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<title>The clm close manual</title>
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<p style="text-align:right">
16 May 2014&nbsp;&nbsp;&nbsp;
<a class="local" href="clmclose.ps"><b>clm close</b></a>
14-137
</p>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#name">NAME</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#synopsis">SYNOPSIS</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">3.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#description">DESCRIPTION</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">4.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#options">OPTIONS</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">5.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#author">AUTHOR</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">6.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#seealso">SEE ALSO</a>
</div>
</div>

<a name="name"></a>
<h2>NAME</h2>
<p style="margin-bottom:0" class="asd_par">
clm close &mdash; Fetch connected components from graphs or subgraphs</p>
<p style="margin-bottom:0" class="asd_par">clmclose is not in actual fact a program. This manual
page documents the behaviour and options of the clm program when
invoked in mode <i>close</i>. The options <b>-h</b>, <b>--apropos</b>,
<b>--version</b>, <b>-set</b>, <b>--nop</b> are accessible
in all <b>clm</b> modes. They are described
in the <a class="local sibling" href="clm.html">clm</a> manual page.</p>

<a name="synopsis"></a>
<h2>SYNOPSIS</h2>
<p style="margin-bottom:0" class="asd_par">
<b>clm close</b> -imx &lt;fname&gt; [options]
</p>
<p style="margin-bottom:0" class="asd_par">
<b>clm close</b>
<a class="intern" href="#opt-imx"><b>-imx</b> fname (<i>specify matrix input</i>)</a>
<a class="intern" href="#opt-abc"><b>-abc</b> fname (<i>specify label input</i>)</a>
<a class="intern" href="#opt-dom"><b>-dom</b> fname (<i>input domain/cluster file</i>)</a>
<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output file</i>)<b>]</b></a>
<a class="intern" href="#opt--is-undirected"><b>[--is-undirected</b> (<i>trust input graph to be undirected</i>)<b>]</b></a>
<a class="intern" href="#opt--write-count"><b>[--write-count</b> (<i>output component count</i>)<b>]</b></a>
<a class="intern" href="#opt--write-sizes"><b>[--write-sizes</b> (<i>output component sizes (default)</i>)<b>]</b></a>
<a class="intern" href="#opt--write-cc"><b>[--write-cc</b> (<i>output components as clustering</i>)<b>]</b></a>
<a class="intern" href="#opt--write-block"><b>[--write-block</b> (<i>output graph restricted to -dom argument</i>)<b>]</b></a>
<a class="intern" href="#opt--write-blockc"><b>[--write-blockc</b> (<i>output graph complement of -dom argument</i>)<b>]</b></a>
<a class="intern" href="#opt-cc-bound"><b>[-cc-bound</b> num (<i>select components with size at least num</i>)<b>]</b></a>
<a class="intern" href="#opt-tf"><b>[-tf</b> spec (<i>apply tf-spec to input matrix</i>)<b>]</b></a>
<a class="intern" href="#opt-h"><b>[-h</b> (<i>print synopsis, exit</i>)<b>]</b></a>
<a class="intern" href="#opt--apropos"><b>[--apropos</b> (<i>print synopsis, exit</i>)<b>]</b></a>
<a class="intern" href="#opt--version"><b>[--version</b> (<i>print version, exit</i>)<b>]</b></a>
</p>

<a name="description"></a>
<h2>DESCRIPTION</h2>
<p style="margin-bottom:0" class="asd_par">
Use <b>clm close</b> to fetch the connected components from a graph. Different
output modes are supported (see below). In matrix mode (i.e. using
the <b>-imx</b> option) the output returned with
<b>--write-cc</b> can be used in conjunction with <b>mcxsubs</b>
to retrieve individual subgraphs corresponding to connected components.
</p>

<a name="options"></a>
<h2>OPTIONS</h2>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-abc"></a><b>-abc</b> &lt;fname&gt; (<i>label input</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
The file name for input that is in label format.</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> &lt;fname&gt; (<i>input matrix</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
The file name for input that is in mcl native matrix format.</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-o"></a><b>-o</b> fname (<i>output file</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Specify the file where output is sent to. The default is STDOUT.
</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-dom"></a><b>-dom</b> fname (<i>input domain/cluster file</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
If this option is used, clm close will, as a first step,
for each of the domains in file&nbsp;<i>fname</i> retrieve the associated
subgraph from the input graph. These are then further decomposed into
connected components, and the program will process these in the normal
manner.
</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-count"></a><b>--write-count</b> (<i>output component count</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-sizes"></a><b>--write-sizes</b> (<i>output component sizes (default)</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-cc"></a><b>--write-cc</b> (<i>output components as clustering</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-block"></a><b>--write-block</b> (<i>output graph restricted to -dom argument</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--write-blockc"></a><b>--write-blockc</b> (<i>output graph complement of -dom argument</i>)</div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
The default behaviour is currently to output the sizes of the
connected components. It is also possible to simply output
the number of components with <b>--write-count</b> or to
write the components as a clustering in mcl format with
<b>-write-cc</b>. Even more options exist: it is possible
to output the restriction of the input graph to a domain, or
to output the complement of this restriction.
</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--is-undirected"></a><b>--is-undirected</b> (<i>omit graph undirected check</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
With this option the transformation to make sure
that the input is undirected is omitted. This will
be slightly faster. Using this option while the
input is directed may lead to erronenous results.
</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-cc-bound"></a><b>-cc-bound</b> num (<i>select components with size at least num</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
Transform the input matrix values according
to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.
</div>
</div>

<a name="author"></a>
<h2>AUTHOR</h2>
<p style="margin-bottom:0" class="asd_par">
Stijn van Dongen.
</p>

<a name="seealso"></a>
<h2>SEE ALSO</h2>
<p style="margin-bottom:0" class="asd_par">
<a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
and the utilities in the mcl family.
</p>
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