From 0b3bc08010f3aba0300a4cf48d6decd6fe1f5160 Mon Sep 17 00:00:00 2001 From: Karl Berry Date: Fri, 7 Jul 2017 21:06:52 +0000 Subject: gotoh (7jul17) git-svn-id: svn://tug.org/texlive/trunk@44764 c570f23f-e606-0410-a88d-b1316a301751 --- Master/texmf-dist/doc/latex/gotoh/README.md | 2 +- Master/texmf-dist/doc/latex/gotoh/gotoh.pdf | Bin 0 -> 291216 bytes Master/texmf-dist/source/latex/gotoh/gotoh.dtx | 510 ++++++++++++++----------- Master/texmf-dist/tex/latex/gotoh/gotoh.sty | 356 ++++++++--------- 4 files changed, 461 insertions(+), 407 deletions(-) create mode 100644 Master/texmf-dist/doc/latex/gotoh/gotoh.pdf (limited to 'Master/texmf-dist') diff --git a/Master/texmf-dist/doc/latex/gotoh/README.md b/Master/texmf-dist/doc/latex/gotoh/README.md index ffe849bf8c3..de1766a3d29 100644 --- a/Master/texmf-dist/doc/latex/gotoh/README.md +++ b/Master/texmf-dist/doc/latex/gotoh/README.md @@ -1,4 +1,4 @@ -# Package Gotoh (v1.0) +# Package Gotoh (v1.1) LaTeX package: An implementation of the Gotoh sequence alignment algorithm. diff --git a/Master/texmf-dist/doc/latex/gotoh/gotoh.pdf b/Master/texmf-dist/doc/latex/gotoh/gotoh.pdf new file mode 100644 index 00000000000..1d0f526ced5 Binary files /dev/null and b/Master/texmf-dist/doc/latex/gotoh/gotoh.pdf differ diff --git a/Master/texmf-dist/source/latex/gotoh/gotoh.dtx b/Master/texmf-dist/source/latex/gotoh/gotoh.dtx index 14395318b26..9c35e9a1a35 100644 --- a/Master/texmf-dist/source/latex/gotoh/gotoh.dtx +++ b/Master/texmf-dist/source/latex/gotoh/gotoh.dtx @@ -11,14 +11,14 @@ % % \fi % -% \CheckSum{971} +% \CheckSum{984} % % \changes{v1.0}{2017/05/05}{The first version} % % \iffalse %<*package> \NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{gotoh}[2017/05/05 v1.0 Sequence alignment algorithm] +\ProvidesPackage{gotoh}[2017/07/07 v1.1 Sequence alignment algorithm] % %<*driver> \documentclass[draft]{ltxdoc} @@ -105,16 +105,16 @@ % \section{Calculating the Alignment} % % \DescribeMacro{\Gotoh} -% The |\Gotoh| command simply takes two sequences as its arguments. +% The syntax of |\Gotoh| is shown below. % \begin{quote} -% |\Gotoh|\marg{sequence A}\marg{sequence B} +% |\Gotoh|\oarg{key-value list}\marg{sequence A}\marg{sequence B} % \end{quote} % The command puts the optimal score of the alignment to specified control % sequence (default: |\GotohScore|) after executing the Gotoh algorithm, and % returns the alignment results to other control sequences (default: % |\GotohResultA| and |\GotohResultB|). Note that these assignments are done -% globally. The control sequences to store the score and results can be changed -% with |\GotohConfig| command. +% globally. Using the optional argument, you can change the configuration +% temporary with the same keys in |\GotohConfig| (see the next section). % % \section{Configuration} % @@ -288,7 +288,7 @@ % \begin{macro}{\gth@d} % \begin{macro}{\gth@e} % These are keys for setting the parameters of the algorithm. The default -% values which are shown in equations~(\ref{eq:parameters}) are set here, and +% values which are shown in Equations~(\ref{eq:parameters}) are set here, and % stored in the macros (\emph{not} count registers) respectively. % \begin{macrocode} \define@cmdkeys[gth]{config}[gth@]{match, mismatch, d, e} @@ -393,7 +393,7 @@ % g(l) = -d - (l-1)e. \label{eq:gap} % \end{equation} % In this equation, $d$ and $e$ are parameters of the algorithm, which have -% default values shown in equations~(\ref{eq:parameters}). +% default values shown in Equations~(\ref{eq:parameters}). % \begin{macrocode} \def\gth@gap@penalty#1{% \gth@calc#1\relax @@ -403,10 +403,10 @@ % \end{macrocode} % \end{macro} % -% \subsection{Printing Matrixes} +% \subsection{Printing Matrices} % % \begin{macro}{\gth@print@matrix} -% This command shows the matrixes $M$, $I_x$ or $I_y$ (See +% This command shows the matrices $M$, $I^x$ or $I^y$ (See % section~\ref{sect:algorithm}). The argument of this macro specifies which % matrix to show, so you can detect |m|, |ix|, or |iy|. However, this macro is % currently only for the author of this package to debug. @@ -419,7 +419,7 @@ \mbox{\hbox to\gth@tempdima{\hss #1}}% \egroup} \def\gth@print@matrix#1{% - \bgroup\texttt + \bgroup\ttfamily #1:\\ \gth@tempcnta\z@ \@whilenum\gth@tempcnta<\gth@m\do{% @@ -427,7 +427,7 @@ \@whilenum\gth@tempcntb<\gth@n\do{% \gth@tab{% \gth@nameuse{\gth@sn @#1@\the\gth@tempcnta - @\the\gth@tempcntb}}% + @\the\gth@tempcntb}}% \advance\gth@tempcntb\@ne}\\ \advance\gth@tempcnta\@ne}% \egroup} @@ -437,21 +437,42 @@ % \subsection{Executing the Gotoh Algorithm}\label{sect:algorithm} % % \begin{macro}{\Gotoh} -% This is the user interface to execute the Gotoh algorithm. If the boolean -% switch |\if@gth@uppercase| is true, the arguments are processed by -% |\uppercase| preamble before passing them to |\gth@gotoh| macro. +% \changes{v1.1}{2017/07/07}{Add a new optional argument for changing +% config temporary} +% This is the user interface to execute the Gotoh algorithm. First, the +% `serial number' is incremented. The whole other process executed by this +% macro contained in a group because a number of temporary macros are defined +% during processing. % \begin{macrocode} -\newcommand{\Gotoh}[2]{% +\newcommand{\Gotoh}{% + \gth@increment\gth@sn + \bgroup % \egroup is in \gth@gotoh@pre + \@ifnextchar[{\gth@gotoh@setkeys}{\gth@gotoh@pre}} +% \end{macrocode} +% \end{macro} +% +% \begin{macro}{\gth@gotoh@setkeys} +% \begin{macro}{\gth@gotoh@pre} +% These inner macros are for preparing: |\gth@gotoh@setkeys| process temporary +% configuration specified with the optional argument of |\Gotoh|. In +% |\gth@gotoh@pre|, if the boolean switch |\if@gth@uppercase| is true, the +% arguments are processed by |\uppercase| preamble before passing them to +% |\gth@gotoh| macro. +% \begin{macrocode} +\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{\gth@gotoh{#1}{#2}}% + \uppercase\expandafter{\gth@tmpa}% \else - \gth@gotoh{#1}{#2}% - \fi} + \gth@tmpa + \fi\egroup} % \end{macrocode} % \end{macro} +% \end{macro} % % \begin{macro}{\gth@gotoh} -% This macro actually executes the Gotoh algorithm.~\cite{gotoh1982} The input +% This macro actually executes the Gotoh algorithm~\cite{gotoh1982}. The input % of the algorithm is two biological sequences % \[ % A \defeq a_1a_2a_3\dots a_m,\eqsep B \defeq b_1b_2b_3\dots b_n @@ -462,39 +483,28 @@ % calculation is done in $O(mn)$ time.} to get optimal score of the algorithm: % \begin{equation} % M_{i+1, j+1} -% = \max\left\{M_{ij}, {I_x}_{ij}, {I_y}_{ij}\right\} + c_{a_ib_j} +% = \max\left\{M_{ij}, I^x_{ij}, I^y_{ij}\right\} + c_{ij} % \label{eq:m} % \end{equation} % where % \begin{align} -% {I_x}_{i+1, j} &= \max\left\{ M_{ij}-d, {I_x}_{ij}-e, {I_y}_{ij}-d \right\}, +% I^x_{i+1, j} &= \max\left\{ M_{ij}-d, I^x_{ij}-e, I^y_{ij}-d \right\}, % \label{eq:ix} \\ -% {I_y}_{i, j+1} &= \max\left\{ M_{ij}-d, {I_y}_{ij}-e \right\}, +% I^y_{i, j+1} &= \max\left\{ M_{ij}-d, I^y_{ij}-e \right\}, % \label{eq:iy} % \end{align} -% and $c_{a_ib_j}$ is a score for a pair $(a_i, b_j)$, namely +% and $c_{ij}$ is a score for a pair $(a_i, b_j)$, namely % \[ -% c_{a_ib_j} = \left\{ +% c_{ij} = \left\{ % \begin{array}{rll} % 1 & \text{if\enspace} a_i = b_j & \text{(match)} \\ % -1 & \text{otherwise} & \text{(mismatch)}. \\ % \end{array} % \right. % \] -% -% \begin{macrocode} -\def\gth@gotoh#1#2{% -% \end{macrocode} -% -% \subsubsection{Preparation} -% -% First, the `serial number' is incremented. The whole other part of this macro -% contained in a group because a number of temporary macros are defined during -% processing. -% \begin{macrocode} - \gth@increment\gth@sn - \bgroup -% \end{macrocode} +% Note that the Equations (\ref{eq:ix}) and (\ref{eq:iy}) have asymmetric form +% because the order of inserting \emph{gaps} when alternating $A$ and $B$ does +% not affect the optimal score. % % \subsubsection{Getting sequences} % @@ -504,18 +514,19 @@ % |\gth@seqa@|$a_i$ and |\gth@seqa@|$b_j$, and the lengthes of the sequences % $m, n$ are stored in |\gth@m| and |\gth@n| respectively. % \begin{macrocode} - \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}% +\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}% % \end{macrocode} % \end{macro} % \end{macro} @@ -523,127 +534,127 @@ % \subsubsection{Initialization} % % We have to be careful with initialization because many implementations of the -% Gotoh algorithm have problems here.~\cite{flouri2015} Specifically, the +% Gotoh algorithm have problems here~\cite{flouri2015}. Specifically, the % package initialzes the matrxes with following equations: % \begin{align*} % M_{i0} &= -\infty, M_{0j} = -\infty, M_{00} = 0, \\ -% {I_x}_{i0} &= -g(i), {I_x}_{0j} = -\infty, \\ -% {I_y}_{i0} &= -\infty, {I_y}_{0j} = -g(j). +% I^x_{i0} &= -g(i), I^x_{0j} = -\infty, \\ +% I^y_{i0} &= -\infty, I^y_{0j} = -g(j). % \end{align*} -% Note that function $g(l)$ is a gap penalty (shown in equation~(\ref{eq:gap})) +% Note that function $g(l)$ is a gap penalty (shown in Equation~(\ref{eq:gap})) % and can be calculated with the macro |\gth@gap@penalty|. % % \begin{macrocode} - \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@}% + \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@}% % \end{macrocode} % % \subsubsection{Memoization} % % If the switch |\if@gth@memoization| is true, memoization functions (See -% section~\ref{sect:memofunc}) are called recursively. +% section~\ref{sect:memofunc}) are called recursively. % \begin{macrocode} - \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 + \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 % \end{macrocode} % % \subsubsection{Dynamic Programming} % -% To fill matrxes $M$, $I_x$ and $I_y$ the package use the recurrence formula +% To fill matrxes $M$, $I^x$, and $I^y$ the package use the recurrence formula % % \begin{macrocode} - \else - \gth@tempcnta\@ne - \@whilenum\gth@tempcnta<\gth@m\do{% - \gth@tempcntb\@ne - \@whilenum\gth@tempcntb<\gth@n\do{% -% \end{macrocode} -% First, $I_x$ is calculated with equation (\ref{eq:ix}). -% \begin{macrocode} - \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}% -% \end{macrocode} -% Secondly, $I_y$ is calculated with equation (\ref{eq:iy}). -% \begin{macrocode} - \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}% -% \end{macrocode} -% Finally, $M$ is calculated with equation (\ref{eq:m}) and a loop is completed. -% \begin{macrocode} - \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 + \else + \gth@tempcnta\@ne + \@whilenum\gth@tempcnta<\gth@m\do{% + \gth@tempcntb\@ne + \@whilenum\gth@tempcntb<\gth@n\do{% +% \end{macrocode} +% First, $I^x$ is calculated with Equation (\ref{eq:ix}). +% \begin{macrocode} + \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}% +% \end{macrocode} +% Secondly, $I^y$ is calculated with Equation (\ref{eq:iy}). +% \begin{macrocode} + \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}% +% \end{macrocode} +% Finally, $M$ is calculated with Equation (\ref{eq:m}) and a loop is completed. +% \begin{macrocode} + \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 % \end{macrocode} % -% \subsubsection{Printing Matrixes} +% \subsubsection{Printing Matrices} % % This is piece of code for debugging the package (so usually commented out). % % \begin{macrocode} - %\gth@print@matrix{m}% - %\gth@print@matrix{ix}% - %\gth@print@matrix{iy}% + %\gth@print@matrix{m}% + %\gth@print@matrix{ix}% + %\gth@print@matrix{iy}% % \end{macrocode} % % \subsubsection{Returning the Optimal Score} @@ -651,20 +662,90 @@ % The calculated optimal score of the alignment stored here to the control % sequences which stored in |\gth@score|. % \begin{macrocode} - \bgroup - \gth@decrement\gth@m \gth@decrement\gth@n - \expandafter\xdef\gth@score{% - \gth@nameuse{\gth@sn @m@\gth@m @\gth@n}}% - \egroup + \bgroup + \gth@decrement\gth@m \gth@decrement\gth@n + \expandafter\xdef\gth@score{% + \gth@nameuse{\gth@sn @m@\gth@m @\gth@n}}% + \egroup % \end{macrocode} % % \subsubsection{Trace Back} % +% After processing dynamic programming (or memoization functions), matrices +% $M$, $I^x$, and $I^y$ are all filled. Using these matrices, we can determine +% the `trace' from the optimal score $M_{m,n}$ to the start $M_{0,0}$ and get +% the result of alignment $(x, y)$. +% +% Considering the form of Equation (\ref{eq:m})--(\ref{eq:iy}), the calculation +% formulae of the former values depend on which matrix the `current position' +% exists. In order to take into account these differences, trace back process +% is calculated while switching three modes: default, gap x, and gap y. +% +% First, make sure to empty |\gth@rseq@x| and |\gth@rseq@y| which is going to +% store result alignment sequences $x$ and $y$ respectively. Note that this is +% the trace \emph{back} process, so new characters are prepended to the +% existing sequences in each loop. In the next line, the switches +% |\if@gth@gapx@| and |\if@gth@gapy@| are both turned off (which means +% processing starts from the default mode). % \begin{macrocode} - \let\gth@rseq@x\@empty\let\gth@rseq@y\@empty\let\gth@mode@seq\@empty - \@gth@remain@true\@gth@gapx@false\@gth@gapy@false - \@whilesw\if@gth@remain@\fi{% - \ifnum\gth@m=\z@ + \let\gth@rseq@x\@empty\let\gth@rseq@y\@empty + \@gth@remain@true\@gth@gapx@false\@gth@gapy@false +% \end{macrocode} +% In the main loop of trace back, process the condition either $x$ or $y$ is +% already completed first. In this situation, the other sequence should be +% filled all the remaining with \emph{gaps}. +% \begin{macrocode} + \@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 +% \end{macrocode} +% \paragraph{mode: gap x} +% Prepend former base to $x$ and a \emph{gap} to $y$. If +% $M_{m-1,n}-d>I^x_{m-1,n}-e$ back to default mode. Else if +% $I^x_{m-1,n}-e\gth@tempcntb + \@gth@gapx@false + \else\ifnum\gth@tempcntb<\gth@tempcntc + \@gth@gapx@false\@gth@gapy@true + \fi\fi +% \end{macrocode} +% \paragraph{mode: gap y} +% Prepend a \emph{gap} to $x$ and former base to $y$. If +% $M_{m,n-1}-d>I^y_{m,n-1}-e$ back to default mode and otherwise stay in mode +% gap y. +% \begin{macrocode} + \else\if@gth@gapy@ \gth@decrement\gth@n \expandafter\expandafter\expandafter \ifx\gth@nameuse{seqb@\gth@n}\relax\else @@ -672,82 +753,53 @@ \edef\gth@rseq@y{\gth@nameuse{seqb@\gth@n}% \gth@rseq@y}% \fi - \else\ifnum\gth@n=\z@ + \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 +% \end{macrocode} +% \paragraph{mode: default} +% Prepend former base to $x$ and $y$ respectively. Only if +% $M_{m-1,n-1}>I^x_{m-1,n-1}$ and $M_{m-1,n-1}>I^y_{m-1,n-1}$ stay on default +% mode, and else if $I^x_{m-1,n-1}>I^y_{n-1,m-1}$ go to gap x otherwise go to +% gap y. +% \begin{macrocode} + \else \gth@decrement\gth@m + \gth@decrement\gth@n \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@ - % mode: gap x - \gth@decrement\gth@m \expandafter\expandafter\expandafter - \ifx\gth@nameuse{seqa@\gth@m}\relax\else + \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@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@ - % mode: gap y - \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 - % mode: default - \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 + \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}% + \fi\fi +% \end{macrocode} +% Finally, if we achieve to $M_{0,0}$, exit from the main loop. +% \begin{macrocode} + \ifnum\gth@m<\@ne\ifnum\gth@n<\@ne + \@gth@remain@false + \fi\fi}% % \end{macrocode} % % \subsubsection{Returning Results} @@ -756,9 +808,8 @@ % |\gth@resq@y| are copied globally to the control sequences which stored in % |\gth@resulta| and |\gth@resultb|. % \begin{macrocode} - \expandafter\gth@glet\gth@resulta\gth@rseq@x - \expandafter\gth@glet\gth@resultb\gth@rseq@y - \egroup} + \expandafter\gth@glet\gth@resulta\gth@rseq@x + \expandafter\gth@glet\gth@resultb\gth@rseq@y} % \end{macrocode} % \end{macro} % @@ -767,14 +818,17 @@ % \begin{macro}{\gth@memo@ix} % \begin{macro}{\gth@memo@iy} % \begin{macro}{\gth@memo@m} -% These are memoization functions for calculating $I_x, I_y, M$ respectively. +% These are memoization functions for calculating $I^x, I^y, M$ respectively. +% Since these functions change many `temporary' values, all of the processes +% are wrapped in a group and only the return values and components of matrices +% are assigned globally. % \begin{macrocode} \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 + @\the\gth@tempcntb}\relax \advance\gth@tempcnta\m@ne \gth@memo@ix{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmp@ix@return{\gth@ix@return}% @@ -800,7 +854,7 @@ \gth@tempcnta#1\gth@tempcntb#2\relax \expandafter\expandafter\expandafter \ifx\gth@nameuse{\gth@sn @iy@\the\gth@tempcnta - @\the\gth@tempcntb}\relax + @\the\gth@tempcntb}\relax \advance\gth@tempcntb\m@ne \gth@memo@iy{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmp@iy@return{\gth@iy@return}% @@ -823,7 +877,7 @@ \gth@tempcnta#1\gth@tempcntb#2\relax \expandafter\expandafter\expandafter \ifx\gth@nameuse{\gth@sn @m@\the\gth@tempcnta - @\the\gth@tempcntb}\relax + @\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}% diff --git a/Master/texmf-dist/tex/latex/gotoh/gotoh.sty b/Master/texmf-dist/tex/latex/gotoh/gotoh.sty index b0a3d0905ea..1687ed3f06f 100644 --- a/Master/texmf-dist/tex/latex/gotoh/gotoh.sty +++ b/Master/texmf-dist/tex/latex/gotoh/gotoh.sty @@ -13,7 +13,7 @@ %% This package is distributed under the MIT License. %% \NeedsTeXFormat{LaTeX2e} -\ProvidesPackage{gotoh}[2017/05/05 v1.0 Sequence alignment algorithm] +\ProvidesPackage{gotoh}[2017/07/07 v1.1 Sequence alignment algorithm] \RequirePackage{xkeyval} \def\gth@pkgname{gotoh} \def\gth@warn{\PackageWarningNoLine\gth@pkgname} @@ -74,7 +74,7 @@ \mbox{\hbox to\gth@tempdima{\hss #1}}% \egroup} \def\gth@print@matrix#1{% - \bgroup\texttt + \bgroup\ttfamily #1:\\ \gth@tempcnta\z@ \@whilenum\gth@tempcnta<\gth@m\do{% @@ -82,120 +82,160 @@ \@whilenum\gth@tempcntb<\gth@n\do{% \gth@tab{% \gth@nameuse{\gth@sn @#1@\the\gth@tempcnta - @\the\gth@tempcntb}}% + @\the\gth@tempcntb}}% \advance\gth@tempcntb\@ne}\\ \advance\gth@tempcnta\@ne}% \egroup} -\newcommand{\Gotoh}[2]{% +\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{\gth@gotoh{#1}{#2}}% + \uppercase\expandafter{\gth@tmpa}% \else - \gth@gotoh{#1}{#2}% - \fi} + \gth@tmpa + \fi\egroup} \def\gth@gotoh#1#2{% - \gth@increment\gth@sn - \bgroup - \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@ + \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@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}% + \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}% - \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 + \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 - \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\let\gth@mode@seq\@empty - \@gth@remain@true\@gth@gapx@false\@gth@gapy@false - \@whilesw\if@gth@remain@\fi{% - \ifnum\gth@m=\z@ + \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 @@ -203,91 +243,51 @@ \edef\gth@rseq@y{\gth@nameuse{seqb@\gth@n}% \gth@rseq@y}% \fi - \else\ifnum\gth@n=\z@ + \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 - \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@ - % mode: gap x - \gth@decrement\gth@m \expandafter\expandafter\expandafter - \ifx\gth@nameuse{seqa@\gth@m}\relax\else + \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@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@ - % mode: gap y - \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 - % mode: default - \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 + \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 - \egroup} + \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 + @\the\gth@tempcntb}\relax \advance\gth@tempcnta\m@ne \gth@memo@ix{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmp@ix@return{\gth@ix@return}% @@ -313,7 +313,7 @@ \gth@tempcnta#1\gth@tempcntb#2\relax \expandafter\expandafter\expandafter \ifx\gth@nameuse{\gth@sn @iy@\the\gth@tempcnta - @\the\gth@tempcntb}\relax + @\the\gth@tempcntb}\relax \advance\gth@tempcntb\m@ne \gth@memo@iy{\gth@tempcnta}{\gth@tempcntb}% \edef\gth@tmp@iy@return{\gth@iy@return}% @@ -336,7 +336,7 @@ \gth@tempcnta#1\gth@tempcntb#2\relax \expandafter\expandafter\expandafter \ifx\gth@nameuse{\gth@sn @m@\the\gth@tempcnta - @\the\gth@tempcntb}\relax + @\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}% -- cgit v1.2.3