new latex package seqsplit

git-svn-id: svn://tug.org/texlive/trunk@1938 c570f23f-e606-0410-a88d-b1316a301751

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+% \iffalse
+%<*gobble>
+% $Id: seqsplit.dtx,v 1.3 2006/08/08 00:02:08 boris Exp $
+%
+% Copyright 2006, Boris Veytsman <borisv@lk.net>
+% This work may be distributed and/or modified under the
+% conditions of the LaTeX Project Public License, either
+% version 1.3 of this license or (at your option) any 
+% later version.
+% The latest version of the license is in
+%    http://www.latex-project.org/lppl.txt
+% and version 1.3 or later is part of all distributions of
+% LaTeX version 2003/06/01 or later.
+%
+% This work has the LPPL maintenance status `maintained'.
+%
+% The Current Maintainer of this work is Boris Veytsman
+%
+% This work consists of the file seqsplit.dtx and the
+% derived files seqsplit.sty, seqsplit.dtx. 
+%
+% \fi 
+% \CheckSum{50}
+%
+% \changes{v0.1}{2006/08/07}{The first released version}
+%
+%% \CharacterTable
+%%  {Upper-case    \A\B\C\D\E\F\G\H\I\J\K\L\M\N\O\P\Q\R\S\T\U\V\W\X\Y\Z
+%%   Lower-case    \a\b\c\d\e\f\g\h\i\j\k\l\m\n\o\p\q\r\s\t\u\v\w\x\y\z
+%%   Digits        \0\1\2\3\4\5\6\7\8\9
+%%   Exclamation   \!     Double quote  \"     Hash (number) \#
+%%   Dollar        \$     Percent       \%     Ampersand     \&
+%%   Acute accent  \'     Left paren    \(     Right paren   \)
+%%   Asterisk      \*     Plus          \+     Comma         \,
+%%   Minus         \-     Point         \.     Solidus       \/
+%%   Colon         \:     Semicolon     \;     Less than     \<
+%%   Equals        \=     Greater than  \>     Question mark \?
+%%   Commercial at \@     Left bracket  \[     Backslash     \\
+%%   Right bracket \]     Circumflex    \^     Underscore    \_
+%%   Grave accent  \`     Left brace    \{     Vertical bar  \|
+%%   Right brace   \}     Tilde         \~} 
+%
+%\iffalse
+%    \begin{macrocode}
+\documentclass{ltxdoc}
+\usepackage{array}
+\usepackage{url}
+\usepackage{seqsplit}
+\DoNotIndex{\NeedsTeXFormat, \ProvidesPackage, \def, \hspace}
+\DoNotIndex{\futurelet, \@gobble, \ifx, \else, \fi, \relax}
+\DoNotIndex{\ifmmode, \fi, \allowbreak}
+\PageIndex
+\CodelineIndex
+\RecordChanges
+\EnableCrossrefs
+\begin{document}
+  \DocInput{seqsplit.dtx}
+\end{document}
+%    \end{macrocode}
+%</gobble> 
+% \fi
+% \MakeShortVerb{|}
+%
+%\GetFileInfo{seqsplit.sty}
+% \title{Splitting Long Sequences of Letters (DNA, RNA, Proteins,
+%   Etc.)\thanks{\copyright Boris Veytsman, 2006}}
+% \author{Boris Veytsman}
+% \date{\filedate, \fileversion}
+% \maketitle
+%
+% \begin{abstract}
+%   Sometimes one needs to typeset long sentences of letters, which
+%   should not have spaces between them (like letters in words), but
+%   could be split between lines at any point, and without a
+%   hyphenation character.  This package provides a command for such
+%   sequences. 
+% \end{abstract}
+%
+% \tableofcontents
+%
+% \clearpage
+%
+%\section{Introduction}
+%\label{sec:intro}
+%
+% At a recent Practical\TeX{} conference (Practical\TeX-2006, Rutgers,
+% New Jersey, USA, \url{http://www.tug.org/practicaltex2006}) Klaus
+% H\"oppner asked, how one typesets long sequences like the ones
+% related to DNA code.  Usually there is no space between letters, but
+% a sequence could be split at any point and continued on the next
+% line.   The audience suggested several solutions to this problem.
+% One solution, for example, was to define a new language, where
+% hyphenation is possible at any point, and hyphenation character is
+% empty.  However, this would require regeneration of all \TeX{}
+% formats, which might be not practical or even not possible.  Another
+% solution, suggested, if my memory is right, by Peter Flynn, was to
+% scan the sequence and insert a breaking point after each letter.
+% This later approach is implemented in this package.
+%
+%
+%
+%\section{User Interface}
+%\label{sec:interface}
+%
+%
+%\subsection{Main Command}
+%\label{sec:command}
+%
+% \DescribeMacro{\seqsplit}
+% The main (and actually the only) command in this package is
+% |\seqsplit|.  Its usage is very simple, for example to typeset the
+% gene HBB, related to sickle cell anaemia (actually, the
+% corresponding mRNA Reference Sequence), we use the following:
+% \begin{verbatim}
+% \seqsplit{%
+% acatttgcttctgacacaactgtgttcactagcaacctcaaacagacaccatggtgcatc%
+% tgactcctgaggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaag%
+% ttggtggtgaggccctgggcaggctgctggtggtctacccttggacccagaggttctttg%
+% agtcctttggggatctgtccactcctgatgctgttatgggcaaccctaaggtgaaggctc%
+% atggcaagaaagtgctcggtgcctttagtgatggcctggctcacctggacaacctcaagg%
+% gcacctttgccacactgagtgagctgcactgtgacaagctgcacgtggatcctgagaact%
+% tcaggctcctgggcaacgtgctggtctgtgtgctggcccatcactttggcaaagaattca%
+% ccccaccagtgcaggctgcctatcagaaagtggtggctggtgtggctaatgccctggccc%
+% acaagtatcactaagctcgctttcttgctgtccaatttctattaaaggttcctttgttcc%
+% ctaagtccaactactaaactgggggatattatgaagggccttgagcatctggattctgcc%
+% taataaaaaacatttattttcattgc}.
+% \end{verbatim}
+% which produces
+% \begin{quote}
+% \seqsplit{%
+% acatttgcttctgacacaactgtgttcactagcaacctcaaacagacaccatggtgcatc%
+% tgactcctgaggagaagtctgccgttactgccctgtggggcaaggtgaacgtggatgaag%
+% ttggtggtgaggccctgggcaggctgctggtggtctacccttggacccagaggttctttg%
+% agtcctttggggatctgtccactcctgatgctgttatgggcaaccctaaggtgaaggctc%
+% atggcaagaaagtgctcggtgcctttagtgatggcctggctcacctggacaacctcaagg%
+% gcacctttgccacactgagtgagctgcactgtgacaagctgcacgtggatcctgagaact%
+% tcaggctcctgggcaacgtgctggtctgtgtgctggcccatcactttggcaaagaattca%
+% ccccaccagtgcaggctgcctatcagaaagtggtggctggtgtggctaatgccctggccc%
+% acaagtatcactaagctcgctttcttgctgtccaatttctattaaaggttcctttgttcc%
+% ctaagtccaactactaaactgggggatattatgaagggccttgagcatctggattctgcc%
+% taataaaaaacatttattttcattgc}.
+% \end{quote}
+% Note that the breaking points in the code (commented out by \%) have
+% nothing to do with the breaking points in the typeset sequence and
+% are introduced only for readability of the code.
+%
+% The corresponding protein sequence ($\beta$-globulin) is shorter:
+% \begin{verbatim}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% vkahgkkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahhfg%
+% keftppvqaayqkvvagvanalahkyh}.
+% \end{verbatim}
+% \begin{quote}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% vkahgkkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahhfg%
+% keftppvqaayqkvvagvanalahkyh}.
+% \end{quote}
+%
+% The command works in math mode as well:
+% \begin{verbatim}
+% $\pi = \seqsplit{%
+% 3.
+% 1415926535 8979323846 2643383279 5028841971 6939937510
+% 5820974944 5923078164 0628620899 8628034825 3421170679
+% 8214808651 3282306647 0938446095 5058223172 5359408128
+% 4811174502 8410270193 8521105559 6446229489 5493038196
+% 4428810975 6659334461 2847564823 3786783165 2712019091
+% 4564856692 3460348610 4543266482 1339360726 0249141273
+% 7245870066 0631558817 4881520920 9628292540 9171536436
+% 7892590360 0113305305 4882046652 1384146951 9415116094
+% 3305727036 5759591953 0921861173 8193261179 3105118548
+% 0744623799 6274956735 1885752724 8912279381 8301194912
+% 9833673362 4406566430 8602139494 6395224737 1907021798
+% 6094370277 0539217176 2931767523 8467481846 7669405132
+% 0005681271 4526356082 7785771342 7577896091 7363717872
+% 1468440901 2249534301 4654958537 1050792279 6892589235}
+% \ldots$
+% \end{verbatim}
+% \begin{quote}
+% $\pi = \seqsplit{%
+% 3.
+% 1415926535 8979323846 2643383279 5028841971 6939937510
+% 5820974944 5923078164 0628620899 8628034825 3421170679
+% 8214808651 3282306647 0938446095 5058223172 5359408128
+% 4811174502 8410270193 8521105559 6446229489 5493038196
+% 4428810975 6659334461 2847564823 3786783165 2712019091
+% 4564856692 3460348610 4543266482 1339360726 0249141273
+% 7245870066 0631558817 4881520920 9628292540 9171536436
+% 7892590360 0113305305 4882046652 1384146951 9415116094
+% 3305727036 5759591953 0921861173 8193261179 3105118548
+% 0744623799 6274956735 1885752724 8912279381 8301194912
+% 9833673362 4406566430 8602139494 6395224737 1907021798
+% 6094370277 0539217176 2931767523 8467481846 7669405132
+% 0005681271 4526356082 7785771342 7577896091 7363717872
+% 1468440901 2249534301 4654958537 1050792279 6892589235}
+% \ldots$
+% \end{quote}
+%
+%\subsection{Customization}
+%\label{sec:customization}
+%
+% \DescribeMacro{\seqinsert} The command |\seqsplit| can be customized
+% by redefining the command |\seqinsert|, which is the macro that is
+% inserted between the letters of the sequence.  By default it is
+% defined as |\allowbreak| in math mode and |\hspace{0pt plus 0.02em}|
+% in text mode: a slightly stretchable glue of zero length.  This
+% definition gives \TeX{} a chance to justify the lines.  However,
+% there might be other definitions.  For example, if we want hyphens
+% at the breakpoints in text mode, we can use:
+% \begin{quote}
+%   |\renewcommand{\seqinsert}{\ifmmode\allowbreak\else\-\fi}|
+% \end{quote}
+% which produces for the $\beta$-globulin protein from the previous
+% section the following:
+% \begin{quote}
+%   \renewcommand{\seqinsert}{\ifmmode\allowbreak\else\-\fi}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% vkahgkkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahhfg%
+% keftppvqaayqkvvagvanalahkyh}.
+% \end{quote}
+% Another redefinition,
+% \begin{quote}
+%   |\renewcommand{\seqinsert}{\ifmmode\allowbreak\else{} \fi}|,
+% \end{quote}
+% produces an output with spaces between letters.  Note that there is
+% no space between the last letter and the dot: the package takes care
+% of this:
+% \begin{quote}
+%   \renewcommand{\seqinsert}{\ifmmode\allowbreak\else{} \fi}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% vkahgkkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahhfg%
+% keftppvqaayqkvvagvanalahkyh}.
+% \end{quote}
+% 
+%
+%
+%\subsection{Grouping and Commands}
+%\label{sec:grouping}
+%
+% The command |\seqsplit| does not insert breakpoints between the
+% letters inside braces |{...}|.  Compare the typesetting of
+% $\beta$-globulin in Section~\ref{sec:command} and the following
+% example:
+% \begin{verbatim}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% v{kahg}kkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahhfg%
+% keftppvqaayqkvvagvanalahkyh}.
+% \end{verbatim}
+% \begin{quote}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% v{kahg}kkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvlvcvlahhfg%
+% keftppvqaayqkvvagvanalahkyh}.
+% \end{quote}
+% The braces around |{kahg}| prevented a splitting of this group.
+% This effect can be used for typesetting special substrings inside
+% sequences.
+%
+% The way |\seqsplit| works interferes with formatting commands like
+% |\textit|.  Therefore the sequence |{kahg}| is \emph{not} italicized
+% in the following example:
+% \begin{verbatim}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% v\textit{kahg}kkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvl%
+% vcvlahhfgkeftppvqaayqkvvagvanalahkyh}.
+% \end{verbatim}
+% \begin{quote}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% v\textit{kahg}kkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvl%
+% vcvlahhfgkeftppvqaayqkvvagvanalahkyh}.
+% \end{quote}
+%
+% Using grouping |{\textit{kahg}}| we can save the situation:
+% \begin{verbatim}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% v{\textit{kahg}}kkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvl%
+% vcvlahhfgkeftppvqaayqkvvagvanalahkyh}.
+% \end{verbatim}
+% \begin{quote}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% v{\textit{kahg}}kkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvl%
+% vcvlahhfgkeftppvqaayqkvvagvanalahkyh}.
+% \end{quote}
+%
+% If we want the italicized sequence to be splittable as well, we can
+% use \emph{nested} |\seqsplit|:
+% \begin{verbatim}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% v{\textit{\seqsplit{kahg}}}kkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvl%
+% vcvlahhfgkeftppvqaayqkvvagvanalahkyh}.
+% \end{verbatim}
+% \begin{quote}
+% \seqsplit{%
+% mvhltpeeksavtalwgkvnvdevggealgrllvvypwtqrffesfgdlstpdavmgnpk%
+% v{\textit{\seqsplit{kahg}}}kkvlgafsdglahldnlkgtfatlselhcdklhvdpenfrllgnvl%
+% vcvlahhfgkeftppvqaayqkvvagvanalahkyh}.
+% \end{quote}
+%
+% These tricks allow one to produce splittable sequences with a rather
+% complex formatting.
+%
+%
+%\StopEventually{}
+%
+% \clearpage
+% 
+% \section{Implementation}
+% \label{sec:implementation}
+% 
+%
+%\subsection{Declarations}
+%\label{sec:decl}
+% 
+%  We start with declaration, who we are:
+%
+%
+%    \begin{macrocode}
+%<*style>
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{seqsplit}
+[2006/08/07 v0.1 Splitting long sequences (DNA, RNA, proteins, etc.) ]
+%    \end{macrocode}
+%
+%
+%
+%
+%\subsection{Inserted Text}
+%\label{sec:insertion}
+%
+% 
+% \begin{macro}{\seqinsert}
+%   This is the macro we insert between letters:
+%    \begin{macrocode}
+\def\seqinsert{\ifmmode\allowbreak\else\hspace{0pt plus 0.02em}\fi}
+%    \end{macrocode}
+% \end{macro}
+% 
+% 
+%
+%\subsection{Scanner}
+%\label{sec:scanner}
+%
+% The scanner code is not too trivial.  Here we describe it in detail.
+%
+% \begin{macro}{\seqsplit}
+%   The main (actually, the only) user-space macro just starts the
+%   scanner.
+%    \begin{macrocode}
+\def\seqsplit#1{\SQSPL@scan#1\SQSPL@end}
+%    \end{macrocode}
+% \end{macro}
+%
+% The macro |\SQSPL@end| is never expanded, it is just a marker.  
+% \begin{macro}{\SQSPL@scan}
+%   The macro |\SQSPL@scan| saves the next token in the special
+%   register |\SQSPL@next|, so we can decide what to do with it:
+%    \begin{macrocode}
+\def\SQSPL@scan{\futurelet\SQSPL@next\SQSPL@scani}
+%    \end{macrocode}
+% \end{macro}
+% \begin{macro}{\SQSPL@scani}
+%   Now since we know the next token, we can decide to either stop the
+%   expansion if we met the end, or continue it if we did not.
+%    \begin{macrocode}
+\def\SQSPL@scani#1{%
+  \ifx \SQSPL@end \SQSPL@next \def\SQSPL@process{\@gobble}%
+  \else \def\SQSPL@process{\SQSPL@doprocess}\fi%
+  \SQSPL@process{#1}}
+%    \end{macrocode}
+% \end{macro}
+% \begin{macro}{\SQSPL@doprocess}
+%   The processing of a letter depends on what is the next letter.  If
+%   the sequence is finished, we should not insert anything after the
+%   last letter: we do not want to break the line between the sequence
+%   and, say, a comma.  Therefore we insert a special smart macro:
+%    \begin{macrocode}
+\def\SQSPL@doprocess#1{#1\SQSPL@insert}
+%    \end{macrocode}
+% \end{macro}
+% \begin{macro}{\SQSPL@insert}
+%   The macro |\SQSPL@insert| uses |\futurelet| to check whether the
+%   processed letter is the last one in the sentence:
+%    \begin{macrocode}
+\def\SQSPL@insert{\futurelet\SQSPL@next\SQSPL@doinsert}
+%    \end{macrocode}
+% \end{macro}
+% \begin{macro}{\SQSPL@doinsert}
+%   And this is the macro that inserts |\seqinsert| and continues
+%   scanning:
+%    \begin{macrocode}
+\def\SQSPL@doinsert{%
+  \ifx \SQSPL@end \SQSPL@next \relax%
+  \else \seqinsert \fi%
+  \SQSPL@scan}
+%    \end{macrocode}
+% \end{macro}
+%
+%
+%\subsection{The Last Words}
+%\label{sec:last}
+%
+%
+%
+%    \begin{macrocode}
+%</style>
+%    \end{macrocode}
+%\Finale
+%\clearpage
+%
+%\PrintChanges
+%\clearpage
+%\PrintIndex
+%
+\endinput