/usr/share/doc/cassiopee/html/classTreeNode.html is in libcassie-doc 1.0.7-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.13"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>Cassiopee: TreeNode Class Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/searchdata.js"></script>
<script type="text/javascript" src="search/search.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Cassiopee
 <span id="projectnumber">1.0</span>
</div>
<div id="projectbrief">Suffix indexer and search tool</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.13 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
$(function() {
initMenu('',true,false,'search.php','Search');
$(document).ready(function() { init_search(); });
});
</script>
<div id="main-nav"></div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
</div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pub-attribs">Public Attributes</a> |
<a href="#friends">Friends</a> |
<a href="classTreeNode-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">TreeNode Class Reference</div> </div>
</div><!--header-->
<div class="contents">
<p><code>#include <<a class="el" href="Cassiopee_8h_source.html">Cassiopee.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:a0588566e906d9dc6930cb8d265f2612a"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classTreeNode.html#a0588566e906d9dc6930cb8d265f2612a">TreeNode</a> (char nc)</td></tr>
<tr class="separator:a0588566e906d9dc6930cb8d265f2612a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a83e684ed666dae18b48d8ea544abe732"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classTreeNode.html#a83e684ed666dae18b48d8ea544abe732">TreeNode</a> (char nc, long pos)</td></tr>
<tr class="separator:a83e684ed666dae18b48d8ea544abe732"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-attribs"></a>
Public Attributes</h2></td></tr>
<tr class="memitem:a3faf767e3b730aeb112edc656273ab03"><td class="memItemLeft" align="right" valign="top">char </td><td class="memItemRight" valign="bottom"><a class="el" href="classTreeNode.html#a3faf767e3b730aeb112edc656273ab03">c</a></td></tr>
<tr class="separator:a3faf767e3b730aeb112edc656273ab03"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac5aaf0f2dcfdc73ce827bc357fff456f"><td class="memItemLeft" align="right" valign="top">list< long > </td><td class="memItemRight" valign="bottom"><a class="el" href="classTreeNode.html#ac5aaf0f2dcfdc73ce827bc357fff456f">positions</a></td></tr>
<tr class="separator:ac5aaf0f2dcfdc73ce827bc357fff456f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad4653b8cfd5f2fe1d1d2d333545897a6"><td class="memItemLeft" align="right" valign="top">long </td><td class="memItemRight" valign="bottom"><a class="el" href="classTreeNode.html#ad4653b8cfd5f2fe1d1d2d333545897a6">next_pos</a></td></tr>
<tr class="separator:ad4653b8cfd5f2fe1d1d2d333545897a6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abcdf798306e96401e94544f87ad914be"><td class="memItemLeft" align="right" valign="top">long </td><td class="memItemRight" valign="bottom"><a class="el" href="classTreeNode.html#abcdf798306e96401e94544f87ad914be">next_length</a></td></tr>
<tr class="separator:abcdf798306e96401e94544f87ad914be"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="friends"></a>
Friends</h2></td></tr>
<tr class="memitem:ac98d07dd8f7b70e16ccb9a01abf56b9c"><td class="memItemLeft" align="right" valign="top"><a id="ac98d07dd8f7b70e16ccb9a01abf56b9c"></a>
class </td><td class="memItemRight" valign="bottom"><b>boost::serialization::access</b></td></tr>
<tr class="separator:ac98d07dd8f7b70e16ccb9a01abf56b9c"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Node in the suffix tree</p>
<p>If tree is reduced (DO_REDUCTION=1), memory usage is highly reduced, keeping in memory only the branching nodes. Search is made after that looking at branch nodes and sequence content between nodes. In addition, data from file are analysed per chunk, limiting again loaded data in memory.</p>
<p>This treatment requires however more disk usage (reads) and tree manipulations, increasing the index and search time for a gain on memory requirements. </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="a0588566e906d9dc6930cb8d265f2612a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a0588566e906d9dc6930cb8d265f2612a">◆ </a></span>TreeNode() <span class="overload">[1/2]</span></h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">TreeNode::TreeNode </td>
<td>(</td>
<td class="paramtype">char </td>
<td class="paramname"><em>nc</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Creates a node from a char</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">nc</td><td>character for this node </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a83e684ed666dae18b48d8ea544abe732"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a83e684ed666dae18b48d8ea544abe732">◆ </a></span>TreeNode() <span class="overload">[2/2]</span></h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">TreeNode::TreeNode </td>
<td>(</td>
<td class="paramtype">char </td>
<td class="paramname"><em>nc</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">long </td>
<td class="paramname"><em>pos</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Creates a node from a char</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">nc</td><td>character for this node </td></tr>
<tr><td class="paramname">pos</td><td>position of the character in the sequence </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<h2 class="groupheader">Member Data Documentation</h2>
<a id="a3faf767e3b730aeb112edc656273ab03"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a3faf767e3b730aeb112edc656273ab03">◆ </a></span>c</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">char TreeNode::c</td>
</tr>
</table>
</div><div class="memdoc">
<p>Character to match </p>
</div>
</div>
<a id="abcdf798306e96401e94544f87ad914be"></a>
<h2 class="memtitle"><span class="permalink"><a href="#abcdf798306e96401e94544f87ad914be">◆ </a></span>next_length</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">long TreeNode::next_length</td>
</tr>
</table>
</div><div class="memdoc">
<p>Length of remaining data to read in sequence file </p>
</div>
</div>
<a id="ad4653b8cfd5f2fe1d1d2d333545897a6"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ad4653b8cfd5f2fe1d1d2d333545897a6">◆ </a></span>next_pos</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">long TreeNode::next_pos</td>
</tr>
</table>
</div><div class="memdoc">
<p>When tree is reduced, store the location of next characters in input sequence file. Reduction can be made from a branch up to the leaf or between 2 branches. If next_pos is equal to -1, then no reduction is made. </p>
</div>
</div>
<a id="ac5aaf0f2dcfdc73ce827bc357fff456f"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac5aaf0f2dcfdc73ce827bc357fff456f">◆ </a></span>positions</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">list<long> TreeNode::positions</td>
</tr>
</table>
</div><div class="memdoc">
<p>List of positions in sequence matching this node </p>
</div>
</div>
<hr/>The documentation for this class was generated from the following files:<ul>
<li>src/<a class="el" href="Cassiopee_8h_source.html">Cassiopee.h</a></li>
<li>src/cassiopee.cxx</li>
</ul>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.13
</small></address>
</body>
</html>
|