This file is indexed.

/usr/share/doc/mcl/html/clmoptics.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
211
212
213
214
215
216
217
218
<!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 clm optics manual</title>
</head>
<body>
<p style="text-align:right">
16 May 2014&nbsp;&nbsp;&nbsp;
<a class="local" href="clmoptics.ps"><b>clm optics</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 optics &mdash; implementation of the OPTICS reachability ordering</p>
<p style="margin-bottom:0" class="asd_par">clmoptics is not in actual fact a program. This manual
page documents the behaviour and options of the clm program when
invoked in mode <i>optics</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 optics</b> -imx &lt;fname&gt; [options]
</p>
<p style="margin-bottom:0" class="asd_par">
<b>clm optics</b>
<a class="intern" href="#opt-imx"><b>-imx</b> fname (<i>input graph file name</i>)</a>
<a class="intern" href="#opt-max-eps"><b>-max-eps</b> &lt;num&gt; (<i>maximum distance considered</i>)</a>
<a class="intern" href="#opt-min-eps"><b>-min-eps</b> &lt;num&gt; (<i>minimum similarity considered</i>)</a>
<a class="intern" href="#opt-min-pts"><b>-min-pts</b> &lt;int&gt; (<i>minimum eps-neighbourhood size</i>)</a>
<a class="intern" href="#opt-icl"><b>[-icl</b> fname (<i>input clustering name</i>)<b>]</b></a>
<a class="intern" href="#opt-o"><b>[-o</b> fname (<i>output name</i>)<b>]</b></a>
<a class="intern" href="#opt-ps"><b>[-ps</b> fname (<i>PostScript output name</i>)<b>]</b></a>
<a class="intern" href="#opt-psx"><b>[-psx</b> fname (<i>scaling factor x axis</i>)<b>]</b></a>
<a class="intern" href="#opt-psy"><b>[-psy</b> fname (<i>scaling factor y axis</i>)<b>]</b></a>
<a class="intern" href="#opt-ps-rows"><b>[-ps-rows</b> &lt;num&gt; (<i>split reachability plot into &lt;num&gt; rows</i>)<b>]</b></a>
<a class="intern" href="#opt--ps-labels"><b>[--ps-labels</b> (<i>show identifiers in PS output</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">
This programs computes the reachability ordering according to the <b>OPTICS</b>
clustering method. It can additionally output a PostScript plot of the reachability
landscape. This plot can be annotated with a user-supplied clustering.
The program does not implement the clustering method that is associated
with <b>OPTICS</b>. It is part of <b>mcl-edge</b> primarily as a visualisation aid.
</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-imx"></a><b>-imx</b> fname (<i>input file</i>)</div></div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
The input file, encoding a graph in native format.
</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-max-eps"></a><b>-max-eps</b> &lt;num&gt; (<i>maximum distance considered</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-min-eps"></a><b>-min-eps</b> &lt;num&gt; (<i>minimum similarity considered</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-min-pts"></a><b>-min-pts</b> &lt;int&gt; (<i>minimum eps-neighbourhood size</i>)</div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
These encode the <b>OPTICS</b> parameters. Use <b>-max-eps</b> if the
edge weights encode a distance (for example the Euclidean distance between
points), use <b>-min-eps</b> if the edge weights encode a similarity.
</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-o"></a><b>-o</b> fname (<i>output file name</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-ps"></a><b>-ps</b> fname (<i>PostScript file name</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-icl"></a><b>-icl</b> fname (<i>input clustering name</i>)</div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
The <b>-o</b>&nbsp;<i>fname</i> option controls the name of the file in which the reachability
values are written. By default these values are written to STDOUT.
</p>
<p style="margin-bottom:0" class="asd_par">
If <b>-ps</b>&nbsp;<i>fname</i> is supplied the program will additionally output a visualisation
of the reachability landscape plot in a PostScript file.
</p>
<p style="margin-bottom:0" class="asd_par">
It is possible, in addition to <b>-ps</b>, to specify a clustering with <b>-icl</b>&nbsp;<i>fname</i>.
Each vertical bar in the landscape plot will be coloured according to cluster membership,
that is, nodes in the same cluster will have the same colour. This can be a useful way
to visualise separation properties of clusterings.
</p>
</div>
<div style="margin-top:0em">&nbsp;</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-psx"></a><b>-psx</b> fname (<i>scaling factor x axis</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-psy"></a><b>-psy</b> fname (<i>scaling factor y axis</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt--ps-labels"></a><b>--ps-labels</b> (<i>show identifiers in PS output</i>)</div><div class=" item_cascade item_leftalign nowrap" ><a name="opt-ps-rows"></a><b>-ps-rows</b> &lt;num&gt; (<i>split reachability plot into &lt;num&gt; rows</i>)</div>
<div class=" item_text " style="margin-left:2em">
<p style="margin-top:0em; margin-bottom:0em">
By default the PostScript output will be scaled to fit onto an A3 page.
The scaling options <b>-psx</b> and <b>-psy</b> can be used as additional
scaling factors. By default these are set <tt>1.0</tt>.
</p>
<p style="margin-bottom:0" class="asd_par">
The <b>--ps-labels</b> can be used to annotate each vertical bar in the landscape
plot with the <b>mcl-edge</b> identifier of the corresponding node.
</p>
<p style="margin-bottom:0" class="asd_par">
The <b>-ps-rows</b> option sets the number of rows. This is the primary
option affect the width of a bar.
</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="mclfamily.html">mclfamily</a> for an overview of all the documentation
and the utilities in the mcl family.</p>
</body>
</html>