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<title>Cassiopee: CassieSearch Class Reference</title>
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<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>
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var searchBox = new SearchBox("searchBox", "search",false,'Search');
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$(document).ready(function() { init_search(); });
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onmouseover="return searchBox.OnSearchSelectShow()"
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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="classCassieSearch-members.html">List of all members</a> </div>
<div class="headertitle">
<div class="title">CassieSearch 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:af63d70d0891eb7f063a1def5caf0e6c6"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#af63d70d0891eb7f063a1def5caf0e6c6">CassieSearch</a> (<a class="el" href="classCassieIndexer.html">CassieIndexer</a> *index_ref)</td></tr>
<tr class="separator:af63d70d0891eb7f063a1def5caf0e6c6"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad30b72b9965e1938b921a8260a027580"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#ad30b72b9965e1938b921a8260a027580">removeDuplicates</a> ()</td></tr>
<tr class="separator:ad30b72b9965e1938b921a8260a027580"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac5cf07a153f4021af5a0f511ec93ee8b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#ac5cf07a153f4021af5a0f511ec93ee8b">search</a> (string suffix, bool clear)</td></tr>
<tr class="separator:ac5cf07a153f4021af5a0f511ec93ee8b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5b3d92321ddb079559dc7cf53eb74563"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#a5b3d92321ddb079559dc7cf53eb74563">search</a> (string suffix)</td></tr>
<tr class="separator:a5b3d92321ddb079559dc7cf53eb74563"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aeda2101931351dd1f96dd4c250686fde"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#aeda2101931351dd1f96dd4c250686fde">search</a> (string suffixes[])</td></tr>
<tr class="separator:aeda2101931351dd1f96dd4c250686fde"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a96fcf0c3c1e61e54992a0f9c500ee159"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#a96fcf0c3c1e61e54992a0f9c500ee159">isequal</a> (char a, char b)</td></tr>
<tr class="separator:a96fcf0c3c1e61e54992a0f9c500ee159"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a66106eb57decacbf1ee551d9de72636b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#a66106eb57decacbf1ee551d9de72636b">sort</a> ()</td></tr>
<tr class="separator:a66106eb57decacbf1ee551d9de72636b"><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:a7a255b24d1a8105aa65cfbef424ac9b4"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classMatch.html">Match</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#a7a255b24d1a8105aa65cfbef424ac9b4">match_limits</a></td></tr>
<tr class="separator:a7a255b24d1a8105aa65cfbef424ac9b4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ada26ba9785a133260873a878585d9601"><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="classCassieSearch.html#ada26ba9785a133260873a878585d9601">matches</a></td></tr>
<tr class="separator:ada26ba9785a133260873a878585d9601"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad14e3b94ac939780540c181d0ed61ecd"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#ad14e3b94ac939780540c181d0ed61ecd">ambiguity</a></td></tr>
<tr class="separator:ad14e3b94ac939780540c181d0ed61ecd"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a730a851a7e6833e6248562e0900a8711"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#a730a851a7e6833e6248562e0900a8711">nmax</a></td></tr>
<tr class="separator:a730a851a7e6833e6248562e0900a8711"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af5c05901c78ae753a583a78e1ed65b41"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#af5c05901c78ae753a583a78e1ed65b41">mode</a></td></tr>
<tr class="separator:af5c05901c78ae753a583a78e1ed65b41"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa075533c107d532be5366ac760cc4822"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#aa075533c107d532be5366ac760cc4822">max_indel</a></td></tr>
<tr class="separator:aa075533c107d532be5366ac760cc4822"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af96f96f0438a4b98d2bd92355671bb83"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classCassieSearch.html#af96f96f0438a4b98d2bd92355671bb83">max_subst</a></td></tr>
<tr class="separator:af96f96f0438a4b98d2bd92355671bb83"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aadc44a312485a4febf246b89610567d4"><td class="memItemLeft" align="right" valign="top"><a id="aadc44a312485a4febf246b89610567d4"></a>
long </td><td class="memItemRight" valign="bottom"><b>pattern_length</b></td></tr>
<tr class="separator:aadc44a312485a4febf246b89610567d4"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Search object </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
<a id="af63d70d0891eb7f063a1def5caf0e6c6"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af63d70d0891eb7f063a1def5caf0e6c6">◆ </a></span>CassieSearch()</h2>
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<div class="memproto">
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<td class="memname">CassieSearch::CassieSearch </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classCassieIndexer.html">CassieIndexer</a> * </td>
<td class="paramname"><em>index_ref</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Main constructor</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">index_ref</td><td>Indexer for sequence </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a id="a96fcf0c3c1e61e54992a0f9c500ee159"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a96fcf0c3c1e61e54992a0f9c500ee159">◆ </a></span>isequal()</h2>
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<td class="memname">bool CassieSearch::isequal </td>
<td>(</td>
<td class="paramtype">char </td>
<td class="paramname"><em>a</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">char </td>
<td class="paramname"><em>b</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Compare two chars, with ambiguity is option is set </p>
</div>
</div>
<a id="ad30b72b9965e1938b921a8260a027580"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ad30b72b9965e1938b921a8260a027580">◆ </a></span>removeDuplicates()</h2>
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<td class="memname">void CassieSearch::removeDuplicates </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Remove matches with same position and same length. </p>
</div>
</div>
<a id="ac5cf07a153f4021af5a0f511ec93ee8b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ac5cf07a153f4021af5a0f511ec93ee8b">◆ </a></span>search() <span class="overload">[1/3]</span></h2>
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<td class="memname">void CassieSearch::search </td>
<td>(</td>
<td class="paramtype">string </td>
<td class="paramname"><em>suffix</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>clear</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Search for a string in the indexed sequence</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">suffix</td><td>pattern to search </td></tr>
<tr><td class="paramname">clear</td><td>Clear existing matches? </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a5b3d92321ddb079559dc7cf53eb74563"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5b3d92321ddb079559dc7cf53eb74563">◆ </a></span>search() <span class="overload">[2/3]</span></h2>
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<td class="memname">void CassieSearch::search </td>
<td>(</td>
<td class="paramtype">string </td>
<td class="paramname"><em>suffix</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Search for a string in the indexed sequence. Clear all previous matches.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">suffix</td><td>pattern to search </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="aeda2101931351dd1f96dd4c250686fde"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aeda2101931351dd1f96dd4c250686fde">◆ </a></span>search() <span class="overload">[3/3]</span></h2>
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<td class="memname">void CassieSearch::search </td>
<td>(</td>
<td class="paramtype">string </td>
<td class="paramname"><em>suffixes</em>[]</td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Search for multiple strings</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">array</td><td>of patterns to search </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a66106eb57decacbf1ee551d9de72636b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a66106eb57decacbf1ee551d9de72636b">◆ </a></span>sort()</h2>
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<td class="memname">void CassieSearch::sort </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Sort matches according to positions i nascending order </p>
</div>
</div>
<h2 class="groupheader">Member Data Documentation</h2>
<a id="ad14e3b94ac939780540c181d0ed61ecd"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ad14e3b94ac939780540c181d0ed61ecd">◆ </a></span>ambiguity</h2>
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<td class="memname">bool CassieSearch::ambiguity</td>
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</table>
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<p>Allow alphabet ambiguity search. False by default. N are by default ignored. To allow N matching, the nmax attribute must be set </p>
</div>
</div>
<a id="a7a255b24d1a8105aa65cfbef424ac9b4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a7a255b24d1a8105aa65cfbef424ac9b4">◆ </a></span>match_limits</h2>
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<td class="memname"><a class="el" href="classMatch.html">Match</a>* CassieSearch::match_limits</td>
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</table>
</div><div class="memdoc">
<p>Used to store max errors allowed </p>
</div>
</div>
<a id="ada26ba9785a133260873a878585d9601"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ada26ba9785a133260873a878585d9601">◆ </a></span>matches</h2>
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<td class="memname">list<<a class="el" href="classMatch.html">Match</a>*> CassieSearch::matches</td>
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<p>List of positions in original sequence matching the search </p>
</div>
</div>
<a id="aa075533c107d532be5366ac760cc4822"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aa075533c107d532be5366ac760cc4822">◆ </a></span>max_indel</h2>
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<td class="memname">int CassieSearch::max_indel</td>
</tr>
</table>
</div><div class="memdoc">
<p>Maximum number of insertion or deletion </p>
</div>
</div>
<a id="af96f96f0438a4b98d2bd92355671bb83"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af96f96f0438a4b98d2bd92355671bb83">◆ </a></span>max_subst</h2>
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<td class="memname">int CassieSearch::max_subst</td>
</tr>
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<p>Maximum number of substitution </p>
</div>
</div>
<a id="af5c05901c78ae753a583a78e1ed65b41"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af5c05901c78ae753a583a78e1ed65b41">◆ </a></span>mode</h2>
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<td class="memname">int CassieSearch::mode</td>
</tr>
</table>
</div><div class="memdoc">
<p>Search mode:</p>
<ul>
<li>0: DNA</li>
<li>1: RNA</li>
<li>2: Protein </li>
</ul>
</div>
</div>
<a id="a730a851a7e6833e6248562e0900a8711"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a730a851a7e6833e6248562e0900a8711">◆ </a></span>nmax</h2>
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<td class="memname">int CassieSearch::nmax</td>
</tr>
</table>
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<p>Allow N matching with alphabet ambiguity. nmax defines the maximum number of consecutive N allowed in match. </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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