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