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@ -36,7 +36,7 @@ has been generated for details. |
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\endpreamble |
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\generate{ |
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\file{flygenet.cls}{\from{flygenet.dtx}{class}} |
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\file{flygenet.sty}{\from{flygenet.dtx}{package}} |
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} |
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\endgroup |
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@ -46,6 +46,7 @@ has been generated for details. |
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\ProvidesFile{flygenet.dtx}[2013/07/14 v0.1 Fly genetics notation] |
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\documentclass[a4paper]{ltxdoc} |
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\usepackage{hyperref} |
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\usepackage{flygenet} |
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\EnableCrossrefs |
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\CodelineIndex |
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\RecordChanges |
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@ -55,7 +56,7 @@ has been generated for details. |
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%</driver> |
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% \fi |
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% |
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% \CheckSum{0} |
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% \CheckSum{110} |
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% |
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% \CharacterTable |
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% {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 |
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@ -73,17 +74,27 @@ has been generated for details. |
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% Grave accent \` Left brace \{ Vertical bar \| |
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% Right brace \} Tilde \~} |
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% |
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% \DoNotIndex{\active} |
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% \DoNotIndex{\begingroup} |
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% \DoNotIndex{\catcode} |
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% \DoNotIndex{\DeclareOption,\def} |
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% \DoNotIndex{\else,\empty,\end,\endgroup} |
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% \DoNotIndex{\fi,\frac} |
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% \DoNotIndex{\gdef} |
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% \DoNotIndex{\ifx} |
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% \DoNotIndex{\let} |
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% \DoNotIndex{\mars,\mathchardef,\mathit,\mercury} |
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% \DoNotIndex{\NeedsTeXFormat} |
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% \DoNotIndex{\ProcessOptions,\ProvidesClass} |
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% \DoNotIndex{\RequirePackage} |
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% \DoNotIndex{\ProcessOptions,\ProvidesPackage} |
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% \DoNotIndex{\RequirePackage,\relax} |
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% \DoNotIndex{\venus} |
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% |
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% \changes{0.1}{2013/07/14}{Initial version.} |
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% |
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% \GetFileInfo{flygenet.dtx} |
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% |
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% \title{^^A |
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% The \textsf{flygenet} class\thanks{^^A |
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% The \textsf{flygenet} package\thanks{^^A |
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% This file has version number \fileversion, last revised \filedate.}} |
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% \author{^^A |
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% Damien Goutte-Gattat\thanks{^^A |
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@ -94,13 +105,96 @@ has been generated for details. |
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% |
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% \maketitle |
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% |
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% \abstract{The abstract} |
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% |
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% \tableofcontents |
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% |
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% \section{Introduction} |
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% The introduction. |
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% |
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% Fly geneticists conventionally denote fly genotypes using a math-like |
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% notation, as in the following example: |
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% |
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% $$ |
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% \genotype{C(1)RM,y^2/Y; In(2LR)O, Cy cn^2 sp^2/Sco; ci^D/ey^D} |
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% $$ |
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% |
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% Consequently, \LaTeX's math mode (and especially displayed math mode, |
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% as above) is well suited to typeset such notation. |
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% |
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% However, typesetting a genotype can be quite tedious, as it requires |
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% many calls to the |\frac| macro (or the |\over| primitive) and |
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% constant use of manual spacing to override \TeX's |
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% math-mode spacing. |
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% |
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% This package is intended to reduce the amount of code needed to |
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% typeset a genotype. For example, the genotype above is the result of |
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% the following code: |
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% |
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% \begin{verbatim} |
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% \genotype{C(1)RM,y^2/Y; In(2LR)O,Cy cn^2 sp^2/Sco; ci^D/ey^D} |
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% \end{verbatim} |
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% |
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% A complete genotype can thus be written in a very intuitive way, the |
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% only \TeX ism being the exponentiation symbol (|^|). |
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% |
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% |
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% \section{User interface} |
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% |
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% The main user-level macro is |\genotype|. It accepts a single argument |
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% which is the genotype to typeset, with semi-colons to separate |
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% chromosome pairs and slashes to separate the two chromosomes of a |
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% pair. |
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% |
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% The macros |\female|, |\male|, and |\virgin| are used in the same way |
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% and perform the same task as |\genotype|, but they insert a female |
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% (\venus), male (\mars), or virgin female (\mercury) symbol in front of |
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% the genotype: |
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% |
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% $$ |
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% \female{cn bw/;TM2/tra} |
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% \quad |
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% \virgin{cn bw/;TM2/tra} |
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% \quad |
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% \male{FM7a/Y;In(2LR)O,Cy/+} |
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% $$ |
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% |
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% The plural forms of these macros (|\females|, |\males|, and |
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% |\virgins|) are similar but insert \emph{two} symbols, thus denotating |
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% several individuals of the indicated genotype. |
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% |
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% |
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% \section{Limitations} |
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% |
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% Homozygous chromosome must be written with an ending slash, as in the |
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% following example: |
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% |
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% \begin{minipage}{.6\textwidth} |
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% \begin{verbatim} |
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% \genotype{cn bw/;TM2/tra} |
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% \end{verbatim} |
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% \end{minipage} |
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% \begin{minipage}{.3\textwidth} |
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% $$ |
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% \genotype{cn bw/;TM2/tra} |
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% $$ |
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% \end{minipage} |
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% |
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% \bigskip |
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% When used as an argument to another macro, |\genotype| cannot control |
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% spacing; spaces between gene symbols must be added manually. |
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% |
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% \begin{minipage}{.6\textwidth} |
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% \begin{verbatim} |
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% \underbrace{\genotype{cn bw/;TM2/tra}} |
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% \quad |
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% \underbrace{\genotype{cn\ bw/;TM2/tra}} |
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% \end{verbatim} |
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% \end{minipage} |
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% \begin{minipage}{.3\textwidth} |
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% $$ |
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% \underbrace{\genotype{cn bw/;TM2/tra}} |
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% \quad |
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% \underbrace{\genotype{cn\ bw/;TM2/tra}} |
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% $$ |
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% \end{minipage} |
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% |
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% ^^A Inserts the LPPL text. |
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% \providecommand{\LPPLsection}{\section} |
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@ -114,11 +208,120 @@ has been generated for details. |
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% \section{The code} |
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% |
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% \subsection{Initialization code} |
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% We start by identifying the class. |
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% We start by identifying the package. |
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% \begin{macrocode} |
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\NeedsTeXFormat{LaTeX2e}[2003/12/01] |
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\ProvidesClass{flygenet}[2013/07/14 v0.1 Fly genetics notation] |
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\ProvidesPackage{flygenet}[2013/07/14 v0.1 Fly genetics notation] |
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% \end{macrocode} |
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% |
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% We load the |wasysym| package, that we will use to typeset the female |
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% (\venus), male (\mars) and virgin female (\mercury) symbols. |
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% \begin{macrocode} |
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\RequirePackage{wasysym} |
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% \end{macrocode} |
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% |
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% \subsection{Typesetting genotypes} |
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% |
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% \begin{macro}{\fly@printchromosome} |
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% This macro typesets a single chromosome pair, as a mathematical |
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% fraction. |
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% \begin{macrocode} |
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\def\fly@printchromosome#1/#2\end{% |
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\def\fly@argii{#2}% |
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\ifx\fly@argii\empty\mathit{#1}\else\frac{\mathit{#1}}{\mathit{#2}}\fi} |
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% \end{macrocode} |
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% \end{macro} |
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% |
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% \begin{macro}{\fly@parsechromosome} |
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% This macro parses a genotype notation (chromosome pairs separated by |
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% semi-colons), and calls the |\fly@printchromosome| for each chromosome |
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% pair. |
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% \begin{macrocode} |
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\def\fly@parsechromosome#1;#2\end{% |
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\fly@printchromosome#1\end% |
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\def\fly@argii{#2}% |
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\ifx\fly@argii\empty\else; \fly@parsechromosome#2\end\fi} |
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% \end{macrocode} |
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% \end{macro} |
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% |
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% \begin{macro}{\mhyphen} |
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% \begin{macro}{\mcolon} |
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% These two macros are used to typeset actual hyphens and colons in math |
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% mode. |
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% \begin{macrocode} |
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\mathchardef\mhyphen="2D |
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\mathchardef\mcolon="3A |
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% \end{macrocode} |
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% \end{macro} |
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% \end{macro} |
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% |
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% \begin{macro}{\fly@endgenotype} |
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% This macro is called at the end of the |\genotype| macro. It performs |
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% the task of parsing and typesetting the genotype and reset the |
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% modified catcodes. |
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% \begin{macrocode} |
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\def\fly@endgenotype#1{% |
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\fly@parsechromosome#1;\end% |
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\catcode`\ =10\relax% |
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\catcode`\-=12\relax% |
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\catcode`\:=12\relax} |
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% \end{macrocode} |
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% \end{macro} |
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% |
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% \begin{macro}{\genotype} |
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% This macro is the main user interface to typeset a genotype. Its |
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% declaration is enclosed in a group since we need to locally modify the |
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% catcodes of some characters. For the same reason, the macro cannot be |
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% declared as expecting an argument (otherwise, the argument would be |
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% parsed before the catcodes are modified)---the argument is parsed when |
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% calling the |\fly@endgenotype| macro. |
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% \begin{macrocode} |
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\begingroup |
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\catcode`\ =\active |
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\catcode`\-=\active |
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\catcode`\:=\active |
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\gdef\genotype{% |
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\catcode`\ =\active\let =\ % |
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\catcode`\-=\active\let-=\mhyphen% |
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\catcode`\:=\active\let:=\mcolon% |
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\fly@endgenotype} |
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\endgroup |
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% \end{macrocode} |
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% \end{macro} |
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% |
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% \subsection{Gender symbols} |
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% |
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% \begin{macro}{\female} |
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% \begin{macro}{\male} |
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% \begin{macro}{\virgin} |
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% These macros typeset a genotype as |\genotype| does, but insert a |
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% female (\venus), male (\mars) or virgin female (\mercury) symbol at |
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% the beginning. This is intended as an abstraction layer above the |
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% |wasysym| package providing these symbols. |
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% \begin{macrocode} |
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\def\female{\venus\;\genotype} |
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\def\male{\mars\;\genotype} |
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\def\virgin{\mercury\;\genotype} |
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% \end{macrocode} |
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% \end{macro} |
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% \end{macro} |
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% \end{macro} |
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% |
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% \begin{macro}{\females} |
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% \begin{macro}{\males} |
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% \begin{macro}{\virgins} |
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% These macros are similar to their singular forms above, but inserts |
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% two female, male or virgin female symbols at the beginning. By |
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% convention, this is used to represent several individuals of the |
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% indicated genotype. |
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% \begin{macrocode} |
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\def\females{\venus\venus\;\genotype} |
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\def\males{\mars\mars\;\genotype} |
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\def\virgins{\mercury\mercury\;\genotype} |
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% \end{macrocode} |
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% \end{macro} |
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% \end{macro} |
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% \end{macro} |
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% |
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% \Finale |
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\endinput |
