1% Typography. 2\newcommand{\ccode}[1]{{\smaller\texttt{#1}}} 3\newcommand{\ccodeincmd}[1]{{\texttt{#1}}} 4\newcommand{\emcode}[1]{{\smaller\texttt{\textbf{#1}}}} 5\newcommand{\itcode}[1]{{\smaller\texttt{\textit{#1}}}} 6\newcommand{\itbfcode}[1]{{\smaller\texttt{\textit{\bfseries #1}}}} 7\newcommand{\esldef}[1]{\textbf{#1}} % Define/introduce a term (to be indexed) 8\newcommand{\prog}[1]{{\smaller\textsc{#1}}} 9\newcommand{\eslmod}[1]{{\smaller\textsf{\textup{\textbf{#1}}}}} 10\newcommand{\eslmodincmd}[1]{{\smaller\textsf{\textup{\textbf{#1}}}}} 11\newcommand{\user}[1]{\indent\indent{\small\bfseries\texttt{> #1}}} 12\newcommand{\response}[1]{\indent\indent{\small\texttt{#1}}} 13 14\newcommand{\Easel} {Easel} 15\newcommand{\HMMER} {HMMER} 16\newcommand{\Infernal} {Infernal} 17\newcommand{\Pfam} {Pfam} 18\newcommand{\Rfam} {Rfam} 19 20% \api* functions are for the API summary tables. 21\newcommand{\apisubhead}[1]{\multicolumn{2}{|c|}{\rule[-0.4em]{0em}{1.5em}\textbf{#1}}} 22 23\def\argmax{\mathop{\mathrm{argmax}}\limits} 24\def\argmin{\mathop{\mathrm{argmin}}\limits} 25 26\DefineVerbatimEnvironment{cchunk} {Verbatim}{fontsize=\scriptsize,numbers=left,xleftmargin=1.0\parindent}% 27\DefineVerbatimEnvironment{userchunk} {Verbatim}{fontsize=\small,fontseries=b,,xleftmargin=1.0\parindent}% 28\DefineVerbatimEnvironment{responsechunk}{Verbatim}{fontsize=\small,xleftmargin=1.0\parindent}% 29\DefineVerbatimEnvironment{asciiart} {Verbatim}{fontsize=\scriptsize,xleftmargin=1.0\parindent}% 30 31% Set the color, size of the numbering of source code figures 32\renewcommand{\theFancyVerbLine}{\tiny\textcolor{SkyBlue}{\arabic{FancyVerbLine}}} 33 34 35% Description-like environment for documenting functions/APIs. 36% puts the description label in a minipage with a large hanging 37% indent. 38% Good christ this took a long time to develop. 39% hanging indent trick stolen from Peter Wilson's hanging.sty @CTAN 40% minipage allows multi-line label, and puts item on next line. 41% customized list inspired by Kopka/Daly _Guide to LaTeX_ p.213 42% SRE, Wed Dec 27 11:37:18 2000 43% 44\newenvironment{sreapi}{% 45 \begin{list}{}{% 46 \renewcommand{\makelabel}[1]{% 47 \begin{minipage}{\textwidth}% 48 \hangindent10em\hangafter1\noindent% 49 {\bfseries\texttt{##1}\vspace{0.8em}}% 50 \end{minipage}% 51 }}}% 52 {\end{list}} 53 54 55% Description-like environment for producing lists like: 56% 57% label stuff, stuff, stuff 58% 59% label2 more stuff, more stuff, 60% more stuff. 61% \begin{sreitems}{Longest label} \item[label] stuff, ... \end{sreitems} 62% SRE, Wed Dec 27 11:59:43 2000 63% 64\newenvironment{sreitems}[1]{% 65 \begin{list}{}{% 66 \settowidth{\labelwidth}{#1}% 67 \setlength{\leftmargin}{\labelwidth}% 68 \addtolength{\leftmargin}{\labelsep}% 69 }} 70 {\end{list}} 71