{GR} % G and R are similar to A
\DNAsims{G}{AR} % A and R are similar to G
\DNAsims{R}{AG} % A and G are similar to R
\DNAsims{C}{TY} % T and Y are similar to C
\DNAsims{T}{CY} % C and Y are similar to T
\DNAsims{Y}{CT} % C and T are similar to Y
}
\catcode`\@=12
\endinput
%%
%% End of file `texshade.sty'.
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