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|
%%
%% 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'.
|
