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% Typography.
\newcommand{\ccode}[1]{{\smaller\texttt{#1}}}
\newcommand{\ccodeincmd}[1]{{\texttt{#1}}}
\newcommand{\emcode}[1]{{\smaller\texttt{\textbf{#1}}}}
\newcommand{\itcode}[1]{{\smaller\texttt{\textit{#1}}}}
\newcommand{\itbfcode}[1]{{\smaller\texttt{\textit{\bfseries #1}}}}
\newcommand{\esldef}[1]{\textbf{#1}} % Define/introduce a term (to be indexed)
\newcommand{\prog}[1]{{\smaller\textsc{#1}}}
\newcommand{\eslmod}[1]{{\smaller\textsf{\textup{\textbf{#1}}}}}
\newcommand{\eslmodincmd}[1]{{\smaller\textsf{\textup{\textbf{#1}}}}}
\newcommand{\user}[1]{\indent\indent{\small\bfseries\texttt{> #1}}}
\newcommand{\response}[1]{\indent\indent{\small\texttt{#1}}}
\newcommand{\Easel} {Easel}
\newcommand{\HMMER} {HMMER}
\newcommand{\Infernal} {Infernal}
\newcommand{\Pfam} {Pfam}
\newcommand{\Rfam} {Rfam}
% \api* functions are for the API summary tables.
\newcommand{\apisubhead}[1]{\multicolumn{2}{|c|}{\rule[-0.4em]{0em}{1.5em}\textbf{#1}}}
\def\argmax{\mathop{\mathrm{argmax}}\limits}
\def\argmin{\mathop{\mathrm{argmin}}\limits}
\DefineVerbatimEnvironment{cchunk} {Verbatim}{fontsize=\scriptsize,numbers=left,xleftmargin=1.0\parindent}%
\DefineVerbatimEnvironment{userchunk} {Verbatim}{fontsize=\small,fontseries=b,,xleftmargin=1.0\parindent}%
\DefineVerbatimEnvironment{responsechunk}{Verbatim}{fontsize=\small,xleftmargin=1.0\parindent}%
\DefineVerbatimEnvironment{asciiart} {Verbatim}{fontsize=\scriptsize,xleftmargin=1.0\parindent}%
% Set the color, size of the numbering of source code figures
\renewcommand{\theFancyVerbLine}{\tiny\textcolor{SkyBlue}{\arabic{FancyVerbLine}}}
% Description-like environment for documenting functions/APIs.
% puts the description label in a minipage with a large hanging
% indent.
% Good christ this took a long time to develop.
% hanging indent trick stolen from Peter Wilson's hanging.sty @CTAN
% minipage allows multi-line label, and puts item on next line.
% customized list inspired by Kopka/Daly _Guide to LaTeX_ p.213
% SRE, Wed Dec 27 11:37:18 2000
%
\newenvironment{sreapi}{%
\begin{list}{}{%
\renewcommand{\makelabel}[1]{%
\begin{minipage}{\textwidth}%
\hangindent10em\hangafter1\noindent%
{\bfseries\texttt{##1}\vspace{0.8em}}%
\end{minipage}%
}}}%
{\end{list}}
% Description-like environment for producing lists like:
%
% label stuff, stuff, stuff
%
% label2 more stuff, more stuff,
% more stuff.
% \begin{sreitems}{Longest label} \item[label] stuff, ... \end{sreitems}
% SRE, Wed Dec 27 11:59:43 2000
%
\newenvironment{sreitems}[1]{%
\begin{list}{}{%
\settowidth{\labelwidth}{#1}%
\setlength{\leftmargin}{\labelwidth}%
\addtolength{\leftmargin}{\labelsep}%
}}
{\end{list}}
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