libcassie-doc 1.0.7-1 / usr / share / doc / cassiopee / html / functions.html

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<!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: Class Members</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
   &#160;<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>
</div><!-- top -->
<!-- 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 class="contents">
<div class="textblock">Here is a list of all documented class members with links to the class documentation for each member:</div>

<h3><a id="index_a"></a>- a -</h3><ul>
<li>ambiguity
: <a class="el" href="classCassieSearch.html#ad14e3b94ac939780540c181d0ed61ecd">CassieSearch</a>
</li>
</ul>


<h3><a id="index_c"></a>- c -</h3><ul>
<li>c
: <a class="el" href="classTreeNode.html#a3faf767e3b730aeb112edc656273ab03">TreeNode</a>
</li>
<li>CassieIndexer()
: <a class="el" href="classCassieIndexer.html#a2c259abfde72f1dfd2cf3b35dc354268">CassieIndexer</a>
</li>
<li>CassieSearch()
: <a class="el" href="classCassieSearch.html#af63d70d0891eb7f063a1def5caf0e6c6">CassieSearch</a>
</li>
</ul>


<h3><a id="index_d"></a>- d -</h3><ul>
<li>del
: <a class="el" href="classMatch.html#a9d275c862cc10ddc94186b4808363411">Match</a>
</li>
<li>do_reduction
: <a class="el" href="classCassieIndexer.html#a09cce9f97298b7f1f2ccb15435e0719a">CassieIndexer</a>
</li>
</ul>


<h3><a id="index_f"></a>- f -</h3><ul>
<li>filltree()
: <a class="el" href="classCassieIndexer.html#a2839d16de46c5f0b1843f236214b2833">CassieIndexer</a>
</li>
</ul>


<h3><a id="index_g"></a>- g -</h3><ul>
<li>getCharAtSuffix()
: <a class="el" href="classCassieIndexer.html#a47a624ee9b7c108d965af6f3e10d8c59">CassieIndexer</a>
</li>
<li>getSuffix()
: <a class="el" href="classCassieIndexer.html#adbfbc9c4c3b73d7e3300347faa40bfb1">CassieIndexer</a>
</li>
<li>getTree()
: <a class="el" href="classCassieIndexer.html#a149883d1037f6a7246e47536717ec98a">CassieIndexer</a>
</li>
<li>graph()
: <a class="el" href="classCassieIndexer.html#a03a3bf5690b95a241ac270a74895ab6d">CassieIndexer</a>
</li>
</ul>


<h3><a id="index_i"></a>- i -</h3><ul>
<li>in
: <a class="el" href="classMatch.html#aa88040760fb141bd06119335a6224599">Match</a>
</li>
<li>index()
: <a class="el" href="classCassieIndexer.html#a421f7d6a4a1056529bbf50667afdeba3">CassieIndexer</a>
</li>
<li>index_loaded_from_file()
: <a class="el" href="classCassieIndexer.html#a8efad6379cef074e8922698e4c7840b1">CassieIndexer</a>
</li>
<li>isequal()
: <a class="el" href="classAmbiguous.html#acf06ed5199258d399b4899a06cda11a6">Ambiguous</a>
, <a class="el" href="classCassieSearch.html#a96fcf0c3c1e61e54992a0f9c500ee159">CassieSearch</a>
</li>
</ul>


<h3><a id="index_l"></a>- l -</h3><ul>
<li>load()
: <a class="el" href="classCassieIndexer.html#aa7c7d09f58a6fb3bafe015656b0d6911">CassieIndexer</a>
</li>
</ul>


<h3><a id="index_m"></a>- m -</h3><ul>
<li>match_limits
: <a class="el" href="classCassieSearch.html#a7a255b24d1a8105aa65cfbef424ac9b4">CassieSearch</a>
</li>
<li>matches
: <a class="el" href="classCassieIndexer.html#a9bcb8811e2179ec6a22e69497f6158c5">CassieIndexer</a>
, <a class="el" href="classCassieSearch.html#ada26ba9785a133260873a878585d9601">CassieSearch</a>
</li>
<li>max_depth
: <a class="el" href="classCassieIndexer.html#a3826371cabc94c7165b042661601642f">CassieIndexer</a>
</li>
<li>max_indel
: <a class="el" href="classCassieSearch.html#aa075533c107d532be5366ac760cc4822">CassieSearch</a>
</li>
<li>max_index_depth
: <a class="el" href="classCassieIndexer.html#a21c8aab233976b1ea2cface6fae59119">CassieIndexer</a>
</li>
<li>max_subst
: <a class="el" href="classCassieSearch.html#af96f96f0438a4b98d2bd92355671bb83">CassieSearch</a>
</li>
<li>mode
: <a class="el" href="classCassieSearch.html#af5c05901c78ae753a583a78e1ed65b41">CassieSearch</a>
</li>
</ul>


<h3><a id="index_n"></a>- n -</h3><ul>
<li>next_length
: <a class="el" href="classTreeNode.html#abcdf798306e96401e94544f87ad914be">TreeNode</a>
</li>
<li>next_pos
: <a class="el" href="classTreeNode.html#ad4653b8cfd5f2fe1d1d2d333545897a6">TreeNode</a>
</li>
<li>nmax
: <a class="el" href="classCassieSearch.html#a730a851a7e6833e6248562e0900a8711">CassieSearch</a>
</li>
</ul>


<h3><a id="index_o"></a>- o -</h3><ul>
<li>operator==()
: <a class="el" href="classMatch.html#a1d33abedbfcdacc9b3f55479fb8c6c75">Match</a>
</li>
</ul>


<h3><a id="index_p"></a>- p -</h3><ul>
<li>positions
: <a class="el" href="classTreeNode.html#ac5aaf0f2dcfdc73ce827bc357fff456f">TreeNode</a>
</li>
</ul>


<h3><a id="index_r"></a>- r -</h3><ul>
<li>removeDuplicates()
: <a class="el" href="classCassieSearch.html#ad30b72b9965e1938b921a8260a027580">CassieSearch</a>
</li>
</ul>


<h3><a id="index_s"></a>- s -</h3><ul>
<li>save()
: <a class="el" href="classCassieIndexer.html#a481f1dd85b429fbf6dc069f28acd2d83">CassieIndexer</a>
</li>
<li>search()
: <a class="el" href="classCassieSearch.html#ac5cf07a153f4021af5a0f511ec93ee8b">CassieSearch</a>
</li>
<li>sort()
: <a class="el" href="classCassieSearch.html#a66106eb57decacbf1ee551d9de72636b">CassieSearch</a>
</li>
<li>subst
: <a class="el" href="classMatch.html#a49c59d7e78506851688892c7834d275c">Match</a>
</li>
</ul>


<h3><a id="index_t"></a>- t -</h3><ul>
<li>transform_fasta()
: <a class="el" href="classCassiopeeUtils.html#a9a4f7ecf4f46ec454de598271be4bca5">CassiopeeUtils</a>
</li>
<li>TreeNode()
: <a class="el" href="classTreeNode.html#a0588566e906d9dc6930cb8d265f2612a">TreeNode</a>
</li>
</ul>
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