Rewrite the genotype macro

Rewrite the genotype macro so that it uses the FGChrPair macro to
typeset chromosome pairs.

flygenet.dtx

@@ -102,6 +102,7 @@ has been generated for details.
 %     2 rue Robert Escarpit, 33607 Pessac, France}\\
 %   \texttt{d.goutte-gattat@iecb.u-bordeaux.fr}}
 % \date{\filedate}
+% \let\ts\textsuperscript
 %
 % \maketitle
 %
@@ -113,7 +114,7 @@ has been generated for details.
 % notation, as in the following example:
 %
 % $$
-% \genotype{C(1)RM,y^2/Y; In(2LR)O, Cy cn^2 sp^2/Sco; ci^D/ey^D}
+% \genotype{C(1)RM,y\ts2/Y; In(2LR)O, Cy cn\ts2 sp\ts2/Sco; ci\ts D/ey\ts D}
 % $$
 %
 % Consequently, \LaTeX's math mode (and especially displayed math mode,
@@ -129,11 +130,13 @@ has been generated for details.
 % the following code:
 %
 % \begin{verbatim}
-% \genotype{C(1)RM,y^2/Y; In(2LR)O,Cy cn^2 sp^2/Sco; ci^D/ey^D}
+% \genotype{C(1)RM,y\ts2/Y; In(2LR)O,Cy cn\ts2 sp\ts2/Sco; ci\ts D/ey\ts D}
 % \end{verbatim}
 %
 % A complete genotype can thus be written in a very intuitive way, the
-% only \TeX ism being the exponentiation symbol (|^|).
+% only \TeX ism being the exponentiation macro, |\ts|, which is an alias
+% for the |\textsuperscript| macro (this alias is \emph{not} defined by
+% this package).
 %
 %
 % \section{User interface}
@@ -177,25 +180,6 @@ has been generated for details.
 % $$
 % \end{minipage}
 %
-% \bigskip
-% When used as an argument to another macro, |\genotype| cannot control
-% spacing; spaces between gene symbols must be added manually.
-%
-% \begin{minipage}{.6\textwidth}
-% \begin{verbatim}
-% \underbrace{\genotype{cn bw/;TM2/tra}}
-% \quad
-% \underbrace{\genotype{cn\ bw/;TM2/tra}}
-% \end{verbatim}
-% \end{minipage}
-% \begin{minipage}{.3\textwidth}
-% $$
-% \underbrace{\genotype{cn bw/;TM2/tra}}
-% \quad
-% \underbrace{\genotype{cn\ bw/;TM2/tra}}
-% $$
-% \end{minipage}
-%
 % ^^A Inserts the LPPL text.
 % \providecommand{\LPPLsection}{\section}
 % \providecommand{\LPPLsubsection}{\subsection}
@@ -256,10 +240,10 @@ has been generated for details.
 % \end{macro}
 %
 % \begin{macro}{\FGXYPair}
-% This macro typesets a Y chromosome genotype. It is intended to look
-% like a half-fraction, with the genotype as the numerator and without a
-% denumerator, and with a downward hook at the right end of the fraction
-% bar.
+% This macro typesets a pair of X/Y sexual chromosomes. It is intended
+% to look like a half-fraction, with the genotype as the numerator and
+% without a denumerator, and with a downward hook at the right end of
+% the fraction bar.
 %
 % We first define two helper macros that will do the actual work of
 % drawing the genotype.
@@ -308,70 +292,30 @@ has been generated for details.
 %
 % \subsection{Typesetting genotypes}
 %
-% \begin{macro}{\fly@printchromosome}
-% This macro typesets a single chromosome pair, as a mathematical
-% fraction.
+% \begin{macro}{\FG@printchromosome}
+% This macro typesets a single chromosome pair, presented as delimited
+% arguments.
 %    \begin{macrocode}
-\def\fly@printchromosome#1/#2\end{%
-\def\fly@argii{#2}%
-\ifx\fly@argii\empty\mathit{#1}\else\frac{\mathit{#1}}{\mathit{#2}}\fi}
+\def\FG@printchromosome#1/#2\end{\FGChrPair{#1}{#2}}
 %    \end{macrocode}
 % \end{macro}
 %
-% \begin{macro}{\fly@parsechromosome}
+% \begin{macro}{\FG@parsechromosome}
 % This macro parses a genotype notation (chromosome pairs separated by
-% semi-colons), and calls the |\fly@printchromosome| for each chromosome
+% semi-colons), and calls the |\FG@printchromosome| for each chromosome
 % pair.
 %    \begin{macrocode}
-\def\fly@parsechromosome#1;#2\end{%
-\fly@printchromosome#1\end%
-\def\fly@argii{#2}%
-\ifx\fly@argii\empty\else; \fly@parsechromosome#2\end\fi}
-%    \end{macrocode}
-% \end{macro}
-%
-% \begin{macro}{\mhyphen}
-% \begin{macro}{\mcolon}
-% These two macros are used to typeset actual hyphens and colons in math
-% mode.
-%    \begin{macrocode}
-\mathchardef\mhyphen="2D
-\mathchardef\mcolon="3A
-%    \end{macrocode}
-% \end{macro}
-% \end{macro}
-%
-% \begin{macro}{\fly@endgenotype}
-% This macro is called at the end of the |\genotype| macro. It performs
-% the task of parsing and typesetting the genotype and reset the
-% modified catcodes.
-%    \begin{macrocode}
-\def\fly@endgenotype#1{%
-\fly@parsechromosome#1;\end%
-\catcode`\ =10\relax%
-\catcode`\-=12\relax%
-\catcode`\:=12\relax}
+\def\FG@parsechromosome#1;#2\end{%
+\FG@printchromosome#1\end%
+\def\FG@argii{#2}%
+\ifx\FG@argii\empty\else; \FG@parsechromosome#2\end\fi}
 %    \end{macrocode}
 % \end{macro}
 %
 % \begin{macro}{\genotype}
-% This macro is the main user interface to typeset a genotype. Its
-% declaration is enclosed in a group since we need to locally modify the
-% catcodes of some characters. For the same reason, the macro cannot be
-% declared as expecting an argument (otherwise, the argument would be
-% parsed before the catcodes are modified)---the argument is parsed when
-% calling the |\fly@endgenotype| macro.
+% This macro is the main user interface to typeset a genotype.
 %    \begin{macrocode}
-\begingroup
-\catcode`\ =\active
-\catcode`\-=\active
-\catcode`\:=\active
-\gdef\genotype{%
-\catcode`\ =\active\let =\ %
-\catcode`\-=\active\let-=\mhyphen%
-\catcode`\:=\active\let:=\mcolon%
-\fly@endgenotype}
-\endgroup
+\def\genotype#1{\FG@parsechromosome#1;\end}
 %    \end{macrocode}
 % \end{macro}
 %