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commit 6c15190477566e4de97fcdafdd79e29124fb94b9 1 parent 9545828
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145 api/doc/html/classhal_1_1_mapped_segment-members.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">
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+ <ul>
+<li class="navelem"><a class="el" href="namespacehal.html">hal</a></li><li class="navelem"><a class="el" href="classhal_1_1_mapped_segment.html">MappedSegment</a></li> </ul>
+</div>
+</div><!-- top -->
+<div class="header">
+ <div class="headertitle">
+<div class="title">hal::MappedSegment Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html#a7299677ca802d4bee638dd11e06d652f">canMergeRightWith</a>(const MappedSegmentConstPtr &amp;next, const std::set&lt; hal_index_t &gt; *cutSet=NULL, const std::set&lt; hal_index_t &gt; *sourceCutSet=NULL) const =0</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html#a5f8cd3a920643d7e8745d301a59af0e6">copy</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>counted_ptr&lt; const MappedSegment &gt;</b> (defined in <a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
+ <tr bgcolor="#f0f0f0"><td class="entry"><b>counted_ptr&lt; MappedSegment &gt;</b> (defined in <a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html#ae52246d09822b57ffc8079a5a60f2f0c">equals</a>(const MappedSegmentConstPtr &amp;other) const =0</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html#ae4c8d0876bbee74685c555bbc7cc7831">flip</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html#ade25d65bf048734a58282625cdbce50a">fullReverse</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a3c6a484cf611ea099ef20ccb8c75af4e">getArrayIndex</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#a26ebe831b8df1a18e6279c0fc7b4e512">getEndOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#add66d5e2d7fbb0257522542a13a2be5e">getEndPosition</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#ae978b16a83930230677cb5746768b572">getGenome</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#ab81920adf7bb6ff0fc089dfeeca30c14">getGenome</a>()=0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#aed488d7c10618754004ccaeba59e75da">getLength</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a154f2fa2a8740af32f4bdecc4467ae1f">getMappedSegments</a>(std::set&lt; MappedSegmentConstPtr &gt; &amp;outSegments, const Genome *tgtGenome, const std::set&lt; const Genome * &gt; *genomesOnPath=NULL, bool doDupes=true, hal_size_t minLength=0) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#a1644d921373f373ff51acba3db136a09">getReversed</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#aa398caf4f4d673628a663502a563b36f">getSequence</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#a95980d7da83e05210a1ba5fbf34b9d7c">getSequence</a>()=0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html#a522bfa220889a15655f9105f9a2551bb">getSource</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#ae0a230c7b336d92a55dc5fb4084780f6">getStartOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a36330fc97cdce2f5be1b6fe01639a41f">getStartPosition</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#afd6fc6bf7084723134218096aff6414a">getString</a>(std::string &amp;outString) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a3fcce27b6fcebaaa49108f6089ed819e">isFirst</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#a200c3c95017edf7ea0c4aa6a55abc0cc">isLast</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#afbb86ebc35841f1ca301abe8bc9656ab">isMissingData</a>(double nThreshold) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#a0e0b2a7126d492be96940e40dc6178db">isTop</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#ad6c49b546dacd77e8a01b3a8e398abe2">leftOf</a>(hal_index_t genomePos) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html#a9039ac6260e639869e260f10617c862c">lessThan</a>(const MappedSegmentConstPtr &amp;other) const =0</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html#aa1549548942a92640cf7b50f6049565b">lessThanBySource</a>(const MappedSegmentConstPtr &amp;other) const =0</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#aea6d5d0be2f936029e68d03cb31cc171">overlaps</a>(hal_index_t genomePos) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html#ac61e2348b75de0569f8dee856f468d6d">print</a>(std::ostream &amp;os) const =0</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#a66f41bba295d2d2f54c8fc2085171667">rightOf</a>(hal_index_t genomePos) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a2d022759a5136ec9a15ae70bd40a20c9">setArrayIndex</a>(Genome *genome, hal_index_t arrayIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#ad9a39b6d7cd828953b15a06bf6a94ddc">setArrayIndex</a>(const Genome *genome, hal_index_t arrayIndex) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a663be727196999cbb3d4f048f8fac3cc">setCoordinates</a>(hal_index_t startPos, hal_size_t length)=0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#a7263b6a7b8d31dcc834e571137625080">slice</a>(hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#a7c5d0a652d00a0492d36bc3f16acf2a4">toReverse</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#aa5bd93fab081d208cdb0c50dba3021e3">toReverseInPlace</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr bgcolor="#f0f0f0"><td class="entry"><b>~MappedSegment</b>()=0 (defined in <a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_mapped_segment.html">hal::MappedSegment</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span><span class="mlabel">pure virtual</span></td></tr>
+ <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~Segment</b>()=0 (defined in <a class="el" href="classhal_1_1_segment.html">hal::Segment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span><span class="mlabel">pure virtual</span></td></tr>
+ <tr bgcolor="#f0f0f0"><td class="entry"><b>~SlicedSegment</b>()=0 (defined in <a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span><span class="mlabel">pure virtual</span></td></tr>
+</table></div><!-- contents -->
+<!-- start footer part -->
+<hr class="footer"/><address class="footer"><small>
+Generated on Thu Dec 5 2013 15:14:36 for halapi by &#160;<a href="http://www.doxygen.org/index.html">
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+</a> 1.8.5
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+</html>
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+<li class="navelem"><a class="el" href="namespacehal.html">hal</a></li><li class="navelem"><a class="el" href="classhal_1_1_mapped_segment.html">MappedSegment</a></li> </ul>
+</div>
+</div><!-- top -->
+<div class="header">
+ <div class="summary">
+<a href="#nested-classes">Classes</a> &#124;
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#friends">Friends</a> &#124;
+<a href="classhal_1_1_mapped_segment-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">hal::MappedSegment Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span></div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="hal_mapped_segment_8h_source.html">halMappedSegment.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for hal::MappedSegment:</div>
+<div class="dyncontent">
+ <div class="center">
+ <img src="classhal_1_1_mapped_segment.png" usemap="#hal::MappedSegment_map" alt=""/>
+ <map id="hal::MappedSegment_map" name="hal::MappedSegment_map">
+<area href="classhal_1_1_sliced_segment.html" alt="hal::SlicedSegment" shape="rect" coords="0,56,129,80"/>
+<area href="classhal_1_1_segment.html" alt="hal::Segment" shape="rect" coords="0,0,129,24"/>
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+ </div></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
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+<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="structhal_1_1_mapped_segment_1_1_equal_to.html">EqualTo</a></td></tr>
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+<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table><table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
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+<tr class="memitem:a522bfa220889a15655f9105f9a2551bb"><td class="memItemLeft" align="right" valign="top">virtual SlicedSegmentConstPtr&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_mapped_segment.html#a522bfa220889a15655f9105f9a2551bb">getSource</a> () const =0</td></tr>
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+<tr class="separator:a66f41bba295d2d2f54c8fc2085171667 inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aea6d5d0be2f936029e68d03cb31cc171 inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#aea6d5d0be2f936029e68d03cb31cc171">overlaps</a> (hal_index_t genomePos) const =0</td></tr>
+<tr class="separator:aea6d5d0be2f936029e68d03cb31cc171 inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a3fcce27b6fcebaaa49108f6089ed819e inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a3fcce27b6fcebaaa49108f6089ed819e">isFirst</a> () const =0</td></tr>
+<tr class="separator:a3fcce27b6fcebaaa49108f6089ed819e inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a200c3c95017edf7ea0c4aa6a55abc0cc inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a200c3c95017edf7ea0c4aa6a55abc0cc">isLast</a> () const =0</td></tr>
+<tr class="separator:a200c3c95017edf7ea0c4aa6a55abc0cc inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:afbb86ebc35841f1ca301abe8bc9656ab inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#afbb86ebc35841f1ca301abe8bc9656ab">isMissingData</a> (double nThreshold) const =0</td></tr>
+<tr class="separator:afbb86ebc35841f1ca301abe8bc9656ab inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a0e0b2a7126d492be96940e40dc6178db inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a0e0b2a7126d492be96940e40dc6178db">isTop</a> () const =0</td></tr>
+<tr class="separator:a0e0b2a7126d492be96940e40dc6178db inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a154f2fa2a8740af32f4bdecc4467ae1f inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual hal_size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a154f2fa2a8740af32f4bdecc4467ae1f">getMappedSegments</a> (std::set&lt; MappedSegmentConstPtr &gt; &amp;outSegments, const <a class="el" href="classhal_1_1_genome.html">Genome</a> *tgtGenome, const std::set&lt; const <a class="el" href="classhal_1_1_genome.html">Genome</a> * &gt; *genomesOnPath=NULL, bool doDupes=true, hal_size_t minLength=0) const =0</td></tr>
+<tr class="separator:a154f2fa2a8740af32f4bdecc4467ae1f inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</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:aa420af5cdfcc9eca79124bb8e5b3530f"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aa420af5cdfcc9eca79124bb8e5b3530f"></a>
+class&#160;</td><td class="memItemRight" valign="bottom"><b>counted_ptr&lt; MappedSegment &gt;</b></td></tr>
+<tr class="separator:aa420af5cdfcc9eca79124bb8e5b3530f"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aebb1dcd62ff069424d6a749cb725a205"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="aebb1dcd62ff069424d6a749cb725a205"></a>
+class&#160;</td><td class="memItemRight" valign="bottom"><b>counted_ptr&lt; const MappedSegment &gt;</b></td></tr>
+<tr class="separator:aebb1dcd62ff069424d6a749cb725a205"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><p>Interface for a mapped segement. A mapped segment keeps track of a homologous region in another genome (from which it was mapped). Mapped segments are used to keep pairwise alignment fragments across the tree as an alternative to the column iterator. </p>
+</div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a7299677ca802d4bee638dd11e06d652f"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual bool hal::MappedSegment::canMergeRightWith </td>
+ <td>(</td>
+ <td class="paramtype">const MappedSegmentConstPtr &amp;&#160;</td>
+ <td class="paramname"><em>next</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">const std::set&lt; hal_index_t &gt; *&#160;</td>
+ <td class="paramname"><em>cutSet</em> = <code>NULL</code>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">const std::set&lt; hal_index_t &gt; *&#160;</td>
+ <td class="paramname"><em>sourceCutSet</em> = <code>NULL</code>&#160;</td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Test if mapped segment can be merged to the right with input segment. will return false if the right coordinate of this is in either (optional) cutSet. </p>
+
+</div>
+</div>
+<a class="anchor" id="a5f8cd3a920643d7e8745d301a59af0e6"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual MappedSegmentConstPtr hal::MappedSegment::copy </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Return of a copy of the mapped segment </p>
+
+</div>
+</div>
+<a class="anchor" id="ae52246d09822b57ffc8079a5a60f2f0c"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual bool hal::MappedSegment::equals </td>
+ <td>(</td>
+ <td class="paramtype">const MappedSegmentConstPtr &amp;&#160;</td>
+ <td class="paramname"><em>other</em></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Comparison used to determine uniqueness in lists. Tests lessThan in both directions. Note that equality is the same regardless of whether or not we use the source segment as our primary index. </p>
+
+</div>
+</div>
+<a class="anchor" id="ae4c8d0876bbee74685c555bbc7cc7831"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual void hal::MappedSegment::flip </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Flip the mapping direction. This segment becomes the source, and the source becomes this. </p>
+
+</div>
+</div>
+<a class="anchor" id="ade25d65bf048734a58282625cdbce50a"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual void hal::MappedSegment::fullReverse </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Reverse both segments. Also swap their start and end offsets. Note that <a class="el" href="classhal_1_1_sliced_segment.html#a7c5d0a652d00a0492d36bc3f16acf2a4">toReverse()</a> does not reverse the source segment. </p>
+
+</div>
+</div>
+<a class="anchor" id="a522bfa220889a15655f9105f9a2551bb"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual SlicedSegmentConstPtr hal::MappedSegment::getSource </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Get the original segment from which this segment was mapped </p>
+
+</div>
+</div>
+<a class="anchor" id="a9039ac6260e639869e260f10617c862c"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual bool hal::MappedSegment::lessThan </td>
+ <td>(</td>
+ <td class="paramtype">const MappedSegmentConstPtr &amp;&#160;</td>
+ <td class="paramname"><em>other</em></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Comparison used to store in stl sets and maps. We sort based on the coordinate of the mapped segemnt's (target) interval as the primary index and the target genome as the secondary index. </p>
+
+</div>
+</div>
+<a class="anchor" id="aa1549548942a92640cf7b50f6049565b"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual bool hal::MappedSegment::lessThanBySource </td>
+ <td>(</td>
+ <td class="paramtype">const MappedSegmentConstPtr &amp;&#160;</td>
+ <td class="paramname"><em>other</em></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Comparison used to store in STL containers. We sort based on the coordinate of the <em>Source</em> genome interval as the primary index and the target genome as the secondary index. </p>
+
+</div>
+</div>
+<a class="anchor" id="ac61e2348b75de0569f8dee856f468d6d"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual void hal::MappedSegment::print </td>
+ <td>(</td>
+ <td class="paramtype">std::ostream &amp;&#160;</td>
+ <td class="paramname"><em>os</em></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Print contents of segment </p>
+
+<p>Implements <a class="el" href="classhal_1_1_segment.html#a4ecebbc4d405d226abd34267b1650f9c">hal::Segment</a>.</p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>inc/<a class="el" href="hal_mapped_segment_8h_source.html">halMappedSegment.h</a></li>
+</ul>
+</div><!-- contents -->
+<!-- start footer part -->
+<hr class="footer"/><address class="footer"><small>
+Generated on Thu Dec 5 2013 15:14:36 for halapi by &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/>
+</a> 1.8.5
+</small></address>
+</body>
+</html>
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+ <div id="projectname">halapi
+ </div>
+ <div id="projectbrief">hierarchichalalignmentformatapi</div>
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+ <li><a href="index.html"><span>Main&#160;Page</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark">&#160;</span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark">&#160;</span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark">&#160;</span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark">&#160;</span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark">&#160;</span>Pages</a></div>
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+ name="MSearchResults" id="MSearchResults">
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+ <ul>
+<li class="navelem"><a class="el" href="namespacehal.html">hal</a></li><li class="navelem"><a class="el" href="classhal_1_1_sliced_segment.html">SlicedSegment</a></li> </ul>
+</div>
+</div><!-- top -->
+<div class="header">
+ <div class="headertitle">
+<div class="title">hal::SlicedSegment Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a>, including all inherited members.</p>
+<table class="directory">
+ <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>counted_ptr&lt; const SlicedSegment &gt;</b> (defined in <a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
+ <tr bgcolor="#f0f0f0"><td class="entry"><b>counted_ptr&lt; SlicedSegment &gt;</b> (defined in <a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">friend</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#a3c6a484cf611ea099ef20ccb8c75af4e">getArrayIndex</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#a26ebe831b8df1a18e6279c0fc7b4e512">getEndOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#add66d5e2d7fbb0257522542a13a2be5e">getEndPosition</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#ae978b16a83930230677cb5746768b572">getGenome</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#ab81920adf7bb6ff0fc089dfeeca30c14">getGenome</a>()=0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#aed488d7c10618754004ccaeba59e75da">getLength</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#a154f2fa2a8740af32f4bdecc4467ae1f">getMappedSegments</a>(std::set&lt; MappedSegmentConstPtr &gt; &amp;outSegments, const Genome *tgtGenome, const std::set&lt; const Genome * &gt; *genomesOnPath=NULL, bool doDupes=true, hal_size_t minLength=0) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#a1644d921373f373ff51acba3db136a09">getReversed</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#aa398caf4f4d673628a663502a563b36f">getSequence</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a95980d7da83e05210a1ba5fbf34b9d7c">getSequence</a>()=0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#ae0a230c7b336d92a55dc5fb4084780f6">getStartOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a36330fc97cdce2f5be1b6fe01639a41f">getStartPosition</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#afd6fc6bf7084723134218096aff6414a">getString</a>(std::string &amp;outString) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a3fcce27b6fcebaaa49108f6089ed819e">isFirst</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#a200c3c95017edf7ea0c4aa6a55abc0cc">isLast</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#afbb86ebc35841f1ca301abe8bc9656ab">isMissingData</a>(double nThreshold) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#a0e0b2a7126d492be96940e40dc6178db">isTop</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#ad6c49b546dacd77e8a01b3a8e398abe2">leftOf</a>(hal_index_t genomePos) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#aea6d5d0be2f936029e68d03cb31cc171">overlaps</a>(hal_index_t genomePos) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a4ecebbc4d405d226abd34267b1650f9c">print</a>(std::ostream &amp;os) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#a66f41bba295d2d2f54c8fc2085171667">rightOf</a>(hal_index_t genomePos) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a2d022759a5136ec9a15ae70bd40a20c9">setArrayIndex</a>(Genome *genome, hal_index_t arrayIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_segment.html#ad9a39b6d7cd828953b15a06bf6a94ddc">setArrayIndex</a>(const Genome *genome, hal_index_t arrayIndex) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_segment.html#a663be727196999cbb3d4f048f8fac3cc">setCoordinates</a>(hal_index_t startPos, hal_size_t length)=0</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#a7263b6a7b8d31dcc834e571137625080">slice</a>(hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#a7c5d0a652d00a0492d36bc3f16acf2a4">toReverse</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html#aa5bd93fab081d208cdb0c50dba3021e3">toReverseInPlace</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr bgcolor="#f0f0f0"><td class="entry"><b>~Segment</b>()=0 (defined in <a class="el" href="classhal_1_1_segment.html">hal::Segment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span><span class="mlabel">pure virtual</span></td></tr>
+ <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~SlicedSegment</b>()=0 (defined in <a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_sliced_segment.html">hal::SlicedSegment</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">protected</span><span class="mlabel">pure virtual</span></td></tr>
+</table></div><!-- contents -->
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+<li class="navelem"><a class="el" href="namespacehal.html">hal</a></li><li class="navelem"><a class="el" href="classhal_1_1_sliced_segment.html">SlicedSegment</a></li> </ul>
+</div>
+</div><!-- top -->
+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> &#124;
+<a href="#friends">Friends</a> &#124;
+<a href="classhal_1_1_sliced_segment-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">hal::SlicedSegment Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span></div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p><code>#include &lt;<a class="el" href="hal_sliced_segment_8h_source.html">halSlicedSegment.h</a>&gt;</code></p>
+<div class="dynheader">
+Inheritance diagram for hal::SlicedSegment:</div>
+<div class="dyncontent">
+ <div class="center">
+ <img src="classhal_1_1_sliced_segment.png" usemap="#hal::SlicedSegment_map" alt=""/>
+ <map id="hal::SlicedSegment_map" name="hal::SlicedSegment_map">
+<area href="classhal_1_1_segment.html" alt="hal::Segment" shape="rect" coords="107,0,311,24"/>
+<area href="classhal_1_1_mapped_segment.html" alt="hal::MappedSegment" shape="rect" coords="0,112,204,136"/>
+<area href="classhal_1_1_segment_iterator.html" alt="hal::SegmentIterator" shape="rect" coords="214,112,418,136"/>
+<area href="classhal_1_1_bottom_segment_iterator.html" alt="hal::BottomSegmentIterator" shape="rect" coords="0,168,204,192"/>
+<area href="classhal_1_1_gapped_segment_iterator.html" alt="hal::GappedSegmentIterator" shape="rect" coords="214,168,418,192"/>
+<area href="classhal_1_1_top_segment_iterator.html" alt="hal::TopSegmentIterator" shape="rect" coords="428,168,632,192"/>
+<area href="classhal_1_1_gapped_bottom_segment_iterator.html" alt="hal::GappedBottomSegmentIterator" shape="rect" coords="107,224,311,248"/>
+<area href="classhal_1_1_gapped_top_segment_iterator.html" alt="hal::GappedTopSegmentIterator" shape="rect" coords="321,224,525,248"/>
+</map>
+ </div></div>
+<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:a7c5d0a652d00a0492d36bc3f16acf2a4"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_sliced_segment.html#a7c5d0a652d00a0492d36bc3f16acf2a4">toReverse</a> () const =0</td></tr>
+<tr class="separator:a7c5d0a652d00a0492d36bc3f16acf2a4"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aa5bd93fab081d208cdb0c50dba3021e3"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_sliced_segment.html#aa5bd93fab081d208cdb0c50dba3021e3">toReverseInPlace</a> () const =0</td></tr>
+<tr class="separator:aa5bd93fab081d208cdb0c50dba3021e3"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ae0a230c7b336d92a55dc5fb4084780f6"><td class="memItemLeft" align="right" valign="top">virtual hal_offset_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_sliced_segment.html#ae0a230c7b336d92a55dc5fb4084780f6">getStartOffset</a> () const =0</td></tr>
+<tr class="separator:ae0a230c7b336d92a55dc5fb4084780f6"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a26ebe831b8df1a18e6279c0fc7b4e512"><td class="memItemLeft" align="right" valign="top">virtual hal_offset_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_sliced_segment.html#a26ebe831b8df1a18e6279c0fc7b4e512">getEndOffset</a> () const =0</td></tr>
+<tr class="separator:a26ebe831b8df1a18e6279c0fc7b4e512"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a7263b6a7b8d31dcc834e571137625080"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_sliced_segment.html#a7263b6a7b8d31dcc834e571137625080">slice</a> (hal_offset_t startOffset=0, hal_offset_t endOffset=0) const =0</td></tr>
+<tr class="separator:a7263b6a7b8d31dcc834e571137625080"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a1644d921373f373ff51acba3db136a09"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_sliced_segment.html#a1644d921373f373ff51acba3db136a09">getReversed</a> () const =0</td></tr>
+<tr class="separator:a1644d921373f373ff51acba3db136a09"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="inherit_header pub_methods_classhal_1_1_segment"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classhal_1_1_segment')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="classhal_1_1_segment.html">hal::Segment</a></td></tr>
+<tr class="memitem:a2d022759a5136ec9a15ae70bd40a20c9 inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a2d022759a5136ec9a15ae70bd40a20c9">setArrayIndex</a> (<a class="el" href="classhal_1_1_genome.html">Genome</a> *genome, hal_index_t arrayIndex)=0</td></tr>
+<tr class="separator:a2d022759a5136ec9a15ae70bd40a20c9 inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ad9a39b6d7cd828953b15a06bf6a94ddc inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#ad9a39b6d7cd828953b15a06bf6a94ddc">setArrayIndex</a> (const <a class="el" href="classhal_1_1_genome.html">Genome</a> *genome, hal_index_t arrayIndex) const =0</td></tr>
+<tr class="separator:ad9a39b6d7cd828953b15a06bf6a94ddc inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ae978b16a83930230677cb5746768b572 inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual const <a class="el" href="classhal_1_1_genome.html">Genome</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#ae978b16a83930230677cb5746768b572">getGenome</a> () const =0</td></tr>
+<tr class="separator:ae978b16a83930230677cb5746768b572 inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ab81920adf7bb6ff0fc089dfeeca30c14 inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classhal_1_1_genome.html">Genome</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#ab81920adf7bb6ff0fc089dfeeca30c14">getGenome</a> ()=0</td></tr>
+<tr class="separator:ab81920adf7bb6ff0fc089dfeeca30c14 inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aa398caf4f4d673628a663502a563b36f inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual const <a class="el" href="classhal_1_1_sequence.html">Sequence</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#aa398caf4f4d673628a663502a563b36f">getSequence</a> () const =0</td></tr>
+<tr class="separator:aa398caf4f4d673628a663502a563b36f inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a95980d7da83e05210a1ba5fbf34b9d7c inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classhal_1_1_sequence.html">Sequence</a> *&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a95980d7da83e05210a1ba5fbf34b9d7c">getSequence</a> ()=0</td></tr>
+<tr class="separator:a95980d7da83e05210a1ba5fbf34b9d7c inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a36330fc97cdce2f5be1b6fe01639a41f inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual hal_index_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a36330fc97cdce2f5be1b6fe01639a41f">getStartPosition</a> () const =0</td></tr>
+<tr class="separator:a36330fc97cdce2f5be1b6fe01639a41f inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:add66d5e2d7fbb0257522542a13a2be5e inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual hal_index_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#add66d5e2d7fbb0257522542a13a2be5e">getEndPosition</a> () const =0</td></tr>
+<tr class="separator:add66d5e2d7fbb0257522542a13a2be5e inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aed488d7c10618754004ccaeba59e75da inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual hal_size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#aed488d7c10618754004ccaeba59e75da">getLength</a> () const =0</td></tr>
+<tr class="separator:aed488d7c10618754004ccaeba59e75da inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:afd6fc6bf7084723134218096aff6414a inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#afd6fc6bf7084723134218096aff6414a">getString</a> (std::string &amp;outString) const =0</td></tr>
+<tr class="separator:afd6fc6bf7084723134218096aff6414a inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a663be727196999cbb3d4f048f8fac3cc inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a663be727196999cbb3d4f048f8fac3cc">setCoordinates</a> (hal_index_t startPos, hal_size_t length)=0</td></tr>
+<tr class="separator:a663be727196999cbb3d4f048f8fac3cc inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a3c6a484cf611ea099ef20ccb8c75af4e inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual hal_index_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a3c6a484cf611ea099ef20ccb8c75af4e">getArrayIndex</a> () const =0</td></tr>
+<tr class="separator:a3c6a484cf611ea099ef20ccb8c75af4e inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ad6c49b546dacd77e8a01b3a8e398abe2 inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#ad6c49b546dacd77e8a01b3a8e398abe2">leftOf</a> (hal_index_t genomePos) const =0</td></tr>
+<tr class="separator:ad6c49b546dacd77e8a01b3a8e398abe2 inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a66f41bba295d2d2f54c8fc2085171667 inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a66f41bba295d2d2f54c8fc2085171667">rightOf</a> (hal_index_t genomePos) const =0</td></tr>
+<tr class="separator:a66f41bba295d2d2f54c8fc2085171667 inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:aea6d5d0be2f936029e68d03cb31cc171 inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#aea6d5d0be2f936029e68d03cb31cc171">overlaps</a> (hal_index_t genomePos) const =0</td></tr>
+<tr class="separator:aea6d5d0be2f936029e68d03cb31cc171 inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a3fcce27b6fcebaaa49108f6089ed819e inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a3fcce27b6fcebaaa49108f6089ed819e">isFirst</a> () const =0</td></tr>
+<tr class="separator:a3fcce27b6fcebaaa49108f6089ed819e inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a200c3c95017edf7ea0c4aa6a55abc0cc inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a200c3c95017edf7ea0c4aa6a55abc0cc">isLast</a> () const =0</td></tr>
+<tr class="separator:a200c3c95017edf7ea0c4aa6a55abc0cc inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:afbb86ebc35841f1ca301abe8bc9656ab inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#afbb86ebc35841f1ca301abe8bc9656ab">isMissingData</a> (double nThreshold) const =0</td></tr>
+<tr class="separator:afbb86ebc35841f1ca301abe8bc9656ab inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a0e0b2a7126d492be96940e40dc6178db inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual bool&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a0e0b2a7126d492be96940e40dc6178db">isTop</a> () const =0</td></tr>
+<tr class="separator:a0e0b2a7126d492be96940e40dc6178db inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a154f2fa2a8740af32f4bdecc4467ae1f inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual hal_size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a154f2fa2a8740af32f4bdecc4467ae1f">getMappedSegments</a> (std::set&lt; MappedSegmentConstPtr &gt; &amp;outSegments, const <a class="el" href="classhal_1_1_genome.html">Genome</a> *tgtGenome, const std::set&lt; const <a class="el" href="classhal_1_1_genome.html">Genome</a> * &gt; *genomesOnPath=NULL, bool doDupes=true, hal_size_t minLength=0) const =0</td></tr>
+<tr class="separator:a154f2fa2a8740af32f4bdecc4467ae1f inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a4ecebbc4d405d226abd34267b1650f9c inherit pub_methods_classhal_1_1_segment"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_segment.html#a4ecebbc4d405d226abd34267b1650f9c">print</a> (std::ostream &amp;os) const =0</td></tr>
+<tr class="separator:a4ecebbc4d405d226abd34267b1650f9c inherit pub_methods_classhal_1_1_segment"><td class="memSeparator" colspan="2">&#160;</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:a324e8999d1e71a35e4cf66afc83d9f35"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a324e8999d1e71a35e4cf66afc83d9f35"></a>
+class&#160;</td><td class="memItemRight" valign="bottom"><b>counted_ptr&lt; SlicedSegment &gt;</b></td></tr>
+<tr class="separator:a324e8999d1e71a35e4cf66afc83d9f35"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:a4b7f61594eab6f055982021c5b7d2e0d"><td class="memItemLeft" align="right" valign="top"><a class="anchor" id="a4b7f61594eab6f055982021c5b7d2e0d"></a>
+class&#160;</td><td class="memItemRight" valign="bottom"><b>counted_ptr&lt; const SlicedSegment &gt;</b></td></tr>
+<tr class="separator:a4b7f61594eab6f055982021c5b7d2e0d"><td class="memSeparator" colspan="2">&#160;</td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><p>Interface for a sliced segement. This extends the segment interface by allowing slicing (accessing just subintervals of the segmenet), along with reversing. </p>
+</div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a26ebe831b8df1a18e6279c0fc7b4e512"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual hal_offset_t hal::SlicedSegment::getEndOffset </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Get the iterator's end offset. This is used when moving vertically and following the parse index. Any part of the segment after the end offset is ignored by the iterator </p>
+
+</div>
+</div>
+<a class="anchor" id="a1644d921373f373ff51acba3db136a09"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual bool hal::SlicedSegment::getReversed </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Check whether iterator is on segment's reverse complement </p>
+
+</div>
+</div>
+<a class="anchor" id="ae0a230c7b336d92a55dc5fb4084780f6"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual hal_offset_t hal::SlicedSegment::getStartOffset </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Get the iterator's start offset. This is used when moving vertically and following the parse index. Any part of the segment before the start offset is ignored by the iterator </p>
+
+</div>
+</div>
+<a class="anchor" id="a7263b6a7b8d31dcc834e571137625080"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual void hal::SlicedSegment::slice </td>
+ <td>(</td>
+ <td class="paramtype">hal_offset_t&#160;</td>
+ <td class="paramname"><em>startOffset</em> = <code>0</code>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">hal_offset_t&#160;</td>
+ <td class="paramname"><em>endOffset</em> = <code>0</code>&#160;</td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>Set the iterator's start and end offsets </p>
+<dl class="params"><dt>Parameters</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">startOffset</td><td>offset from beginning of segment </td></tr>
+ <tr><td class="paramname">endOffset</td><td>offset from end of segment </td></tr>
+ </table>
+ </dd>
+</dl>
+
+</div>
+</div>
+<a class="anchor" id="a7c5d0a652d00a0492d36bc3f16acf2a4"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual void hal::SlicedSegment::toReverse </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>switch to segment's reverse complement </p>
+
+</div>
+</div>
+<a class="anchor" id="aa5bd93fab081d208cdb0c50dba3021e3"></a>
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual void hal::SlicedSegment::toReverseInPlace </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td> const</td>
+ </tr>
+ </table>
+ </td>
+ <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span> </td>
+ </tr>
+</table>
+</div><div class="memdoc">
+<p>switch to segment's reverse complement without affecting the coordinates in the forward strand. Unless the segment is sliced this will have an identical effect to <a class="el" href="classhal_1_1_sliced_segment.html#a7c5d0a652d00a0492d36bc3f16acf2a4">toReverse()</a>. Both methods can be useful in different situations but the distinction is confusing. For example, if the segment represents range [0, 10] on the forward strand but is sliced to to the subregion [3,8], then <a class="el" href="classhal_1_1_sliced_segment.html#a7c5d0a652d00a0492d36bc3f16acf2a4">toReverse()</a> will result in the the region [7,2], but to <a class="el" href="classhal_1_1_sliced_segment.html#aa5bd93fab081d208cdb0c50dba3021e3">toReverseInPlace()</a> would yield [8,3]. </p>
+
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>inc/<a class="el" href="hal_sliced_segment_8h_source.html">halSlicedSegment.h</a></li>
+</ul>
+</div><!-- contents -->
+<!-- start footer part -->
+<hr class="footer"/><address class="footer"><small>
+Generated on Thu Dec 5 2013 15:14:38 for halapi by &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/>
+</a> 1.8.5
+</small></address>
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+Generated on Thu Dec 5 2013 15:14:39 for halapi by &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="doxygen.png" alt="doxygen"/>
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