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<li class="navelem"><a class="el" href="namespace_bam_tools.html">BamTools</a></li><li class="navelem"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html">SamSequenceDictionary</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<p>Container of <a class="el" href="struct_bam_tools_1_1_sam_sequence.html" title="Represents a SAM sequence entry. ">SamSequence</a> entries.
<a href="class_bam_tools_1_1_sam_sequence_dictionary.html#details">More...</a></p>
<p><code>#include <<a class="el" href="_sam_sequence_dictionary_8h_source.html">SamSequenceDictionary.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:ab399b241a263bd8ebce0882b6487d505"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#ab399b241a263bd8ebce0882b6487d505">SamSequenceDictionary</a> (void)</td></tr>
<tr class="memdesc:ab399b241a263bd8ebce0882b6487d505"><td class="mdescLeft"> </td><td class="mdescRight">constructor <a href="#ab399b241a263bd8ebce0882b6487d505">More...</a><br /></td></tr>
<tr class="separator:ab399b241a263bd8ebce0882b6487d505"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6a0d705a286a708f2419fd51ff854fed"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a6a0d705a286a708f2419fd51ff854fed">SamSequenceDictionary</a> (const <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html">SamSequenceDictionary</a> &other)</td></tr>
<tr class="memdesc:a6a0d705a286a708f2419fd51ff854fed"><td class="mdescLeft"> </td><td class="mdescRight">copy constructor <a href="#a6a0d705a286a708f2419fd51ff854fed">More...</a><br /></td></tr>
<tr class="separator:a6a0d705a286a708f2419fd51ff854fed"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aac6817f77a73450387eb9c1eefda361a"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#aac6817f77a73450387eb9c1eefda361a">~SamSequenceDictionary</a> (void)</td></tr>
<tr class="memdesc:aac6817f77a73450387eb9c1eefda361a"><td class="mdescLeft"> </td><td class="mdescRight">destructor <a href="#aac6817f77a73450387eb9c1eefda361a">More...</a><br /></td></tr>
<tr class="separator:aac6817f77a73450387eb9c1eefda361a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8923d4d50ecae78117387369c3c01e80"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a8923d4d50ecae78117387369c3c01e80">Add</a> (const <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> &sequence)</td></tr>
<tr class="memdesc:a8923d4d50ecae78117387369c3c01e80"><td class="mdescLeft"> </td><td class="mdescRight">Appends a sequence to the dictionary. <a href="#a8923d4d50ecae78117387369c3c01e80">More...</a><br /></td></tr>
<tr class="separator:a8923d4d50ecae78117387369c3c01e80"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a2ffecfe6dd28cb56e1fb65d81221730e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a2ffecfe6dd28cb56e1fb65d81221730e">Add</a> (const std::string &name, const int &length)</td></tr>
<tr class="memdesc:a2ffecfe6dd28cb56e1fb65d81221730e"><td class="mdescLeft"> </td><td class="mdescRight">Appends a sequence to the dictionary. <a href="#a2ffecfe6dd28cb56e1fb65d81221730e">More...</a><br /></td></tr>
<tr class="separator:a2ffecfe6dd28cb56e1fb65d81221730e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8d2bfed8df28aeb053c2156528dfc271"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a8d2bfed8df28aeb053c2156528dfc271">Add</a> (const <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html">SamSequenceDictionary</a> &sequences)</td></tr>
<tr class="memdesc:a8d2bfed8df28aeb053c2156528dfc271"><td class="mdescLeft"> </td><td class="mdescRight">Appends another sequence dictionary to this one. <a href="#a8d2bfed8df28aeb053c2156528dfc271">More...</a><br /></td></tr>
<tr class="separator:a8d2bfed8df28aeb053c2156528dfc271"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5722d0129d953534f7874ed80630c35b"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a5722d0129d953534f7874ed80630c35b">Add</a> (const std::vector< <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> > &sequences)</td></tr>
<tr class="memdesc:a5722d0129d953534f7874ed80630c35b"><td class="mdescLeft"> </td><td class="mdescRight">Appends multiple sequences to the dictionary. <a href="#a5722d0129d953534f7874ed80630c35b">More...</a><br /></td></tr>
<tr class="separator:a5722d0129d953534f7874ed80630c35b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a969636fd9c2422c2704d3ff010b50255"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a969636fd9c2422c2704d3ff010b50255">Add</a> (const std::map< std::string, int > &sequenceMap)</td></tr>
<tr class="memdesc:a969636fd9c2422c2704d3ff010b50255"><td class="mdescLeft"> </td><td class="mdescRight">Appends multiple sequences to the dictionary. <a href="#a969636fd9c2422c2704d3ff010b50255">More...</a><br /></td></tr>
<tr class="separator:a969636fd9c2422c2704d3ff010b50255"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab5f1c55fa25c85a6b112fef669644f15"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#ab5f1c55fa25c85a6b112fef669644f15">Clear</a> (void)</td></tr>
<tr class="memdesc:ab5f1c55fa25c85a6b112fef669644f15"><td class="mdescLeft"> </td><td class="mdescRight">Clears all sequence entries. <a href="#ab5f1c55fa25c85a6b112fef669644f15">More...</a><br /></td></tr>
<tr class="separator:ab5f1c55fa25c85a6b112fef669644f15"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a07a9db64543d83e9f5ea4c3fd60fb879"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a07a9db64543d83e9f5ea4c3fd60fb879">Contains</a> (const <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> &sequence) const</td></tr>
<tr class="memdesc:a07a9db64543d83e9f5ea4c3fd60fb879"><td class="mdescLeft"> </td><td class="mdescRight">Returns true if dictionary contains sequence (matches on name). <a href="#a07a9db64543d83e9f5ea4c3fd60fb879">More...</a><br /></td></tr>
<tr class="separator:a07a9db64543d83e9f5ea4c3fd60fb879"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aff18163f91950c1357540bd465b587d3"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#aff18163f91950c1357540bd465b587d3">Contains</a> (const std::string &sequenceName) const</td></tr>
<tr class="memdesc:aff18163f91950c1357540bd465b587d3"><td class="mdescLeft"> </td><td class="mdescRight">Returns true if dictionary contains sequence. <a href="#aff18163f91950c1357540bd465b587d3">More...</a><br /></td></tr>
<tr class="separator:aff18163f91950c1357540bd465b587d3"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a28eb68e5e7d6a0b5fb212482851d1f60"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a28eb68e5e7d6a0b5fb212482851d1f60">IsEmpty</a> (void) const</td></tr>
<tr class="memdesc:a28eb68e5e7d6a0b5fb212482851d1f60"><td class="mdescLeft"> </td><td class="mdescRight">Returns <code>true</code> if dictionary contains no sequences. <a href="#a28eb68e5e7d6a0b5fb212482851d1f60">More...</a><br /></td></tr>
<tr class="separator:a28eb68e5e7d6a0b5fb212482851d1f60"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a415299173023d7960b0d539eaeebee07"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a415299173023d7960b0d539eaeebee07">Remove</a> (const <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> &sequence)</td></tr>
<tr class="memdesc:a415299173023d7960b0d539eaeebee07"><td class="mdescLeft"> </td><td class="mdescRight">Removes sequence from dictionary, if found (matches on name). <a href="#a415299173023d7960b0d539eaeebee07">More...</a><br /></td></tr>
<tr class="separator:a415299173023d7960b0d539eaeebee07"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad1de8f1c41355973678506853ee088ca"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#ad1de8f1c41355973678506853ee088ca">Remove</a> (const std::string &sequenceName)</td></tr>
<tr class="memdesc:ad1de8f1c41355973678506853ee088ca"><td class="mdescLeft"> </td><td class="mdescRight">Removes sequence from dictionary, if found. <a href="#ad1de8f1c41355973678506853ee088ca">More...</a><br /></td></tr>
<tr class="separator:ad1de8f1c41355973678506853ee088ca"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a1cf18da743407b1d3d562a71a56ef09e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a1cf18da743407b1d3d562a71a56ef09e">Remove</a> (const std::vector< <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> > &sequences)</td></tr>
<tr class="memdesc:a1cf18da743407b1d3d562a71a56ef09e"><td class="mdescLeft"> </td><td class="mdescRight">Removes multiple sequences from dictionary. <a href="#a1cf18da743407b1d3d562a71a56ef09e">More...</a><br /></td></tr>
<tr class="separator:a1cf18da743407b1d3d562a71a56ef09e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a44b5cc63517b55bade6bd64423c81f01"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a44b5cc63517b55bade6bd64423c81f01">Remove</a> (const std::vector< std::string > &sequenceNames)</td></tr>
<tr class="memdesc:a44b5cc63517b55bade6bd64423c81f01"><td class="mdescLeft"> </td><td class="mdescRight">Removes multiple sequences from dictionary. <a href="#a44b5cc63517b55bade6bd64423c81f01">More...</a><br /></td></tr>
<tr class="separator:a44b5cc63517b55bade6bd64423c81f01"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6b9e73245ea8199577f2fd944c276d0d"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a6b9e73245ea8199577f2fd944c276d0d">Size</a> (void) const</td></tr>
<tr class="memdesc:a6b9e73245ea8199577f2fd944c276d0d"><td class="mdescLeft"> </td><td class="mdescRight">Returns number of sequences in dictionary. <a href="#a6b9e73245ea8199577f2fd944c276d0d">More...</a><br /></td></tr>
<tr class="separator:a6b9e73245ea8199577f2fd944c276d0d"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac1a53cc4e0499d5e548993a902a5aa32"><td class="memItemLeft" align="right" valign="top"><a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#ac1a53cc4e0499d5e548993a902a5aa32">operator[]</a> (const std::string &sequenceName)</td></tr>
<tr class="memdesc:ac1a53cc4e0499d5e548993a902a5aa32"><td class="mdescLeft"> </td><td class="mdescRight">Retrieves the modifiable <a class="el" href="struct_bam_tools_1_1_sam_sequence.html" title="Represents a SAM sequence entry. ">SamSequence</a> that matches <em>sequenceName</em>. <a href="#ac1a53cc4e0499d5e548993a902a5aa32">More...</a><br /></td></tr>
<tr class="separator:ac1a53cc4e0499d5e548993a902a5aa32"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa751a16ecf3363966a0e06f28dd163dc"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespace_bam_tools.html#a80bfb49ef575b0fc7b9b4fa111f47308">SamSequenceIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#aa751a16ecf3363966a0e06f28dd163dc">Begin</a> (void)</td></tr>
<tr class="separator:aa751a16ecf3363966a0e06f28dd163dc"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0f267a26d796f075ebe0309ca6465e5e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespace_bam_tools.html#a6a7821c6bf43e5e9b3ea2b2216554360">SamSequenceConstIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a0f267a26d796f075ebe0309ca6465e5e">Begin</a> (void) const</td></tr>
<tr class="separator:a0f267a26d796f075ebe0309ca6465e5e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a46bf50d51b95aec15776a69356486baa"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespace_bam_tools.html#a6a7821c6bf43e5e9b3ea2b2216554360">SamSequenceConstIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a46bf50d51b95aec15776a69356486baa">ConstBegin</a> (void) const</td></tr>
<tr class="separator:a46bf50d51b95aec15776a69356486baa"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5ec55747eeb43d2c9684b21c4fb54cac"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespace_bam_tools.html#a80bfb49ef575b0fc7b9b4fa111f47308">SamSequenceIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a5ec55747eeb43d2c9684b21c4fb54cac">End</a> (void)</td></tr>
<tr class="separator:a5ec55747eeb43d2c9684b21c4fb54cac"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abeda49771289614fcbe50253b1287e21"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespace_bam_tools.html#a6a7821c6bf43e5e9b3ea2b2216554360">SamSequenceConstIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#abeda49771289614fcbe50253b1287e21">End</a> (void) const</td></tr>
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<tr class="memitem:ae806b3dad8fee543be4c15b97aaf6cf3"><td class="memItemLeft" align="right" valign="top"><a class="el" href="namespace_bam_tools.html#a6a7821c6bf43e5e9b3ea2b2216554360">SamSequenceConstIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#ae806b3dad8fee543be4c15b97aaf6cf3">ConstEnd</a> (void) const</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Container of <a class="el" href="struct_bam_tools_1_1_sam_sequence.html" title="Represents a SAM sequence entry. ">SamSequence</a> entries. </p>
<p>Provides methods for operating on a collection of <a class="el" href="struct_bam_tools_1_1_sam_sequence.html" title="Represents a SAM sequence entry. ">SamSequence</a> entries. </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#ab399b241a263bd8ebce0882b6487d505">◆ </a></span>SamSequenceDictionary() <span class="overload">[1/2]</span></h2>
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<td class="memname">SamSequenceDictionary::SamSequenceDictionary </td>
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<td class="paramtype">void </td>
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<p>constructor </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a6a0d705a286a708f2419fd51ff854fed">◆ </a></span>SamSequenceDictionary() <span class="overload">[2/2]</span></h2>
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<td class="memname">SamSequenceDictionary::SamSequenceDictionary </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html">SamSequenceDictionary</a> & </td>
<td class="paramname"><em>other</em></td><td>)</td>
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<p>copy constructor </p>
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<h2 class="memtitle"><span class="permalink"><a href="#aac6817f77a73450387eb9c1eefda361a">◆ </a></span>~SamSequenceDictionary()</h2>
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<td class="memname">SamSequenceDictionary::~SamSequenceDictionary </td>
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<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
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<p>destructor </p>
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<h2 class="groupheader">Member Function Documentation</h2>
<a id="a8923d4d50ecae78117387369c3c01e80"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8923d4d50ecae78117387369c3c01e80">◆ </a></span>Add() <span class="overload">[1/5]</span></h2>
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<td class="memname">void SamSequenceDictionary::Add </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> & </td>
<td class="paramname"><em>sequence</em></td><td>)</td>
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<p>Appends a sequence to the dictionary. </p>
<p>Duplicate entries are silently discarded.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">sequence</td><td>entry to be added </td></tr>
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</dd>
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<h2 class="memtitle"><span class="permalink"><a href="#a2ffecfe6dd28cb56e1fb65d81221730e">◆ </a></span>Add() <span class="overload">[2/5]</span></h2>
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<td class="memname">void SamSequenceDictionary::Add </td>
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<td class="paramtype">const std::string & </td>
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<td class="paramtype">const int & </td>
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<p>Appends a sequence to the dictionary. </p>
<p>This is an overloaded function.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">name</td><td>name of sequence entry to be added </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">length</td><td>length of sequence entry to be added </td></tr>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a8923d4d50ecae78117387369c3c01e80" title="Appends a sequence to the dictionary. ">Add()</a> </dd></dl>
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<td class="memname">void SamSequenceDictionary::Add </td>
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<td class="paramtype">const <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html">SamSequenceDictionary</a> & </td>
<td class="paramname"><em>sequences</em></td><td>)</td>
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<p>Appends another sequence dictionary to this one. </p>
<p>This is an overloaded function.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">sequences</td><td>sequence dictionary to be appended </td></tr>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a8923d4d50ecae78117387369c3c01e80" title="Appends a sequence to the dictionary. ">Add()</a> </dd></dl>
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<td class="memname">void SamSequenceDictionary::Add </td>
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<td class="paramtype">const std::vector< <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> > & </td>
<td class="paramname"><em>sequences</em></td><td>)</td>
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<p>Appends multiple sequences to the dictionary. </p>
<p>This is an overloaded function.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">sequences</td><td>entries to be added </td></tr>
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</dd>
</dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a8923d4d50ecae78117387369c3c01e80" title="Appends a sequence to the dictionary. ">Add()</a> </dd></dl>
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<td class="memname">void SamSequenceDictionary::Add </td>
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<td class="paramtype">const std::map< std::string, int > & </td>
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<p>Appends multiple sequences to the dictionary. </p>
<p>This is an overloaded function.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">sequenceMap</td><td>map of sequence entries (name => length) to be added </td></tr>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a8923d4d50ecae78117387369c3c01e80" title="Appends a sequence to the dictionary. ">Add()</a> </dd></dl>
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<td class="memname"><a class="el" href="namespace_bam_tools.html#a80bfb49ef575b0fc7b9b4fa111f47308">SamSequenceIterator</a> SamSequenceDictionary::Begin </td>
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<dl class="section return"><dt>Returns</dt><dd>an STL iterator pointing to the first sequence </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a46bf50d51b95aec15776a69356486baa">ConstBegin()</a>, <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a5ec55747eeb43d2c9684b21c4fb54cac">End()</a> </dd></dl>
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<td class="memname"><a class="el" href="namespace_bam_tools.html#a6a7821c6bf43e5e9b3ea2b2216554360">SamSequenceConstIterator</a> SamSequenceDictionary::Begin </td>
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<dl class="section return"><dt>Returns</dt><dd>an STL const_iterator pointing to the first sequence</dd></dl>
<p>This is an overloaded function.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a46bf50d51b95aec15776a69356486baa">ConstBegin()</a>, <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a5ec55747eeb43d2c9684b21c4fb54cac">End()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ab5f1c55fa25c85a6b112fef669644f15">◆ </a></span>Clear()</h2>
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<td class="memname">void SamSequenceDictionary::Clear </td>
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<p>Clears all sequence entries. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a46bf50d51b95aec15776a69356486baa">◆ </a></span>ConstBegin()</h2>
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<td class="memname"><a class="el" href="namespace_bam_tools.html#a6a7821c6bf43e5e9b3ea2b2216554360">SamSequenceConstIterator</a> SamSequenceDictionary::ConstBegin </td>
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<dl class="section return"><dt>Returns</dt><dd>an STL const_iterator pointing to the first sequence </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#aa751a16ecf3363966a0e06f28dd163dc">Begin()</a>, <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#ae806b3dad8fee543be4c15b97aaf6cf3">ConstEnd()</a> </dd></dl>
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<td class="memname"><a class="el" href="namespace_bam_tools.html#a6a7821c6bf43e5e9b3ea2b2216554360">SamSequenceConstIterator</a> SamSequenceDictionary::ConstEnd </td>
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<dl class="section return"><dt>Returns</dt><dd>an STL const_iterator pointing to the imaginary entry after the last sequence </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a5ec55747eeb43d2c9684b21c4fb54cac">End()</a>, <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a46bf50d51b95aec15776a69356486baa">ConstBegin()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a07a9db64543d83e9f5ea4c3fd60fb879">◆ </a></span>Contains() <span class="overload">[1/2]</span></h2>
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<td class="memname">bool SamSequenceDictionary::Contains </td>
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<td class="paramtype">const <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> & </td>
<td class="paramname"><em>sequence</em></td><td>)</td>
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<p>Returns true if dictionary contains sequence (matches on name). </p>
<p>This is an overloaded function.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">sequence</td><td>search for this sequence </td></tr>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if dictionary contains sequence (matching on name) </dd></dl>
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<p>Returns true if dictionary contains sequence. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">sequenceName</td><td>search for sequence matching this name </td></tr>
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<dl class="section return"><dt>Returns</dt><dd><code>true</code> if dictionary contains a sequence with this name </dd></dl>
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<td class="memname"><a class="el" href="namespace_bam_tools.html#a80bfb49ef575b0fc7b9b4fa111f47308">SamSequenceIterator</a> SamSequenceDictionary::End </td>
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<dl class="section return"><dt>Returns</dt><dd>an STL iterator pointing to the imaginary entry after the last sequence </dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#aa751a16ecf3363966a0e06f28dd163dc">Begin()</a>, <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#ae806b3dad8fee543be4c15b97aaf6cf3">ConstEnd()</a> </dd></dl>
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<td class="memname"><a class="el" href="namespace_bam_tools.html#a6a7821c6bf43e5e9b3ea2b2216554360">SamSequenceConstIterator</a> SamSequenceDictionary::End </td>
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<dl class="section return"><dt>Returns</dt><dd>an STL const_iterator pointing to the imaginary entry after the last sequence</dd></dl>
<p>This is an overloaded function.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#aa751a16ecf3363966a0e06f28dd163dc">Begin()</a>, <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#ae806b3dad8fee543be4c15b97aaf6cf3">ConstEnd()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a28eb68e5e7d6a0b5fb212482851d1f60">◆ </a></span>IsEmpty()</h2>
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<td class="memname">bool SamSequenceDictionary::IsEmpty </td>
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<p>Returns <code>true</code> if dictionary contains no sequences. </p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a6b9e73245ea8199577f2fd944c276d0d" title="Returns number of sequences in dictionary. ">Size()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#ac1a53cc4e0499d5e548993a902a5aa32">◆ </a></span>operator[]()</h2>
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<td class="memname"><a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> & SamSequenceDictionary::operator[] </td>
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<p>Retrieves the modifiable <a class="el" href="struct_bam_tools_1_1_sam_sequence.html" title="Represents a SAM sequence entry. ">SamSequence</a> that matches <em>sequenceName</em>. </p>
<dl class="section note"><dt>Note</dt><dd>If the dictionary contains no sequence matching this name, this function inserts a new one with this name (length:0), and returns a reference to it. If you want to avoid this insertion behavior, check the result of <a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a07a9db64543d83e9f5ea4c3fd60fb879" title="Returns true if dictionary contains sequence (matches on name). ">Contains()</a> before using this operator.</dd></dl>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">sequenceName</td><td>name of sequence to retrieve </td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>a modifiable reference to the <a class="el" href="struct_bam_tools_1_1_sam_sequence.html" title="Represents a SAM sequence entry. ">SamSequence</a> associated with the name </dd></dl>
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<td class="memname">void SamSequenceDictionary::Remove </td>
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<td class="paramtype">const <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> & </td>
<td class="paramname"><em>sequence</em></td><td>)</td>
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<p>Removes sequence from dictionary, if found (matches on name). </p>
<p>This is an overloaded function.</p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">sequence</td><td><a class="el" href="struct_bam_tools_1_1_sam_sequence.html" title="Represents a SAM sequence entry. ">SamSequence</a> to remove (matching on name) </td></tr>
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<a id="ad1de8f1c41355973678506853ee088ca"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ad1de8f1c41355973678506853ee088ca">◆ </a></span>Remove() <span class="overload">[2/4]</span></h2>
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<td class="memname">void SamSequenceDictionary::Remove </td>
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<td class="paramtype">const std::string & </td>
<td class="paramname"><em>sequenceName</em></td><td>)</td>
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<p>Removes sequence from dictionary, if found. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramdir">[in]</td><td class="paramname">sequenceName</td><td>name of sequence to remove </td></tr>
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<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a415299173023d7960b0d539eaeebee07" title="Removes sequence from dictionary, if found (matches on name). ">Remove()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a1cf18da743407b1d3d562a71a56ef09e">◆ </a></span>Remove() <span class="overload">[3/4]</span></h2>
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<td class="memname">void SamSequenceDictionary::Remove </td>
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<td class="paramtype">const std::vector< <a class="el" href="struct_bam_tools_1_1_sam_sequence.html">SamSequence</a> > & </td>
<td class="paramname"><em>sequences</em></td><td>)</td>
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<p>Removes multiple sequences from dictionary. </p>
<p>This is an overloaded function.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">sequences</td><td>sequences to remove </td></tr>
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</dd>
</dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a415299173023d7960b0d539eaeebee07" title="Removes sequence from dictionary, if found (matches on name). ">Remove()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a44b5cc63517b55bade6bd64423c81f01">◆ </a></span>Remove() <span class="overload">[4/4]</span></h2>
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<td class="memname">void SamSequenceDictionary::Remove </td>
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<td class="paramtype">const std::vector< std::string > & </td>
<td class="paramname"><em>sequenceNames</em></td><td>)</td>
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<p>Removes multiple sequences from dictionary. </p>
<p>This is an overloaded function.</p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">sequenceNames</td><td>names of the sequences to remove </td></tr>
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</dd>
</dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a415299173023d7960b0d539eaeebee07" title="Removes sequence from dictionary, if found (matches on name). ">Remove()</a> </dd></dl>
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<h2 class="memtitle"><span class="permalink"><a href="#a6b9e73245ea8199577f2fd944c276d0d">◆ </a></span>Size()</h2>
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<td class="memname">int SamSequenceDictionary::Size </td>
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<td class="paramtype">void </td>
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<p>Returns number of sequences in dictionary. </p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="class_bam_tools_1_1_sam_sequence_dictionary.html#a28eb68e5e7d6a0b5fb212482851d1f60" title="Returns true if dictionary contains no sequences. ">IsEmpty()</a> </dd></dl>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="_sam_sequence_dictionary_8h_source.html">SamSequenceDictionary.h</a></li>
<li><a class="el" href="_sam_sequence_dictionary_8cpp.html">SamSequenceDictionary.cpp</a></li>
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