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\: what's with the funny name index.in.azm ?
\: this document is a regular manual page in the roff edition;
\: the html edition is not however, as it uses tables (coded ad hoc).
\: as a result the macro code below looks messy - more so
\: becaues the html edition is split into two incarnations,
\: a 'distribution index' and an 'installed index'.
\: the incarnations correspond with the keys dist#0 and install#0.
\import{mcx.zmm}
\if{\defined{key}{dist}}{
\set{modal}{Install with}
\set{subtitle}{Distribution index \"mcx::stamp"}
}{}
\if{\defined{key}{install}}{
\set{modal}{Documentation only available if installed with}
\set{subtitle}{Installation index \"mcx::stamp"}
}{}
\${html}{
\set{mkentry#3}{\@{<tr>
<td><b>\1</b> - \3</td>
<td><a href="\1.html">html</a></td>
<td><a href="\1.ps">ps</a></td>
</tr>}}
\set{mkheader#3}{\@{<tr>
<th colspan="3">}
\bf{\1} - \2 \bf{\3}
\@{</th>
</tr>}}
\set{utsection#1}{\@{
<h3 style="margin-top:2em">}\1\@{</h3>
<table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
}}
\set{modsection#1}{\@{
<h3 style="margin-top:2em">}\1\@{</h3>
<table width="100%" border=1 cellpadding=3 rules=all style="margin-top:0em">
}}
\set{utend}{\@{</table>}}
\set{modend}{\@{</table>}}
\@{\w}
\@{<html>
<head>
<title>MCL manuals</title>
<style type="text/css">
body
{ text-align: justify;
color: #001111;
background: white;
margin-left: 8%;
margin-right: 8%;
}
h3 { margin-top:1em; }
h2 { margin-top:2em; }
</style>
</head>
<body>
}
\@{
<hr noshade size=1>
<h1> MCL user manuals </h1>
<h3> \&{\subtitle} </h3>
<hr noshade size=1>
}
}
\${roff}{
\begin{pud::man}{
{name}{mclindex}
{author}{Stijn van Dongen}
{section}{7}
\man_share
}
\sec{name}{NAME}
\NAME{mclindex}{a list of the utilities and modules present in the MCL distribution.}
\par
For more information, consult \mysib{mclfamily}.
\set{utsection#1}{\par\sec{}{\1}
\par
\begin{itemize}{{compact}{1}{contiguous}{1}{w1}{14}{w2}{1}}
}
\set{modsection#1}{\par\sec{}{\1}
\~\par
\begin{itemize}{{compact}{1}{contiguous}{1}{w1}{18}{w2}{1}}
}
\set{mkentry#3}{\item{\bf{\1(\2)}} \3}
\set{mkheader#3}{\bf{\1} - \2 \bf{\3}\|}
\set{utend}{\end{itemize}}
\set{modend}{\end{itemize}}
}
\utsection{Generic stuff}
\mkentry{mcl}{1}{the mcl manual page}
\mkentry{mclfaq}{7}{the mcl FAQ}
\mkentry{mcxio}{5}{the mcl matrix format specification}
\mkentry{mclpipeline}{1}{generic pipeline (parsing/matrix creation/clustering/display)}
\mkentry{mcx}{1}{interface to basic matrix operations}
\mkentry{mcxassemble}{1}{prepare input matrix from cooccurrence scores}
\mkentry{mcxdump}{1}{dump matrices, optionally map indices to labels}
\mkentry{mcxarray}{1}{transform array data to MCL matrices}
\mkentry{mcxconvert}{1}{convert between ascii/binary storage types}
\utend
\utsection{Dealing with clustering results}
\mkentry{clmformat}{1}{display clusterings in browsable format}
\mkentry{clmdist}{1}{compute distances between clusterings}
\mkentry{clminfo}{1}{performance measures for clusterings}
\mkentry{clmmeet}{1}{compute intersection of clusterings}
\mkentry{clmmate}{1}{compute best matches between two clusterings}
\mkentry{clmimac}{1}{Interpret Matrices (c.q. MCL iterands) As Clusterings}
\mkentry{clmresidue}{1}{extend subgraph clusterings onto encompassing graph}
\mkentry{clmorder}{1}{reorder indices to represent blocks from different clusterings}
\mkentry{clmclose}{1}{fetch connected components from graphs or subgraphs}
\utend
\utsection{Dealing with matrices}
\mkentry{mcxio}{5}{the mcl matrix format specification}
\mkentry{mcx}{1}{interface to basic matrix operations}
\mkentry{mcxsubs}{1}{extract submatrices by specifying sets of nodes and clusters}
\mkentry{mcxmap}{1}{remap matrix indices / relabel graph nodes}
\mkentry{mcxassemble}{1}{prepare input matrix from cooccurrence scores}
\utend
\modsection{Application specific parsers and wrappers}
\mkheader{BLAST package}{\modal}{--enable-blast}
\${roff}{\v{__________________}\|}
\mkentry{mclblastline}{1}{pipeline for clustering from blast files}
\mkentry{mcxdeblast}{1}{prepare input from blast files}
\modend
\${html}{\@{
</body>
</html>
}}
\${roff}{\end{pud::man}}
|
