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regenerate doxygen docs

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1 parent 7415d13 commit 9545828e1ec7fdcd81aa03fd19107b2b6a4a4d71 @glennhickey committed Dec 5, 2013
Showing with 2,628 additions and 1,679 deletions.
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View
65 api/doc/html/annotated.html
@@ -3,7 +3,7 @@
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
-<meta name="generator" content="Doxygen 1.8.3"/>
+<meta name="generator" content="Doxygen 1.8.5"/>
<title>halapi: Class List</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
@@ -31,7 +31,7 @@
</table>
</div>
<!-- end header part -->
-<!-- Generated by Doxygen 1.8.3 -->
+<!-- Generated by Doxygen 1.8.5 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
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@@ -89,39 +89,46 @@
<div class="contents">
<div class="textblock">Here are the classes, structs, unions and interfaces with brief descriptions:</div><div class="directory">
<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span>]</div><table class="directory">
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-<tr id="row_0_0_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_alignment.html" target="_self">Alignment</a></td><td class="desc"></td></tr>
-<tr id="row_0_1_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_bottom_segment.html" target="_self">BottomSegment</a></td><td class="desc"></td></tr>
-<tr id="row_0_2_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_bottom_segment_iterator.html" target="_self">BottomSegmentIterator</a></td><td class="desc"></td></tr>
-<tr id="row_0_3_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img id="arr_0_3_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_3_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_c_l_parser.html" target="_self">CLParser</a></td><td class="desc"></td></tr>
-<tr id="row_0_3_0_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structhal_1_1_c_l_parser_1_1_argument.html" target="_self">Argument</a></td><td class="desc"></td></tr>
-<tr id="row_0_3_1_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structhal_1_1_c_l_parser_1_1_option.html" target="_self">Option</a></td><td class="desc"></td></tr>
-<tr id="row_0_4_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_column_iterator.html" target="_self">ColumnIterator</a></td><td class="desc"></td></tr>
-<tr id="row_0_5_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_d_n_a_iterator.html" target="_self">DNAIterator</a></td><td class="desc"></td></tr>
-<tr id="row_0_6_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_gapped_bottom_segment_iterator.html" target="_self">GappedBottomSegmentIterator</a></td><td class="desc"></td></tr>
-<tr id="row_0_7_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_gapped_segment_iterator.html" target="_self">GappedSegmentIterator</a></td><td class="desc"></td></tr>
-<tr id="row_0_8_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_gapped_top_segment_iterator.html" target="_self">GappedTopSegmentIterator</a></td><td class="desc"></td></tr>
-<tr id="row_0_9_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_genome.html" target="_self">Genome</a></td><td class="desc"></td></tr>
-<tr id="row_0_10_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_meta_data.html" target="_self">MetaData</a></td><td class="desc"></td></tr>
-<tr id="row_0_11_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_position_cache.html" target="_self">PositionCache</a></td><td class="desc"></td></tr>
-<tr id="row_0_12_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_rearrangement.html" target="_self">Rearrangement</a></td><td class="desc"></td></tr>
-<tr id="row_0_13_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_segment.html" target="_self">Segment</a></td><td class="desc"></td></tr>
-<tr id="row_0_14_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_segmented_sequence.html" target="_self">SegmentedSequence</a></td><td class="desc"></td></tr>
-<tr id="row_0_15_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_segment_iterator.html" target="_self">SegmentIterator</a></td><td class="desc"></td></tr>
-<tr id="row_0_16_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img id="arr_0_16_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_16_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_sequence.html" target="_self">Sequence</a></td><td class="desc"></td></tr>
-<tr id="row_0_16_0_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structhal_1_1_sequence_1_1_info.html" target="_self">Info</a></td><td class="desc"></td></tr>
-<tr id="row_0_16_1_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structhal_1_1_sequence_1_1_update_info.html" target="_self">UpdateInfo</a></td><td class="desc"></td></tr>
-<tr id="row_0_17_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_sequence_iterator.html" target="_self">SequenceIterator</a></td><td class="desc"></td></tr>
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-<tr id="row_0_19_" class="even"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_top_segment_iterator.html" target="_self">TopSegmentIterator</a></td><td class="desc"></td></tr>
+<tr id="row_0_" class="even"><td class="entry"><img id="arr_0_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_')"/><img src="ftv2ns.png" alt="N" width="24" height="22" /><a class="el" href="namespacehal.html" target="_self">hal</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_alignment.html" target="_self">Alignment</a></td><td class="desc"></td></tr>
+<tr id="row_0_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_bottom_segment.html" target="_self">BottomSegment</a></td><td class="desc"></td></tr>
+<tr id="row_0_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_bottom_segment_iterator.html" target="_self">BottomSegmentIterator</a></td><td class="desc"></td></tr>
+<tr id="row_0_3_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_3_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_3_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_c_l_parser.html" target="_self">CLParser</a></td><td class="desc"></td></tr>
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+<tr id="row_0_3_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structhal_1_1_c_l_parser_1_1_option.html" target="_self">Option</a></td><td class="desc"></td></tr>
+<tr id="row_0_4_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_column_iterator.html" target="_self">ColumnIterator</a></td><td class="desc"></td></tr>
+<tr id="row_0_5_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_d_n_a_iterator.html" target="_self">DNAIterator</a></td><td class="desc"></td></tr>
+<tr id="row_0_6_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_gapped_bottom_segment_iterator.html" target="_self">GappedBottomSegmentIterator</a></td><td class="desc"></td></tr>
+<tr id="row_0_7_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_gapped_segment_iterator.html" target="_self">GappedSegmentIterator</a></td><td class="desc"></td></tr>
+<tr id="row_0_8_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_gapped_top_segment_iterator.html" target="_self">GappedTopSegmentIterator</a></td><td class="desc"></td></tr>
+<tr id="row_0_9_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_genome.html" target="_self">Genome</a></td><td class="desc"></td></tr>
+<tr id="row_0_10_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_10_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_10_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_mapped_segment.html" target="_self">MappedSegment</a></td><td class="desc"></td></tr>
+<tr id="row_0_10_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structhal_1_1_mapped_segment_1_1_equal_to.html" target="_self">EqualTo</a></td><td class="desc"></td></tr>
+<tr id="row_0_10_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structhal_1_1_mapped_segment_1_1_less.html" target="_self">Less</a></td><td class="desc"></td></tr>
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+<tr id="row_0_13_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_rearrangement.html" target="_self">Rearrangement</a></td><td class="desc"></td></tr>
+<tr id="row_0_14_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_segment.html" target="_self">Segment</a></td><td class="desc"></td></tr>
+<tr id="row_0_15_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_segmented_sequence.html" target="_self">SegmentedSequence</a></td><td class="desc"></td></tr>
+<tr id="row_0_16_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_segment_iterator.html" target="_self">SegmentIterator</a></td><td class="desc"></td></tr>
+<tr id="row_0_17_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_17_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_17_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_sequence.html" target="_self">Sequence</a></td><td class="desc"></td></tr>
+<tr id="row_0_17_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structhal_1_1_sequence_1_1_info.html" target="_self">Info</a></td><td class="desc"></td></tr>
+<tr id="row_0_17_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structhal_1_1_sequence_1_1_update_info.html" target="_self">UpdateInfo</a></td><td class="desc"></td></tr>
+<tr id="row_0_18_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_sequence_iterator.html" target="_self">SequenceIterator</a></td><td class="desc"></td></tr>
+<tr id="row_0_19_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_sliced_segment.html" target="_self">SlicedSegment</a></td><td class="desc"></td></tr>
+<tr id="row_0_20_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_top_segment.html" target="_self">TopSegment</a></td><td class="desc"></td></tr>
+<tr id="row_0_21_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="classhal_1_1_top_segment_iterator.html" target="_self">TopSegmentIterator</a></td><td class="desc"></td></tr>
+<tr id="row_1_" class="even"><td class="entry"><img id="arr_1_" src="ftv2mlastnode.png" alt="\" width="16" height="22" onclick="toggleFolder('1_')"/><img src="ftv2ns.png" alt="N" width="24" height="22" /><b>std</b></td><td class="desc"></td></tr>
+<tr id="row_1_0_"><td class="entry"><img src="ftv2blank.png" alt="&#160;" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="structstd_1_1less_3_01hal_1_1_mapped_segment_const_ptr_01_4.html" target="_self">less&lt; hal::MappedSegmentConstPtr &gt;</a></td><td class="desc"></td></tr>
</table>
</div><!-- directory -->
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
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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">
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54 api/doc/html/classes.html
@@ -3,7 +3,7 @@
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
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+<meta name="generator" content="Doxygen 1.8.5"/>
<title>halapi: Class Index</title>
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@@ -31,7 +31,7 @@
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</div>
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+<!-- Generated by Doxygen 1.8.5 -->
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@@ -87,42 +87,44 @@
<div class="title">Class Index</div> </div>
</div><!--header-->
<div class="contents">
-<div class="qindex"><a class="qindex" href="#letter_A">A</a>&#160;|&#160;<a class="qindex" href="#letter_B">B</a>&#160;|&#160;<a class="qindex" href="#letter_C">C</a>&#160;|&#160;<a class="qindex" href="#letter_D">D</a>&#160;|&#160;<a class="qindex" href="#letter_G">G</a>&#160;|&#160;<a class="qindex" href="#letter_I">I</a>&#160;|&#160;<a class="qindex" href="#letter_M">M</a>&#160;|&#160;<a class="qindex" href="#letter_O">O</a>&#160;|&#160;<a class="qindex" href="#letter_P">P</a>&#160;|&#160;<a class="qindex" href="#letter_R">R</a>&#160;|&#160;<a class="qindex" href="#letter_S">S</a>&#160;|&#160;<a class="qindex" href="#letter_T">T</a>&#160;|&#160;<a class="qindex" href="#letter_U">U</a></div>
+<div class="qindex"><a class="qindex" href="#letter_A">A</a>&#160;|&#160;<a class="qindex" href="#letter_B">B</a>&#160;|&#160;<a class="qindex" href="#letter_C">C</a>&#160;|&#160;<a class="qindex" href="#letter_D">D</a>&#160;|&#160;<a class="qindex" href="#letter_E">E</a>&#160;|&#160;<a class="qindex" href="#letter_G">G</a>&#160;|&#160;<a class="qindex" href="#letter_I">I</a>&#160;|&#160;<a class="qindex" href="#letter_L">L</a>&#160;|&#160;<a class="qindex" href="#letter_M">M</a>&#160;|&#160;<a class="qindex" href="#letter_O">O</a>&#160;|&#160;<a class="qindex" href="#letter_P">P</a>&#160;|&#160;<a class="qindex" href="#letter_R">R</a>&#160;|&#160;<a class="qindex" href="#letter_S">S</a>&#160;|&#160;<a class="qindex" href="#letter_T">T</a>&#160;|&#160;<a class="qindex" href="#letter_U">U</a></div>
<table style="margin: 10px; white-space: nowrap;" align="center" width="95%" border="0" cellspacing="0" cellpadding="0">
<tr><td rowspan="2" valign="bottom"><a name="letter_A"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">&#160;&#160;A&#160;&#160;</div></td></tr></table>
-</td><td valign="top"><a class="el" href="classhal_1_1_column_iterator.html">ColumnIterator</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td><td rowspan="2" valign="bottom"><a name="letter_I"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">&#160;&#160;I&#160;&#160;</div></td></tr></table>
-</td><td rowspan="2" valign="bottom"><a name="letter_R"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">&#160;&#160;R&#160;&#160;</div></td></tr></table>
-</td><td rowspan="2" valign="bottom"><a name="letter_T"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">&#160;&#160;T&#160;&#160;</div></td></tr></table>
+</td><td rowspan="2" valign="bottom"><a name="letter_D"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">&#160;&#160;D&#160;&#160;</div></td></tr></table>
+</td><td rowspan="2" valign="bottom"><a name="letter_I"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">&#160;&#160;I&#160;&#160;</div></td></tr></table>
+</td><td rowspan="2" valign="bottom"><a name="letter_O"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">&#160;&#160;O&#160;&#160;</div></td></tr></table>
+</td><td valign="top"><a class="el" href="classhal_1_1_segmented_sequence.html">SegmentedSequence</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td></tr>
+<tr><td valign="top"><a class="el" href="classhal_1_1_segment_iterator.html">SegmentIterator</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td></tr>
+<tr><td valign="top"><a class="el" href="classhal_1_1_alignment.html">Alignment</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td><td valign="top"><a class="el" href="classhal_1_1_d_n_a_iterator.html">DNAIterator</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td><td valign="top"><a class="el" href="structhal_1_1_sequence_1_1_info.html">Sequence::Info</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td><td valign="top"><a class="el" href="structhal_1_1_c_l_parser_1_1_option.html">CLParser::Option</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td><td valign="top"><a class="el" href="classhal_1_1_sequence.html">Sequence</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td></tr>
+<tr><td valign="top"><a class="el" href="structhal_1_1_c_l_parser_1_1_argument.html">CLParser::Argument</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td><td rowspan="2" valign="bottom"><a name="letter_E"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">&#160;&#160;E&#160;&#160;</div></td></tr></table>
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+</td><td valign="top"><a class="el" href="classhal_1_1_sequence_iterator.html">SequenceIterator</a> (<a class="el" href="namespacehal.html">hal</a>)&#160;&#160;&#160;</td></tr>
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11 api/doc/html/classhal_1_1_alignment-members.html
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+ <tr class="even"><td class="entry"><a class="el" href="classhal_1_1_alignment.html#a53a3c97e0f85d6e865f07845ba13336b">updateBranchLength</a>(const std::string &amp;parentName, const std::string &amp;childName, double length)=0</td><td class="entry"><a class="el" href="classhal_1_1_alignment.html">hal::Alignment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
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58 api/doc/html/classhal_1_1_alignment.html
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<tr class="memitem:a15b39bbdd00e5165631822df5b8cc3f8"><td class="memItemLeft" align="right" valign="top">virtual std::vector&lt; std::string &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classhal_1_1_alignment.html#a15b39bbdd00e5165631822df5b8cc3f8">getChildNames</a> (const std::string &amp;name) const =0</td></tr>
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@@ -865,15 +867,63 @@ <h2 class="groupheader">Member Function Documentation</h2>
</div>
</div>
+<a class="anchor" id="a53a3c97e0f85d6e865f07845ba13336b"></a>
+<div class="memitem">
+<div class="memproto">
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+ <tr>
+ <td class="mlabels-left">
+ <table class="memname">
+ <tr>
+ <td class="memname">virtual void hal::Alignment::updateBranchLength </td>
+ <td>(</td>
+ <td class="paramtype">const std::string &amp;&#160;</td>
+ <td class="paramname"><em>parentName</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">const std::string &amp;&#160;</td>
+ <td class="paramname"><em>childName</em>, </td>
+ </tr>
+ <tr>
+ <td class="paramkey"></td>
+ <td></td>
+ <td class="paramtype">double&#160;</td>
+ <td class="paramname"><em>length</em>&#160;</td>
+ </tr>
+ <tr>
+ <td></td>
+ <td>)</td>
+ <td></td><td></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>Change the branch length between two genomes in the phylogeny </p>
+<dl class="params"><dt>Parameters</dt><dd>
+ <table class="params">
+ <tr><td class="paramname">parentName</td><td>name of parent genome </td></tr>
+ <tr><td class="paramname">childName</td><td>name of child genome </td></tr>
+ </table>
+ </dd>
+</dl>
+
+</div>
+</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>inc/<a class="el" href="hal_alignment_8h_source.html">halAlignment.h</a></li>
</ul>
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57 api/doc/html/classhal_1_1_bottom_segment-members.html
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@@ -105,37 +105,40 @@
<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_bottom_segment.html#a0b956a4a67bdb69fd4d2b7aecdbef940">getLeftChildIndex</a>(hal_size_t i) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a32744c5e19a0b72bfb79d2370c142cdc">getNumChildren</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a9ba870a58ca8dcc1fd887d59ccec29c1">getRightChildIndex</a>(hal_size_t i) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_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_bottom_segment.html#a0b1f0edb6f6c76f60ab27afe39ef738e">getTopParseIndex</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a78406bf324b95234f44ede654a0b2a25">getTopParseOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
- <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a7b958595d1213dc4e939d22ede37e807">hasChild</a>(hal_size_t child) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a854ca7ad2f293c0b0b07fe83ec6f41a4">hasChildG</a>(const Genome *childGenome) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
- <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#af412268ba89c81b0229a5b6b8a66520e">hasParseUp</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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#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><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 class="even"><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><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_bottom_segment.html#a32744c5e19a0b72bfb79d2370c142cdc">getNumChildren</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a9ba870a58ca8dcc1fd887d59ccec29c1">getRightChildIndex</a>(hal_size_t i) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_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><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 class="even"><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a0b1f0edb6f6c76f60ab27afe39ef738e">getTopParseIndex</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a78406bf324b95234f44ede654a0b2a25">getTopParseOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a7b958595d1213dc4e939d22ede37e807">hasChild</a>(hal_size_t child) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a854ca7ad2f293c0b0b07fe83ec6f41a4">hasChildG</a>(const Genome *childGenome) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#af412268ba89c81b0229a5b6b8a66520e">hasParseUp</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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#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 class="even"><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><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 class="even"><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a95ca9a41dd50651cf12d07a4bae08d83">setChildIndex</a>(hal_size_t i, hal_index_t childIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
- <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#ae0875a5ef630ea63cf278fb319cd2695">setChildReversed</a>(hal_size_t child, bool isReversed)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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#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><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#ac83b5c218df47514e7810879df312147">setTopParseIndex</a>(hal_index_t parseIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
- <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~BottomSegment</b>()=0 (defined in <a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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>~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><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_bottom_segment.html#a95ca9a41dd50651cf12d07a4bae08d83">setChildIndex</a>(hal_size_t i, hal_index_t childIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#ae0875a5ef630ea63cf278fb319cd2695">setChildReversed</a>(hal_size_t child, bool isReversed)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#ac83b5c218df47514e7810879df312147">setTopParseIndex</a>(hal_index_t parseIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr bgcolor="#f0f0f0"><td class="entry"><b>~BottomSegment</b>()=0 (defined in <a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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>
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+Generated on Thu Dec 5 2013 15:14:34 for halapi by &#160;<a href="http://www.doxygen.org/index.html">
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14 api/doc/html/classhal_1_1_bottom_segment.html
@@ -3,7 +3,7 @@
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<title>halapi: hal::BottomSegment Class Reference</title>
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@@ -31,7 +31,7 @@
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+<!-- Generated by Doxygen 1.8.5 -->
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@@ -175,6 +175,12 @@
<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>
@@ -622,9 +628,9 @@
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71 api/doc/html/classhal_1_1_bottom_segment_iterator-members.html
@@ -3,7 +3,7 @@
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@@ -106,54 +106,59 @@
<tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#ac316b1abfe2dd47f5f0f3ae9fd3dd435">getChildIndex</a>(hal_size_t i) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a93ebca8c68ae803f8c3091fb0999c8eb">getChildIndexG</a>(const Genome *childGenome) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a3a5e076b36d7fadbf3785c26ec935658">getChildReversed</a>(hal_size_t i) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_iterator.html#aada0eee37263569a41604dff9f08ea5d">getEndOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment_iterator.html">hal::SegmentIterator</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_bottom_segment.html#a0b956a4a67bdb69fd4d2b7aecdbef940">getLeftChildIndex</a>(hal_size_t i) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a32744c5e19a0b72bfb79d2370c142cdc">getNumChildren</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_iterator.html#af6efc88c85bedac56c8144f989eb7210">getReversed</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment_iterator.html">hal::SegmentIterator</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_bottom_segment.html#a9ba870a58ca8dcc1fd887d59ccec29c1">getRightChildIndex</a>(hal_size_t i) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_segment_iterator.html#a19949421e1d351b98474b3062a47595a">getStartOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment_iterator.html">hal::SegmentIterator</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#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><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 class="even"><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a0b1f0edb6f6c76f60ab27afe39ef738e">getTopParseIndex</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
- <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a78406bf324b95234f44ede654a0b2a25">getTopParseOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a7b958595d1213dc4e939d22ede37e807">hasChild</a>(hal_size_t child) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
- <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a854ca7ad2f293c0b0b07fe83ec6f41a4">hasChildG</a>(const Genome *childGenome) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#af412268ba89c81b0229a5b6b8a66520e">hasParseUp</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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#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_bottom_segment.html#a32744c5e19a0b72bfb79d2370c142cdc">getNumChildren</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a9ba870a58ca8dcc1fd887d59ccec29c1">getRightChildIndex</a>(hal_size_t i) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a0b1f0edb6f6c76f60ab27afe39ef738e">getTopParseIndex</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a78406bf324b95234f44ede654a0b2a25">getTopParseOffset</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a7b958595d1213dc4e939d22ede37e807">hasChild</a>(hal_size_t child) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#a854ca7ad2f293c0b0b07fe83ec6f41a4">hasChildG</a>(const Genome *childGenome) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#af412268ba89c81b0229a5b6b8a66520e">hasParseUp</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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#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><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 class="even"><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><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 class="even"><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><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 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_bottom_segment.html#a95ca9a41dd50651cf12d07a4bae08d83">setChildIndex</a>(hal_size_t i, hal_index_t childIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#ae0875a5ef630ea63cf278fb319cd2695">setChildReversed</a>(hal_size_t child, bool isReversed)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_bottom_segment.html#ac83b5c218df47514e7810879df312147">setTopParseIndex</a>(hal_index_t parseIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_iterator.html#a0d80d83afa8d7c31a590569e6077cfd7">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_segment_iterator.html">hal::SegmentIterator</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_iterator.html#ab6386a92b6546c22987da777ca99d411">toLeft</a>(hal_index_t leftCutoff=NULL_INDEX) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment_iterator.html">hal::SegmentIterator</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
- <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment_iterator.html#a4b174bf61c029172b93e5612daee6243">toParent</a>(TopSegmentIteratorConstPtr ts) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment_iterator.html">hal::BottomSegmentIterator</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_bottom_segment_iterator.html#af9a7393eaafc9fe36eacfd8cabdde0fc">toParseDown</a>(TopSegmentIteratorConstPtr ts) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment_iterator.html">hal::BottomSegmentIterator</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_iterator.html#a27181042bb713d2433828577700cf680">toReverse</a>() const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment_iterator.html">hal::SegmentIterator</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#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><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 class="even"><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><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 class="even"><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#a95ca9a41dd50651cf12d07a4bae08d83">setChildIndex</a>(hal_size_t i, hal_index_t childIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#ae0875a5ef630ea63cf278fb319cd2695">setChildReversed</a>(hal_size_t child, bool isReversed)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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#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><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html#ac83b5c218df47514e7810879df312147">setTopParseIndex</a>(hal_index_t parseIndex)=0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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_segment_iterator.html#ab6386a92b6546c22987da777ca99d411">toLeft</a>(hal_index_t leftCutoff=NULL_INDEX) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment_iterator.html">hal::SegmentIterator</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_bottom_segment_iterator.html#a4b174bf61c029172b93e5612daee6243">toParent</a>(TopSegmentIteratorConstPtr ts) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment_iterator.html">hal::BottomSegmentIterator</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+ <tr><td class="entry"><a class="el" href="classhal_1_1_bottom_segment_iterator.html#af9a7393eaafc9fe36eacfd8cabdde0fc">toParseDown</a>(TopSegmentIteratorConstPtr ts) const =0</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment_iterator.html">hal::BottomSegmentIterator</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#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><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 class="even"><td class="entry"><a class="el" href="classhal_1_1_segment_iterator.html#a3cc3a8ad71b6004727c6494f09228001">toRight</a>(hal_index_t rightCutoff=NULL_INDEX) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment_iterator.html">hal::SegmentIterator</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_iterator.html#a2c3a9fc175fee37494918255cd6d2af7">toSite</a>(hal_index_t position, bool slice=true) const =0</td><td class="entry"><a class="el" href="classhal_1_1_segment_iterator.html">hal::SegmentIterator</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
<tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~BottomSegment</b>()=0 (defined in <a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</a>)</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment.html">hal::BottomSegment</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>~BottomSegmentIterator</b>()=0 (defined in <a class="el" href="classhal_1_1_bottom_segment_iterator.html">hal::BottomSegmentIterator</a>)</td><td class="entry"><a class="el" href="classhal_1_1_bottom_segment_iterator.html">hal::BottomSegmentIterator</a></td><td