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%BioCon.sty: Biological Conventions.
%
%This package tries to automatically typeset some biological entities. Currently (v0.04), only
%species are supported, but plans are to include genes and their products (and maybe even more).
%
%Although, it is not a real convention, this package gives the full name of a species the first
%time it is used in a document. After that, it uses the abbreviated form consisting of the
%first letter of the genus followed by the epiteton.
%The species name is written emphasized.
%
%The workings of this package are fairly simple. To introduce a new species, use the
%\newspecies[optional identifier]{Genus epiteton} command. If no identifier is given, the first
%letter of the genus in capital followed by the first letter of the epiteton in lowercase are used.
%For example, to introduce Drosophilla melanogaster, type \newspecies[Dros]{Drosophilla melanogaster}
%or \newspecies{Drosophila melanogaster}.
%Then, every time you want to use this species, type \species{Abbreviation}. In the above
%example this would be \species{Dm}.
%
%Of course, long or short names can be forced. This is done through an optional parameter.
%This can be "n" for normal, "l" for long, and "s" for short. Furthermore, the type it was about
%to use by appending a "d" (for "delay") to this.
%
%In the above example, suppose you want to use the full name in the title, and then the first
%time it occurs in the text. In the last sentence, the full name has also to be used:
%\title{The HOX-genes of \species[ld]{Dm}} ([nd] can also be used)
%....
%....
%As a conclusion: Time flies like an arrow and fruit flies like a banana, and so does
%\species[l]{Dm}.
%
%This package is written by Pieter Edelman (PEdelman@dds.nl). Please send me any comments,
%requests and/or suggestions.
%
%This package is released under the GNU General Public License.
\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{biocon}[2000/08/11 Typesets Biological Statements, v.0.04 (stable)]
%global defs:
\newcounter{Option}
\newcommand\ShowHow{n}
\newcommand\Short{s}
\newcommand\Long{l}
\newcommand\Normal{n}
\newcommand\LongDelay{ld}
\newcommand\ShortDelay{sd}
\newcommand\NormalDelay{nd}
\newcommand\isEmpty{}
%These are used to store intermediate variables:
\newcommand\GenusFirst{}
\newcommand\Genus{}
\newcommand\EpitetonFirst{}
\newcommand\Epiteton{}
\newcommand\AbName{}
\newcommand\useDefault{}
%These define how a long and a short name should look like.
\newcommand\FullName[1]{\csname#1Genus\endcsname\ \csname#1Epiteton\endcsname}
\newcommand\ShortName[1]{\csname#1GenusFirst\endcsname. \csname#1Epiteton\endcsname}
\def\setSpeciesParams(#1#2 #3#4){% This sets the various variables using their intermediates.
\uppercase{\renewcommand{\GenusFirst}{#1}}%
\lowercase{\renewcommand{\EpitetonFirst}{#3}}%
\renewcommand{\Genus}{\uppercase{#1}\lowercase{#2}}%
\lowercase{\renewcommand{\Epiteton}{#3#4}}%
}
\newcommand{\newspecies}[2][]{%
\setSpeciesParams(#2)%
\renewcommand{\useDefault}{#1}%
\ifx \useDefault\isEmpty% Find out if abbreviation is provided.
\renewcommand{\AbName}{\GenusFirst\EpitetonFirst}%
\else%
\renewcommand{\AbName}{#1}%
\fi%
\expandafter\newcounter\expandafter{\AbName}% Set new counter using the abbreviated name
\expandafter\let\csname\AbName GenusFirst\endcsname=\GenusFirst% Set intermediates to real values
\expandafter\let\csname\AbName Genus\endcsname=\Genus%
\expandafter\let\csname\AbName Epiteton\endcsname=\Epiteton%
}
\newcommand{\LineInput}[1]{%
\renewcommand\ShowHow{#1}%
\ifx\ShowHow\Short%
\setcounter{Option}{1}%
\fi%
\ifx\ShowHow\Long%
\setcounter{Option}{3}%
\fi%
\ifx\ShowHow\Normal%
\setcounter{Option}{5}%
\fi%
\ifx\ShowHow\ShortDelay%
\setcounter{Option}{0}%
\fi%
\ifx\ShowHow\LongDelay%
\setcounter{Option}{2}%
\fi%
\ifx\ShowHow\NormalDelay%
\setcounter{Option}{4}%
\fi%
}
\newcommand{\species}[2][n]{%
\LineInput{#1}%
%
\ifnum\value{Option}>3% If name is normal
\ifnum\value{#2}=0% If name is used for the first time
\emph{\FullName{#2}}%
\else% If name is used for another time
\emph{\ShortName{#2}}%
\fi%
\else%
\ifnum\value{Option}<2% If name is short
\emph{\ShortName{#2}}%
\else% If name is long
\emph{\FullName{#2}}%
\fi%
\fi%
%
\ifodd\value{Option}%
\stepcounter{#2}%
\fi%
}
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