/usr/share/doc/mcl/html/mcxalter.html is in mcl-doc 1:14-137-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<!-- Copyright (c) 2014 Stijn van Dongen -->
<head>
<meta name="keywords" content="manual">
<style type="text/css">
/* START aephea.base.css */
body
{ text-align: justify;
margin-left: 0%;
margin-right: 0%;
}
a:link { text-decoration: none; }
a:active { text-decoration: none; }
a:visited { text-decoration: none; }
a:link { color: #1111aa; }
a:active { color: #1111aa; }
a:visited { color: #111166; }
a.local:link { color: #11aa11; }
a.local:active { color: #11aa11; }
a.local:visited { color: #116611; }
a.intern:link { color: #1111aa; }
a.intern:active { color: #1111aa; }
a.intern:visited { color: #111166; }
a.extern:link { color: #aa1111; }
a.extern:active { color: #aa1111; }
a.extern:visited { color: #661111; }
a.quiet:link { color: black; }
a.quiet:active { color: black; }
a.quiet:visited { color: black; }
div.verbatim
{ font-family: monospace;
margin-top: 1em;
margin-bottom: 1em;
font-size: 10pt;
margin-left: 2em;
white-space: pre;
}
div.indent
{ margin-left: 8%;
margin-right: 0%;
}
.right { text-align: right; }
.left { text-align: left; }
.nowrap { white-space: nowrap; }
.item_leader
{ position: relative;
margin-left: 8%;
}
.item_compact { position: absolute; vertical-align: baseline; }
.item_cascade { position: relative; }
.item_leftalign { text-align: left; }
.item_rightalign
{ width: 2em;
text-align: right;
}
.item_compact .item_rightalign
{ position: absolute;
width: 52em;
right: -2em;
text-align: right;
}
.item_text
{ position: relative;
margin-left: 3em;
}
.smallcaps { font-size: smaller; text-transform: uppercase }
/* END aephea.base.css */
body { font-family: "Garamond", "Gill Sans", "Verdana", sans-serif; }
body
{ text-align: justify;
margin-left: 8%;
margin-right: 8%;
}
</style>
<title>The mcxalter manual</title>
</head>
<body>
<p style="text-align:right">
16 May 2014
<a class="local" href="mcxalter.ps"><b>mcxalter</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">
mcxalter — various network transformations</p>
<a name="synopsis"></a>
<h2>SYNOPSIS</h2>
<p style="margin-bottom:0" class="asd_par">
<b>mcxalter</b>
<a class="intern" href="#opt-imx"><b>[-imx</b> <fname> (<i>specify matrix/graph input</i>)<b>]</b></a>
<a class="intern" href="#opt-abc"><b>[-abc</b> <fname> (<i>specify label input</i>)<b>]</b></a>
<a class="intern" href="#opt-tab"><b>[-tab</b> <fname> (<i>use tab file</i>)<b>]</b></a>
<a class="intern" href="#opt-icl"><b>[-icl</b> <fname> (<i>specify cluster input</i>)<b>]</b></a>
<a class="intern" href="#opt--block"><b>[--block</b> (<i>use within-cluster edges</i>)<b>]</b></a>
<a class="intern" href="#opt--blockc"><b>[--blockc</b> (<i>use between-cluster edges</i>)<b>]</b></a>
<a class="intern" href="#opt-o"><b>[-o</b> <fname> (<i>output</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>
</p>
<a name="description"></a>
<h2>DESCRIPTION</h2>
<p style="margin-bottom:0" class="asd_par">
This utility supplies various transformations of networks.
</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> <fname> (<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"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-imx"></a><b>-imx</b> <fname> (<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"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tab"></a><b>-tab</b> <fname> (<i>use tab file</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
This option causes the output to be printed with the labels
found in the tab file.
With <b>-abc</b> this option will, additionally, construct
a graph only on the labels found in the tab file.
If this option is used in conjunction with <b>-imx</b> the
tab domain and the matrix domain are required to be identical.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-icl"></a><b>-icl</b> <fname> (<i>specify cluster input</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Read in a cluster file for use with either <b>--block</b> or <b>--blockc</b>.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--block"></a><b>--block</b> (<i>use within-cluster edges</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Remove between-cluster edges from the network. This is done first, before
other transformations take effect.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt--blockc"></a><b>--blockc</b> (<i>use between-cluster edges</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Remove within-cluster edges from the network. This is done first, before
other transformations take effect.
</p>
</div>
<div style="margin-top:0em"> </div><div class=" item_cascade"><div class=" item_leftalign nowrap " ><a name="opt-tf"></a><b>-tf</b> <tf-spec> (<i>transform input matrix values</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
Transform the input matrix values according
to the syntax described in <a class="local sibling" href="mcxio.html">mcxio</a>.
</p>
</div>
<div style="margin-top:0em"> </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">
Output file.</p>
</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="mcxio.html">mcxio</a>,
<a class="local sibling" href="mcx.html">mcx</a>,
<a class="local sibling" href="mcxsubs.html">mcxsubs</a>,
and <a class="local sibling" href="mclfamily.html">mclfamily</a> for an overview of all the documentation
and the utilities in the mcl family.
</p>
</body>
</html>
|