%% %% This is file `gotoh.sty', %% generated with the docstrip utility. %% %% The original source files were: %% %% gotoh.dtx (with options: `package') %% %% Copyright (c) 2017 Takuto ASAKURA (wtsnjp) %% GitHub: https://github.com/wtsnjp %% Twitter: @wtsnjp %% %% This package is distributed under the MIT License. %% \NeedsTeXFormat{LaTeX2e} \ProvidesPackage{gotoh}[2017/07/07 v1.1 Sequence alignment algorithm] \RequirePackage{xkeyval} \def\gth@pkgname{gotoh} \def\gth@warn{\PackageWarningNoLine\gth@pkgname} \def\gth@error{\PackageError\gth@pkgname} \newif\if@gth@first@ \newif\if@gth@remain@ \newif\if@gth@gap@ \newif\if@gth@gapx@ \newif\if@gth@gapy@ \newcount\gth@tempcnta \newcount\gth@tempcntb \newcount\gth@tempcntc \newcount\gth@tempcntd \newcount\gth@calc \edef\gth@sn{\number\z@} \mathchardef\gth@M="7FFF \edef\gth@min{-\number\gth@M} \newdimen\gth@tempdima \define@cmdkeys[gth]{config}[gth@]{match, mismatch, d, e} \setkeys[gth]{config}{match=1, mismatch=-1, d=7, e=1} \define@key[gth]{config}{score}{\def\gth@score{#1}} \define@key[gth]{config}{result A}{\def\gth@resulta{#1}} \define@key[gth]{config}{result B}{\def\gth@resultb{#1}} \setkeys[gth]{config}{ score=\GotohScore, result A=\GotohResultA, result B=\GotohResultB} \define@boolkeys[gth]{config}[@gth@]{memoization, uppercase}[true] \define@key[gth]{config}{gap char}{\def\gth@gap@char{#1}} \setkeys[gth]{config}{memoization=false, uppercase=false, gap char={.}} \def\gth@nameuse#1{\csname gth@#1\endcsname} \def\gth@name@edef#1{\expandafter\edef\csname gth@#1\endcsname} \def\gth@name@xdef#1{\expandafter\xdef\csname gth@#1\endcsname} \def\gth@glet{\global\let} \def\gth@advance#1#2{% \gth@calc#1\advance\gth@calc#2\edef#1{\the\gth@calc}} \def\gth@increment#1{\gth@advance#1\@ne} \def\gth@decrement#1{\gth@advance#1\m@ne} \def\gth@max#1{% \@gth@first@true \@for\gth@member:=#1\do{% \if@gth@first@ \gth@calc\gth@member \@gth@first@false \else \ifnum\gth@member>\gth@calc \gth@calc\gth@member \fi \fi}} \def\gth@gap@penalty#1{% \gth@calc#1\relax \advance\gth@calc\m@ne \multiply\gth@calc-\gth@e \advance\gth@calc-\gth@d} \def\gth@tab#1{% \bgroup \sbox\z@ 0% \expandafter\gth@tempdima\ht\z@ \multiply\gth@tempdima 8% \mbox{\hbox to\gth@tempdima{\hss #1}}% \egroup} \def\gth@print@matrix#1{% \bgroup\ttfamily #1:\\ \gth@tempcnta\z@ \@whilenum\gth@tempcnta<\gth@m\do{% \gth@tempcntb\z@ \@whilenum\gth@tempcntb<\gth@n\do{% \gth@tab{% \gth@nameuse{\gth@sn @#1@\the\gth@tempcnta @\the\gth@tempcntb}}% \advance\gth@tempcntb\@ne}\\ \advance\gth@tempcnta\@ne}% \egroup} \newcommand{\Gotoh}{% \gth@increment\gth@sn \bgroup % \egroup is in \gth@gotoh@pre \@ifnextchar[{\gth@gotoh@setkeys}{\gth@gotoh@pre}} \def\gth@gotoh@setkeys[#1]{\setkeys[gth]{config}{#1}\gth@gotoh@pre} \def\gth@gotoh@pre#1#2{% \edef\gth@tmpa{\noexpand\gth@gotoh{#1}{#2}}% \if@gth@uppercase \uppercase\expandafter{\gth@tmpa}% \else \gth@tmpa \fi\egroup} \def\gth@gotoh#1#2{% \gth@tempcnta\z@ \@tfor\gth@member:=#1\do{% \gth@name@edef{seqa@\the\gth@tempcnta}{\gth@member}% \advance\gth@tempcnta\@ne}% \advance\gth@tempcnta\@ne \edef\gth@m{\the\gth@tempcnta}% \gth@tempcntb\z@ \@tfor\gth@member:=#2\do{% \gth@name@edef{seqb@\the\gth@tempcntb}{\gth@member}% \advance\gth@tempcntb\@ne}% \advance\gth@tempcntb\@ne \edef\gth@n{\the\gth@tempcntb}% \gth@tempcnta\z@ \@whilenum\gth@tempcnta<\gth@m\do{% \gth@gap@penalty{\gth@tempcnta}% \gth@name@xdef{\gth@sn @m@\the\gth@tempcnta @0}{\gth@min}% \gth@name@xdef{\gth@sn @ix@\the\gth@tempcnta @0}{\the\gth@calc}% \gth@name@xdef{\gth@sn @iy@\the\gth@tempcnta @0}{\gth@min}% \advance\gth@tempcnta\@ne}% \gth@tempcntb\z@ \@whilenum\gth@tempcntb<\gth@n\do{% \gth@gap@penalty{\gth@tempcntb}% \gth@name@xdef{\gth@sn @m@0@\the\gth@tempcntb}{\gth@min}% \gth@name@xdef{\gth@sn @ix@0@\the\gth@tempcntb}{\gth@min}% \gth@name@xdef{\gth@sn @iy@0@\the\gth@tempcntb}{\the\gth@calc}% \advance\gth@tempcntb\@ne}% \gth@name@xdef{\gth@sn @m@0@0}{\number\z@}% \if@gth@memoization \gth@decrement\gth@m \gth@decrement\gth@n \gth@memo@ix{\gth@m}{\gth@n}% \gth@memo@iy{\gth@m}{\gth@n}% \gth@memo@m{\gth@m}{\gth@n}% \gth@increment\gth@m \gth@increment\gth@n \else \gth@tempcnta\@ne \@whilenum\gth@tempcnta<\gth@m\do{% \gth@tempcntb\@ne \@whilenum\gth@tempcntb<\gth@n\do{% \advance\gth@tempcnta\m@ne \gth@max{% \gth@nameuse{\gth@sn @m@\the\gth@tempcnta @\the\gth@tempcntb},% \gth@nameuse{\gth@sn @iy@\the\gth@tempcnta @\the\gth@tempcntb}}% \gth@tempcntc\gth@calc \gth@tempcntd \gth@nameuse{\gth@sn @ix@\the\gth@tempcnta @\the\gth@tempcntb}% \advance\gth@tempcntc-\gth@d\advance\gth@tempcntd-\gth@e \advance\gth@tempcnta\@ne \gth@max{\gth@tempcntc,\gth@tempcntd}% \gth@name@xdef{\gth@sn @ix@\the\gth@tempcnta @\the\gth@tempcntb}{% \the\gth@calc}% \advance\gth@tempcntb\m@ne \gth@tempcntc \gth@nameuse{\gth@sn @m@\the\gth@tempcnta @\the\gth@tempcntb}% \gth@tempcntd \gth@nameuse{\gth@sn @iy@\the\gth@tempcnta @\the\gth@tempcntb}% \advance\gth@tempcntc-\gth@d\advance\gth@tempcntd-\gth@e \advance\gth@tempcntb\@ne \gth@max{\gth@tempcntc,\gth@tempcntd}% \gth@name@xdef{\gth@sn @iy@\the\gth@tempcnta @\the\gth@tempcntb}{% \the\gth@calc}% \advance\gth@tempcnta\m@ne\advance\gth@tempcntb\m@ne \gth@max{% \gth@nameuse{\gth@sn @m@\the\gth@tempcnta @\the\gth@tempcntb},% \gth@nameuse{\gth@sn @ix@\the\gth@tempcnta @\the\gth@tempcntb},% \gth@nameuse{\gth@sn @iy@\the\gth@tempcnta @\the\gth@tempcntb}}% \edef\gth@tmpa{\gth@nameuse{seqa@\the\gth@tempcnta}}% \edef\gth@tmpb{\gth@nameuse{seqb@\the\gth@tempcntb}}% \advance\gth@tempcnta\@ne\advance\gth@tempcntb\@ne \ifx\gth@tmpa\gth@tmpb \advance\gth@calc\gth@match \else \advance\gth@calc\gth@mismatch \fi \gth@name@xdef{\gth@sn @m@\the\gth@tempcnta @\the\gth@tempcntb}{% \the\gth@calc}% \advance\gth@tempcntb\@ne}% \advance\gth@tempcnta\@ne}% \fi %\gth@print@matrix{m}% %\gth@print@matrix{ix}% %\gth@print@matrix{iy}% \bgroup \gth@decrement\gth@m \gth@decrement\gth@n \expandafter\xdef\gth@score{% \gth@nameuse{\gth@sn @m@\gth@m @\gth@n}}% \egroup \let\gth@rseq@x\@empty\let\gth@rseq@y\@empty \@gth@remain@true\@gth@gapx@false\@gth@gapy@false \@whilesw\if@gth@remain@\fi{% \ifnum\gth@m=\z@ \gth@decrement\gth@n \expandafter\expandafter\expandafter \ifx\gth@nameuse{seqb@\gth@n}\relax\else \edef\gth@rseq@x{\gth@gap@char\gth@rseq@x}% \edef\gth@rseq@y{\gth@nameuse{seqb@\gth@n}% \gth@rseq@y}% \fi \else\ifnum\gth@n=\z@ \gth@decrement\gth@m \expandafter\expandafter\expandafter \ifx\gth@nameuse{seqa@\gth@m}\relax\else \edef\gth@rseq@x{\gth@nameuse{seqa@\gth@m}% \gth@rseq@x}% \edef\gth@rseq@y{\gth@gap@char\gth@rseq@y}% \fi \else \if@gth@gapx@ \gth@decrement\gth@m \expandafter\expandafter\expandafter \ifx\gth@nameuse{seqa@\gth@m}\relax\else \edef\gth@rseq@x{\gth@nameuse{seqa@\gth@m}% \gth@rseq@x}% \edef\gth@rseq@y{\gth@gap@char\gth@rseq@y}% \fi \gth@tempcnta\gth@nameuse{\gth@sn @m@\gth@m @\gth@n}% \gth@tempcntb\gth@nameuse{\gth@sn @ix@\gth@m @\gth@n}% \gth@tempcntc\gth@nameuse{\gth@sn @iy@\gth@m @\gth@n}% \advance\gth@tempcnta-\gth@d \advance\gth@tempcntb-\gth@e \advance\gth@tempcntc-\gth@d \ifnum\gth@tempcnta>\gth@tempcntb \@gth@gapx@false \else\ifnum\gth@tempcntb<\gth@tempcntc \@gth@gapx@false\@gth@gapy@true \fi\fi \else\if@gth@gapy@ \gth@decrement\gth@n \expandafter\expandafter\expandafter \ifx\gth@nameuse{seqb@\gth@n}\relax\else \edef\gth@rseq@x{\gth@gap@char\gth@rseq@x}% \edef\gth@rseq@y{\gth@nameuse{seqb@\gth@n}% \gth@rseq@y}% \fi \gth@tempcnta\gth@nameuse{\gth@sn @m@\gth@m @\gth@n}% \gth@tempcntb\gth@nameuse{\gth@sn @iy@\gth@m @\gth@n}% \advance\gth@tempcnta-\gth@d\advance\gth@tempcntb-\gth@e \ifnum\gth@tempcnta>\gth@tempcntb \@gth@gapy@false \fi \else \gth@decrement\gth@m \gth@decrement\gth@n \expandafter\expandafter\expandafter \ifx\gth@nameuse{seqa@\gth@m}\relax\else \expandafter\expandafter\expandafter \ifx\gth@nameuse{seqb@\gth@n}\relax\else \edef\gth@rseq@x{\gth@nameuse{seqa@\gth@m}% \gth@rseq@x}% \edef\gth@rseq@y{\gth@nameuse{seqb@\gth@n}% \gth@rseq@y}% \fi \fi \gth@tempcnta\gth@nameuse{\gth@sn @m@\gth@m @\gth@n}% \gth@tempcntb\gth@nameuse{\gth@sn @ix@\gth@m @\gth@n}% \gth@tempcntc\gth@nameuse{\gth@sn @iy@\gth@m @\gth@n}% \@gth@gap@false \ifnum\gth@tempcnta<\gth@tempcntb\@gth@gap@true\fi \ifnum\gth@tempcnta<\gth@tempcntc\@gth@gap@true\fi \if@gth@gap@ \ifnum\gth@tempcntb>\gth@tempcntc \@gth@gapx@true \else \@gth@gapy@true \fi \fi \fi\fi \fi\fi \ifnum\gth@m<\@ne\ifnum\gth@n<\@ne \@gth@remain@false \fi\fi}% \expandafter\gth@glet\gth@resulta\gth@rseq@x \expandafter\gth@glet\gth@resultb\gth@rseq@y} \def\gth@memo@ix#1#2{% \bgroup \gth@tempcnta#1\gth@tempcntb#2\relax \expandafter\expandafter\expandafter \ifx\gth@nameuse{\gth@sn @ix@\the\gth@tempcnta @\the\gth@tempcntb}\relax \advance\gth@tempcnta\m@ne \gth@memo@ix{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmp@ix@return{\gth@ix@return}% \gth@memo@iy{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmp@iy@return{\gth@iy@return}% \gth@memo@m{\gth@tempcnta}{\gth@tempcntb}% \advance\gth@tempcnta\@ne \gth@advance{\gth@m@return}{-\gth@d}% \gth@advance{\gth@tmp@ix@return}{-\gth@e}% \gth@advance{\gth@tmp@iy@return}{-\gth@d}% \gth@max{\gth@m@return,\gth@tmp@ix@return,\gth@tmp@iy@return}% \gth@name@xdef{\gth@sn @ix@\the\gth@tempcnta @\the\gth@tempcntb}{% \the\gth@calc}% \xdef\gth@ix@return{\the\gth@calc} \else \xdef\gth@ix@return{% \gth@nameuse{\gth@sn @ix@\the\gth@tempcnta @\the\gth@tempcntb}} \fi \egroup} \def\gth@memo@iy#1#2{% \bgroup \gth@tempcnta#1\gth@tempcntb#2\relax \expandafter\expandafter\expandafter \ifx\gth@nameuse{\gth@sn @iy@\the\gth@tempcnta @\the\gth@tempcntb}\relax \advance\gth@tempcntb\m@ne \gth@memo@iy{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmp@iy@return{\gth@iy@return}% \gth@memo@m{\gth@tempcnta}{\gth@tempcntb}% \advance\gth@tempcntb\@ne \gth@advance{\gth@m@return}{-\gth@d}% \gth@advance{\gth@tmp@iy@return}{-\gth@e}% \gth@max{\gth@m@return,\gth@tmp@iy@return}% \gth@name@xdef{\gth@sn @iy@\the\gth@tempcnta @\the\gth@tempcntb}{% \the\gth@calc}% \xdef\gth@iy@return{\the\gth@calc}% \else \xdef\gth@iy@return{% \gth@nameuse{\gth@sn @iy@\the\gth@tempcnta @\the\gth@tempcntb}} \fi \egroup} \def\gth@memo@m#1#2{% \bgroup \gth@tempcnta#1\gth@tempcntb#2\relax \expandafter\expandafter\expandafter \ifx\gth@nameuse{\gth@sn @m@\the\gth@tempcnta @\the\gth@tempcntb}\relax \advance\gth@tempcnta\m@ne\advance\gth@tempcntb\m@ne \gth@memo@ix{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmp@ix@return{\gth@ix@return}% \gth@memo@iy{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmp@iy@return{\gth@iy@return}% \gth@memo@m{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmpa{\gth@nameuse{seqa@\the\gth@tempcnta}}% \edef\gth@tmpb{\gth@nameuse{seqb@\the\gth@tempcntb}}% \advance\gth@tempcnta\@ne\advance\gth@tempcntb\@ne \gth@max{\gth@m@return,\gth@tmp@ix@return,\gth@tmp@iy@return}% \ifx\gth@tmpa\gth@tmpb \advance\gth@calc\gth@match \else \advance\gth@calc\gth@mismatch \fi \gth@name@xdef{\gth@sn @m@\the\gth@tempcnta @\the\gth@tempcntb}{% \the\gth@calc}% \xdef\gth@m@return{\the\gth@calc}% \else \xdef\gth@m@return{% \gth@nameuse{\gth@sn @m@\the\gth@tempcnta @\the\gth@tempcntb}}% \fi \egroup} \newcommand{\GotohConfig}[1]{\setkeys[gth]{config}{#1}} \endinput %% %% End of file `gotoh.sty'.