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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/libncl">Debian Med / libncl</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libncl/commit/e20e24f0f8c7f8afbc76866ef760a9a3f57719ee">e20e24f0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-04T18:10:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.21+git20180827.c71b264</pre>
</li>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#77e8487ce4528960ca8e176742ebc54c7a7a59d6">
example/normalizer/normalizer.cpp
</a>
</li>
<li class="file-stats">
<a href="#e6727af2fbb5970de26fc2a95f2f0854c81c70aa">
example/normalizer/normalizer.h
</a>
</li>
<li class="file-stats">
<a href="#f1add6e3bdc52391d2edd77e97473062b9b1a6b4">
example/normalizer/us2ml.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="77e8487ce4528960ca8e176742ebc54c7a7a59d6">
<a href="https://salsa.debian.org/med-team/libncl/commit/e20e24f0f8c7f8afbc76866ef760a9a3f57719ee#77e8487ce4528960ca8e176742ebc54c7a7a59d6"><strong>example/normalizer/normalizer.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,6 +67,7 @@ std::ostream * gCommonOstream = 0L;</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">RELAXED_PHYLIP_EXPORT_FORMAT</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">FASTA_EXPORT_FORMAT</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">NEXML_EXPORT_FORMAT</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">TREE_NEXML_EXPORT_FORMAT</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">UNSUPPORTED_EXPORT_FORMAT</span></span>
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71
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">ExportFormatEnum</span> <span class="n" style="color: #333;">gExportFormat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NEXML_EXPORT_FORMAT</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,9 +82,10 @@ std::ostream * gCommonOstream = 0L;</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="s" style="color: #d14;">"phylip"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"> <span class="s" style="color: #d14;">"relaxedphylip"</span><span class="p">,</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"> <span class="s" style="color: #d14;">"fasta"</span><span class="p">,</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"> <span class="s" style="color: #d14;">"nexml"</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="s" style="color: #d14;">"nexml"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="s" style="color: #d14;">"treenexml"</span></span>
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85
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="p">};</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">gNumExportFormats</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">5</span></span><span class="p">;</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">gNumExportFormats</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">6</span></span><span class="p">;</span></span>
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87
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="n" style="color: #333;">NxsString</span> <span class="n" style="color: #333;">l</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">NxsString</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_lower</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -274,8 +276,12 @@ void processContent(PublicNexusReader & nexusReader, ostream *os, ProcessActions</td>
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274
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">MultiFormatReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">DataFormatType</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MultiFormatReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NEXUS_FORMAT</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gExportFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NEXUS_EXPORT_FORMAT</span><span class="p">)</span></span>
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">exportData</span><span class="p">(</span><span class="n" style="color: #333;">nexusReader</span><span class="p">,</span> <span class="n" style="color: #333;">MultiFormatReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NEXUS_FORMAT</span><span class="p">,</span> <span class="n" style="color: #333;">gInterleaveLen</span><span class="p">,</span> <span class="n" style="color: #333;">gExportPrefix</span><span class="p">,</span> <span class="n" style="color: #333;">gCommonOstream</span><span class="p">,</span> <span class="n" style="color: #333;">gTranslatingConventions</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gExportFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NEXML_EXPORT_FORMAT</span><span class="p">)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gExportFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NEXML_EXPORT_FORMAT</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">gExportFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">TREE_NEXML_EXPORT_FORMAT</span> <span class="p">)</span> <span class="p">{</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gExportFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">TREE_NEXML_EXPORT_FORMAT</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">gTranslatingConventions</span><span class="p">.</span><span class="n" style="color: #333;">emitTreesAndTaxaOnly</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">exportData</span><span class="p">(</span><span class="n" style="color: #333;">nexusReader</span><span class="p">,</span> <span class="n" style="color: #333;">MultiFormatReader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NEXML_FORMAT</span><span class="p">,</span> <span class="n" style="color: #333;">gInterleaveLen</span><span class="p">,</span> <span class="n" style="color: #333;">gExportPrefix</span><span class="p">,</span> <span class="n" style="color: #333;">gCommonOstream</span><span class="p">,</span> <span class="n" style="color: #333;">gTranslatingConventions</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="p">}</span></span>
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279
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gExportFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">PHYLIP_EXPORT_FORMAT</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">fullExportPrefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gExportPrefix</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">fullExportPrefix</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">".dna"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -550,6 +556,7 @@ void printHelp(ostream & out)</td>
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550
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -ephylip Trees and character data in phylip (could result in multiple output files)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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551
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -erelaxedphylip Trees and character data in relaxed phylip (could result in multiple output files)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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552
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -enexml nexml output (this is also the default)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -etreenexml nexml output of trees and taxa only</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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553
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -f<format> specifies the input file format expected:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -fnexus NEXUS (this is also the default)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/libncl/commit/e20e24f0f8c7f8afbc76866ef760a9a3f57719ee#e6727af2fbb5970de26fc2a95f2f0854c81c70aa"><strong>example/normalizer/normalizer.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,8 @@ class TranslatingConventions {</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"> <span class="n" style="color: #333;">currentTreeIndex</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"> <span class="n" style="color: #333;">currentNodeIndex</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"> <span class="n" style="color: #333;">currentEdgeIndex</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"> <span class="n" style="color: #333;">treatNodeLabelsAsStrings</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"> <span class="n" style="color: #333;">treatNodeLabelsAsStrings</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"> <span class="n" style="color: #333;">emitTreesAndTaxaOnly</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">idPrefix</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">globalIncrementingIDs</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,6 +39,7 @@ class TranslatingConventions {</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">currentNodeIndex</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">currentEdgeIndex</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">treatNodeLabelsAsStrings</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">emitTreesAndTaxaOnly</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<li id="f1add6e3bdc52391d2edd77e97473062b9b1a6b4">
<a href="https://salsa.debian.org/med-team/libncl/commit/e20e24f0f8c7f8afbc76866ef760a9a3f57719ee#f1add6e3bdc52391d2edd77e97473062b9b1a6b4"><strong>example/normalizer/us2ml.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -505,32 +505,37 @@ void writeAsNexml(PublicNexusReader & nexusReader, ostream & os, TranslatingConv</td>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">NxsTaxaBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetTaxaBlock</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">NxsAssumptionsBlock</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">assumps</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetNumAssumptionsBlocks</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="cpp"> <span class="n" style="color: #333;">assumps</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetAssumptionsBlock</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">transConv</span><span class="p">.</span><span class="n" style="color: #333;">emitTreesAndTaxaOnly</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetNumAssumptionsBlocks</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"> <span class="n" style="color: #333;">assumps</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetAssumptionsBlock</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="cpp"> <span class="n" style="color: #333;">writeOTUS</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">tb</span><span class="p">,</span> <span class="n" style="color: #333;">assumps</span><span class="p">,</span> <span class="n" style="color: #333;">memo</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">nCharBlocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetNumCharactersBlocks</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nCharBlocks</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">transConv</span><span class="p">.</span><span class="n" style="color: #333;">emitTreesAndTaxaOnly</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="cpp"> <span class="n" style="color: #333;">NxsCharactersBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetCharactersBlock</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">nCharBlocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetNumCharactersBlocks</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nCharBlocks</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"> <span class="p">{</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">NxsCharactersBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetCharactersBlock</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="cpp"> <span class="n" style="color: #333;">assumps</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetNumAssumptionsBlocks</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="cpp"> <span class="n" style="color: #333;">assumps</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetAssumptionsBlock</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">));</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">assumps</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetNumAssumptionsBlocks</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">assumps</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetAssumptionsBlock</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="cpp"> <span class="n" style="color: #333;">writeCharacters</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">cb</span><span class="p">,</span> <span class="n" style="color: #333;">assumps</span><span class="p">,</span> <span class="n" style="color: #333;">memo</span><span class="p">,</span> <span class="n" style="color: #333;">nCharBlocksRead</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="n" style="color: #333;">writeCharacters</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">cb</span><span class="p">,</span> <span class="n" style="color: #333;">assumps</span><span class="p">,</span> <span class="n" style="color: #333;">memo</span><span class="p">,</span> <span class="n" style="color: #333;">nCharBlocksRead</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="p">}</span></span>
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">nTreesBlocks</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetNumTreesBlocks</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">);</span></span>
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526
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nTreesBlocks</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp"> <span class="p">{</span></span>
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528
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="cpp"> <span class="n" style="color: #333;">NxsTreesBlock</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetTreesBlock</span><span class="p">(</span><span class="n" style="color: #333;">tb</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="n" style="color: #333;">assumps</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetNumAssumptionsBlocks</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="cpp"> <span class="n" style="color: #333;">assumps</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetAssumptionsBlock</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">transConv</span><span class="p">.</span><span class="n" style="color: #333;">emitTreesAndTaxaOnly</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetNumAssumptionsBlocks</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="n" style="color: #333;">assumps</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">nexusReader</span><span class="p">.</span><span class="n" style="color: #333;">GetAssumptionsBlock</span><span class="p">(</span><span class="n" style="color: #333;">cb</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp"> <span class="n" style="color: #333;">writeTrees</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">cb</span><span class="p">,</span> <span class="n" style="color: #333;">assumps</span><span class="p">,</span> <span class="n" style="color: #333;">memo</span><span class="p">,</span> <span class="n" style="color: #333;">nTreeBlocksRead</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">transConv</span><span class="p">.</span><span class="n" style="color: #333;">treatNodeLabelsAsStrings</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp"> <span class="p">}</span></span>
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