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<div id="projectname">Cassiopee
 <span id="projectnumber">1.0</span>
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<div id="projectbrief">Suffix indexer and search tool</div>
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<div class="header">
<div class="summary">
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pub-attribs">Public Attributes</a> |
<a href="classCassieIndexer-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">CassieIndexer Class Reference</div> </div>
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<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:a2c259abfde72f1dfd2cf3b35dc354268"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a2c259abfde72f1dfd2cf3b35dc354268">CassieIndexer</a> (const char *path)</td></tr>
<tr class="separator:a2c259abfde72f1dfd2cf3b35dc354268"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a481f1dd85b429fbf6dc069f28acd2d83"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a481f1dd85b429fbf6dc069f28acd2d83">save</a> ()</td></tr>
<tr class="separator:a481f1dd85b429fbf6dc069f28acd2d83"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa7c7d09f58a6fb3bafe015656b0d6911"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#aa7c7d09f58a6fb3bafe015656b0d6911">load</a> ()</td></tr>
<tr class="separator:aa7c7d09f58a6fb3bafe015656b0d6911"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a03a3bf5690b95a241ac270a74895ab6d"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a03a3bf5690b95a241ac270a74895ab6d">graph</a> ()</td></tr>
<tr class="separator:a03a3bf5690b95a241ac270a74895ab6d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a66b34970351f8666b59b95e49bed23ca"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a66b34970351f8666b59b95e49bed23ca">graph</a> (int depth)</td></tr>
<tr class="separator:a66b34970351f8666b59b95e49bed23ca"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adbfbc9c4c3b73d7e3300347faa40bfb1"><td class="memItemLeft" align="right" valign="top">string </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#adbfbc9c4c3b73d7e3300347faa40bfb1">getSuffix</a> (long pos)</td></tr>
<tr class="separator:adbfbc9c4c3b73d7e3300347faa40bfb1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a421f7d6a4a1056529bbf50667afdeba3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a421f7d6a4a1056529bbf50667afdeba3">index</a> ()</td></tr>
<tr class="separator:a421f7d6a4a1056529bbf50667afdeba3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a149883d1037f6a7246e47536717ec98a"><td class="memItemLeft" align="right" valign="top">tree< <a class="el" href="classTreeNode.html">TreeNode</a> > * </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a149883d1037f6a7246e47536717ec98a">getTree</a> ()</td></tr>
<tr class="separator:a149883d1037f6a7246e47536717ec98a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a47a624ee9b7c108d965af6f3e10d8c59"><td class="memItemLeft" align="right" valign="top">char </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a47a624ee9b7c108d965af6f3e10d8c59">getCharAtSuffix</a> (long pos)</td></tr>
<tr class="separator:a47a624ee9b7c108d965af6f3e10d8c59"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2839d16de46c5f0b1843f236214b2833"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a2839d16de46c5f0b1843f236214b2833">filltree</a> (long pos)</td></tr>
<tr class="separator:a2839d16de46c5f0b1843f236214b2833"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8efad6379cef074e8922698e4c7840b1"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a8efad6379cef074e8922698e4c7840b1">index_loaded_from_file</a> ()</td></tr>
<tr class="separator:a8efad6379cef074e8922698e4c7840b1"><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:a9bcb8811e2179ec6a22e69497f6158c5"><td class="memItemLeft" align="right" valign="top">list< <a class="el" href="classMatch.html">Match</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a9bcb8811e2179ec6a22e69497f6158c5">matches</a></td></tr>
<tr class="separator:a9bcb8811e2179ec6a22e69497f6158c5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a09cce9f97298b7f1f2ccb15435e0719a"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a09cce9f97298b7f1f2ccb15435e0719a">do_reduction</a></td></tr>
<tr class="separator:a09cce9f97298b7f1f2ccb15435e0719a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3826371cabc94c7165b042661601642f"><td class="memItemLeft" align="right" valign="top">long </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a3826371cabc94c7165b042661601642f">max_depth</a></td></tr>
<tr class="separator:a3826371cabc94c7165b042661601642f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a21c8aab233976b1ea2cface6fae59119"><td class="memItemLeft" align="right" valign="top">long </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieIndexer.html#a21c8aab233976b1ea2cface6fae59119">max_index_depth</a></td></tr>
<tr class="separator:a21c8aab233976b1ea2cface6fae59119"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a31bc6eea89b691d0dfae7da7e437031e"><td class="memItemLeft" align="right" valign="top"><a id="a31bc6eea89b691d0dfae7da7e437031e"></a>
long </td><td class="memItemRight" valign="bottom"><b>seq_length</b></td></tr>
<tr class="separator:a31bc6eea89b691d0dfae7da7e437031e"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Cassiopee indexer</p>
<p>Index an input file </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="a2c259abfde72f1dfd2cf3b35dc354268"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a2c259abfde72f1dfd2cf3b35dc354268">◆ </a></span>CassieIndexer()</h2>
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<td class="memname">CassieIndexer::CassieIndexer </td>
<td>(</td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>path</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Main contructor</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">path</td><td>Path to the sequence file, sequence must be a one-line sequence. </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="a2839d16de46c5f0b1843f236214b2833"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a2839d16de46c5f0b1843f236214b2833">◆ </a></span>filltree()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
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<td class="memname">void CassieIndexer::filltree </td>
<td>(</td>
<td class="paramtype">long </td>
<td class="paramname"><em>pos</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Fills suffix tree with input suffix</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pos</td><td>Position of suffix in sequence </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a47a624ee9b7c108d965af6f3e10d8c59"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a47a624ee9b7c108d965af6f3e10d8c59">◆ </a></span>getCharAtSuffix()</h2>
<div class="memitem">
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<td class="memname">char CassieIndexer::getCharAtSuffix </td>
<td>(</td>
<td class="paramtype">long </td>
<td class="paramname"><em>pos</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Get char from suffix located at position pos. </p>
</div>
</div>
<a id="adbfbc9c4c3b73d7e3300347faa40bfb1"></a>
<h2 class="memtitle"><span class="permalink"><a href="#adbfbc9c4c3b73d7e3300347faa40bfb1">◆ </a></span>getSuffix()</h2>
<div class="memitem">
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<td class="memname">string CassieIndexer::getSuffix </td>
<td>(</td>
<td class="paramtype">long </td>
<td class="paramname"><em>pos</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Get the suffix content from a position</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">pos</td><td>Position in the file </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>the suffix string </dd></dl>
</div>
</div>
<a id="a149883d1037f6a7246e47536717ec98a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a149883d1037f6a7246e47536717ec98a">◆ </a></span>getTree()</h2>
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<table class="memname">
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<td class="memname">tree< <a class="el" href="classTreeNode.html">TreeNode</a> > * CassieIndexer::getTree </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Get the tree matching the indexed sequence </p>
</div>
</div>
<a id="a03a3bf5690b95a241ac270a74895ab6d"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a03a3bf5690b95a241ac270a74895ab6d">◆ </a></span>graph() <span class="overload">[1/2]</span></h2>
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<td class="memname">void CassieIndexer::graph </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Generates a dot file representing the tree. </p>
</div>
</div>
<a id="a66b34970351f8666b59b95e49bed23ca"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a66b34970351f8666b59b95e49bed23ca">◆ </a></span>graph() <span class="overload">[2/2]</span></h2>
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<td class="memname">void CassieIndexer::graph </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>depth</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Generates a dot file representing the tree up to depth</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">depth</td><td>Max depth to print </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a421f7d6a4a1056529bbf50667afdeba3"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a421f7d6a4a1056529bbf50667afdeba3">◆ </a></span>index()</h2>
<div class="memitem">
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<td class="memname">void CassieIndexer::index </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Launch the indexation of the input sequence </p>
</div>
</div>
<a id="a8efad6379cef074e8922698e4c7840b1"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8efad6379cef074e8922698e4c7840b1">◆ </a></span>index_loaded_from_file()</h2>
<div class="memitem">
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<td class="memname">bool CassieIndexer::index_loaded_from_file </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Checks if index has been loaded from a saved index or if index has been build dynamically </p>
</div>
</div>
<a id="aa7c7d09f58a6fb3bafe015656b0d6911"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aa7c7d09f58a6fb3bafe015656b0d6911">◆ </a></span>load()</h2>
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<td class="memname">void CassieIndexer::load </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Load index from a file </p>
</div>
</div>
<a id="a481f1dd85b429fbf6dc069f28acd2d83"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a481f1dd85b429fbf6dc069f28acd2d83">◆ </a></span>save()</h2>
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<td class="memname">void CassieIndexer::save </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Save the index in a file </p>
</div>
</div>
<h2 class="groupheader">Member Data Documentation</h2>
<a id="a09cce9f97298b7f1f2ccb15435e0719a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a09cce9f97298b7f1f2ccb15435e0719a">◆ </a></span>do_reduction</h2>
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<td class="memname">bool CassieIndexer::do_reduction</td>
</tr>
</table>
</div><div class="memdoc">
<p>Allow tree reduction </p>
</div>
</div>
<a id="a9bcb8811e2179ec6a22e69497f6158c5"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a9bcb8811e2179ec6a22e69497f6158c5">◆ </a></span>matches</h2>
<div class="memitem">
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<td class="memname">list<<a class="el" href="classMatch.html">Match</a>> CassieIndexer::matches</td>
</tr>
</table>
</div><div class="memdoc">
<p>List of positions in original sequence matching the search </p>
</div>
</div>
<a id="a3826371cabc94c7165b042661601642f"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a3826371cabc94c7165b042661601642f">◆ </a></span>max_depth</h2>
<div class="memitem">
<div class="memproto">
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<td class="memname">long CassieIndexer::max_depth</td>
</tr>
</table>
</div><div class="memdoc">
<p>Max depth to graph </p>
</div>
</div>
<a id="a21c8aab233976b1ea2cface6fae59119"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a21c8aab233976b1ea2cface6fae59119">◆ </a></span>max_index_depth</h2>
<div class="memitem">
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<td class="memname">long CassieIndexer::max_index_depth</td>
</tr>
</table>
</div><div class="memdoc">
<p>Max depth to index, can limit index size if pattern to search are known of a maximum size </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>
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