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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b">0af13b84</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-12T18:59:42+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.31+dfsg</pre>
</li>
</ul>
<h4>21 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#595b42362bc80e51259da598ac8ff2dd32cd7358">
res/TemplateBatchFiles/GARD.bf
</a>
</li>
<li class="file-stats">
<a href="#817efc81f1180519a6136b50a447433f20cf679d">
res/TemplateBatchFiles/SelectionAnalyses/FEL.bf
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<li class="file-stats">
<a href="#af43f80c500c4a3acf886ebcfd048a6a7a3cf361">
res/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf
</a>
</li>
<li class="file-stats">
<a href="#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2">
res/TemplateBatchFiles/SelectionAnalyses/MEME.bf
</a>
</li>
<li class="file-stats">
<a href="#95a7c74b0e59bc9dc8d85b6ac4b02d308b4e09fb">
res/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
</a>
</li>
<li class="file-stats">
<a href="#e7b72a8f9f424fe1e9e9e76f25522816189c14c9">
res/TemplateBatchFiles/libv3/tasks/alignments.bf
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</li>
<li class="file-stats">
<a href="#c7933e171033f4eac9d83419583cca5474f9266c">
res/TemplateBatchFiles/libv3/tasks/estimators.bf
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<li class="file-stats">
<a href="#3945e6db8feb0e4ed58719b69ff3d8485bc45e87">
res/TemplateBatchFiles/libv3/tasks/trees.bf
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<li class="file-stats">
<a href="#02cbcb76e8ce1aa3e72d55e6696cda20813d57b6">
src/core/batchlan.cpp
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<li class="file-stats">
<a href="#7474aa77ff4fbb7ca8b12091ad6d5e459fdc18c6">
src/core/dataset.cpp
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<li class="file-stats">
<a href="#a0fe81e4f5076dffb1bf945d1fc8f2b1bef8e630">
src/core/dataset_filter.cpp
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<li class="file-stats">
<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">
src/core/global_things.cpp
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</li>
<li class="file-stats">
<a href="#d96642d31b69af6c250af904868c89a79c200f46">
src/core/include/dataset.h
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<li class="file-stats">
<a href="#f096017b26d15cb3aebe7d7856046904f16536e5">
src/core/include/dataset_filter.h
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<li class="file-stats">
<a href="#390224bdc129deb2ba2cd939305e8b820a0eee6d">
src/core/include/global_things.h
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<li class="file-stats">
<a href="#e0458243bd4e03f3eca3229e56d2bb31c81da1af">
src/core/include/hy_string_buffer.h
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<li class="file-stats">
<a href="#2a8dd324ded753b0b3c559ac3950a2881ccd7a93">
src/core/likefunc.cpp
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<li class="file-stats">
<a href="#a07278be16446012117c4ede345bf6f66c7ec48e">
src/core/nexus.cpp
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</li>
<li class="file-stats">
<a href="#e6d7ca8f3c2b6fd6a56154efe97c9c135f9d663b">
src/core/string_buffer.cpp
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</li>
<li class="file-stats">
<a href="#bda7cb75d6978cc48706b966e994f4c167863cb4">
tests/hbltests/UnitTests/HBLCommands/DataSet.bf
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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="3" 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">@@ -3,6 +3,7 @@ project(HyPhy)</td>
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<td class="old_line diff-line-num" data-linenumber="3" 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">
3
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<td class="new_line diff-line-num" data-linenumber="3" 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">
3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_policy</span><span class="p">(</span>VERSION 3.0.0<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="4" 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">
4
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<td class="new_line diff-line-num" data-linenumber="4" 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">
4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="5" 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">
5
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<td class="new_line diff-line-num" data-linenumber="5" 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">
5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">enable_testing</span><span class="p">()</span></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="6" 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">
</td>
<td class="new_line diff-line-num new" data-linenumber="6" 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">
6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#enable_language(Fortran)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="6" 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="new_line diff-line-num" data-linenumber="7" 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">
7
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="7" 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">
7
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<td class="new_line diff-line-num" data-linenumber="8" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CONFIGURATION_TYPES Release<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="8" 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">
8
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<td class="new_line diff-line-num" data-linenumber="9" 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">
9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" 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="14" 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">@@ -13,6 +14,7 @@ set(CMAKE_CONFIGURATION_TYPES Release)</td>
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<td class="old_line diff-line-num" data-linenumber="13" 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">
13
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<td class="new_line diff-line-num" data-linenumber="14" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>NOAVX OFF<span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="14" 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">
14
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<td class="new_line diff-line-num" data-linenumber="15" 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">
15
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>NOSSE3 OFF<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="15" 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">
15
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<td class="new_line diff-line-num" data-linenumber="16" 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">
16
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>NONEON OFF<span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="16" 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">
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<td class="new_line diff-line-num new" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>NOZLIB OFF<span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="16" 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="new_line diff-line-num" data-linenumber="18" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC18" class="line" lang="cmake"></span>
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<td class="old_line diff-line-num" data-linenumber="17" 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="new_line diff-line-num" data-linenumber="19" 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="LC19" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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<td class="old_line diff-line-num" data-linenumber="18" 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="new_line diff-line-num" data-linenumber="20" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC20" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># SSE MACROS</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="304" 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="306" 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">@@ -304,16 +306,25 @@ endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")</td>
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<td class="old_line diff-line-num" data-linenumber="304" 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="new_line diff-line-num" data-linenumber="306" 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="LC306" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># LIBCurl support</span></span>
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<td class="old_line diff-line-num" data-linenumber="305" 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="new_line diff-line-num" data-linenumber="307" 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="LC307" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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<td class="old_line diff-line-num" data-linenumber="306" 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="LC308" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>CURL<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_FOUND</span><span class="si" style="color: #d14;">}</span> AND NOT APPLE<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>CMAKE_SYSTEM_NAME MATCHES <span class="s2" style="color: #d14;">"FreeBSD"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>DEFAULT_LIBRARIES crypto curl ssl<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span><span class="p">(</span>CMAKE_SYSTEM_NAME MATCHES <span class="s2" style="color: #d14;">"FreeBSD"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>DEFAULT_LIBRARIES dl crypto curl ssl<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>CMAKE_SYSTEM_NAME MATCHES <span class="s2" style="color: #d14;">"FreeBSD"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># set(DEFAULT_LIBRARIES " crypto curl ssl")</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;"># set(DEFAULT_LIBRARIES "dl crypto curl ssl")</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">message</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">string</span><span class="p">(</span>APPEND DEFAULT_LIBRARIES <span class="s2" style="color: #d14;">" "</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D__HYPHYCURL__<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_FOUND</span><span class="si" style="color: #d14;">}</span> AND NOT APPLE<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CURL_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span><span class="p">(</span>NOT NOZLIB<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>ZLIB 1.2.9<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">string</span><span class="p">(</span>APPEND DEFAULT_LIBRARIES <span class="s2" style="color: #d14;">" "</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_INCLUDE_DIRS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span> <span class="p">(</span>-D__ZLIB__<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ZLIB_FOUND</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>NOT NOZLIB<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#-------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># uninstall target</span></span>
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<li id="595b42362bc80e51259da598ac8ff2dd32cd7358">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#595b42362bc80e51259da598ac8ff2dd32cd7358"><strong>res/TemplateBatchFiles/GARD.bf</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">@@ -212,6 +212,8 @@ Will resume search from the end of the previous run.</td>
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">defaultFitFilePath = (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alignment</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">file</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> '</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">best</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">gard');</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("output</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">lf"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Write the best fitting HyPhy analysis snapshot to (default is to save to the same path as the alignment file </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 'best</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">gard')"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">defaultFitFilePath);</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lfFileLocation = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUserForFilePath ("Save the HyPhy analysis snapshot to");</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">@@ -428,7 +430,7 @@ namespace gard {</td>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bestOverallModelSoFar = {1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> startWithBP};</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (i</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> v; in; json</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"breakpointData"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> startWithBP) {</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">+</span></span><span class="c1" style="color: #998; font-style: italic;">i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> startWithBP) {</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> bestOverallModelSoFar</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">(v</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">'bps'</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#817efc81f1180519a6136b50a447433f20cf679d"><strong>res/TemplateBatchFiles/SelectionAnalyses/FEL.bf</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">@@ -286,7 +286,7 @@ selection.io.startTimer (fel.json [terms.json.timers], "FEL analysis", 2);</td>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">apply_proportional_site_constraint (tree_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> node_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> alpha_parameter</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> beta_parameter</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> alpha_factor</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> beta_factor</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> branch_length) {</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length = (branch_length</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> node_name = tree_name </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> node_name;</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands ("</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#af43f80c500c4a3acf886ebcfd048a6a7a3cf361"><strong>res/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf</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">@@ -451,9 +451,17 @@ if (fitter.do_islands) {</td>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">callout)) {</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> // reconstruct ancestors here</span></span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site2partition = {};</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ancestral_caches = {};</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (index</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> partition; in; fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification) {</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (site_index</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> site; in; partition</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site2partition </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {{index__</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">site_index__}};</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ancestral_caches </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">build (fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">three_hit_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">likelihood_function</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">index</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> None);</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_reports = {};</span></span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left">fitter</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">ancestral_cache = ancestral</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">build (fitter</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">three_hit_results</span></span><span class="p"><span class="idiff">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">terms</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">likelihood_function</span></span><span class="p"><span class="idiff">]</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff"> 0</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"> None);</span></span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("fitter"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "sites"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">callout) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " individual " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SingularOrPlural (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">callout) </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "site"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "sites") </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " which showed sufficiently strong preference for multiple</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">hit models");</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_output_options = {</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">@@ -489,8 +497,10 @@ if (utility.Array1D (fitter.callout)) {</td>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_output_options</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">header")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = FALSE;</span></span>
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEachPair (fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">callout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_site_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_value_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _site_map_ = fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site2partition </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_site_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"></span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_reports </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_site_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeSubstitutionBySite (fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ancestral_cache</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">_site_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> None))</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitutions</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_reports </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_site_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeSubstitutionBySite <span class="idiff left">(</span>(fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ancestral_cache<span class="idiff">s</span></span><span class="p"><span class="idiff">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">_site_map_</span></span><span class="p"><span class="idiff">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]]</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">)</span></span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">(</span>_site_<span class="idiff">map_</span></span><span class="p"><span class="idiff">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">)</span></span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> None))</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitutions</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"></span></span>
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">do_islands) {</span></span>
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fprintf(stdout</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FormatTableRow(</span></span>
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<li id="bc98d7300147ce39ef8ee0f9b35f3252bebd01d2">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#bc98d7300147ce39ef8ee0f9b35f3252bebd01d2"><strong>res/TemplateBatchFiles/SelectionAnalyses/MEME.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="511" 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="511" 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">@@ -511,6 +511,8 @@ function meme.apply_proportional_site_constraint.fel (tree_name, node_name, alph</td>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> node_name = tree_name </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> node_name;</span></span>
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands ("</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`alpha_parameter` :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 1e10;</span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`beta_parameter` :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 1e10;</span></span>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`alpha_parameter` := (`alpha_factor`) * meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length__;</span></span>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`beta_parameter` := (`beta_factor`) * meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length__;</span></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ");</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">@@ -524,6 +526,9 @@ function meme.apply_proportional_site_constraint.bsrel (tree_name, node_name, al</td>
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> node_name = tree_name </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> node_name;</span></span>
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="brainfuck"></span>
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ExecuteCommands ("</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`alpha_parameter` :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 1e10;</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`beta_parameter2` :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 1e10;</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`beta_parameter` :</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 1e10;</span></span>
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`alpha_parameter` := (`alpha_factor`) * meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length__;</span></span>
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`beta_parameter` := (`omega_factor`) * `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`alpha_parameter`;</span></span>
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`beta_parameter2` := (`beta_factor`) * meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length__;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="734" 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="739" 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">@@ -734,10 +739,16 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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734
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739
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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735
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740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta_plus" </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha" && ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_mixture_weight" </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">999999) {</span></span>
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="brainfuck"></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /*</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_tree_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">aipysurusLaevis</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha" </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 10000) {</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Export (lfe</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf_bsrel);</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (lfe);</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_START_COMPUTE);</span></span>
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">baseline);</span></span>
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_node_name_; in; ^bsrel_tree_id) {</span></span>
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (((^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches") </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test")) {</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">@@ -747,16 +758,7 @@ lfunction meme.handle_a_site (lf_fel, lf_bsrel, filter_data, partition_index, pa</td>
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /*utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEach (^bsrel_tree_id</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_node_name_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '</span></span>
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"`&partition_index`"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test")) {</span></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _node_name_res_ = meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">compute_branch_EBF (^"`&lf_bsrel`"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"`&bsrel_tree_id`"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _node_name_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"`&baseline`");</span></span>
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (^"`&branch_ebf`")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _node_name_res_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">empirical_bayes_factor")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (^"`&branch_posterior`")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _node_name_res_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">posterior")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> LFCompute (^lf_bsrel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_DONE_COMPUTE);</span></span>
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta_plus" := ^"meme</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha";</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#95a7c74b0e59bc9dc8d85b6ac4b02d308b4e09fb"><strong>res/TemplateBatchFiles/libv3/models/codon/MG_REV.bf</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">@@ -142,10 +142,12 @@ function models.codon.MG_REV.set_branch_length(model, value, parameter) {</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ( null != models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta && null != models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha) {</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha;</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta;</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Type(value) == "AssociativeList") {</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (value</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_scaler</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_constrain) {</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">IsIndependent(models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p)) {</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (Abs(model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) == 0) {</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">@@ -173,11 +175,12 @@ function models.codon.MG_REV.set_branch_length(model, value, parameter) {</td>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lp = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="brainfuck"></span>
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">IsIndependent(models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p)) {</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Eval(models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ":=(" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> value</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_scaler</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ")*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> value</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lp </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1;</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="brainfuck"></span>
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">IsIndependent(models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p)) {</span></span>
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<li id="e7b72a8f9f424fe1e9e9e76f25522816189c14c9">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#e7b72a8f9f424fe1e9e9e76f25522816189c14c9"><strong>res/TemplateBatchFiles/libv3/tasks/alignments.bf</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="103" 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">@@ -103,6 +103,7 @@ lfunction alignments.ReadNucleotideDataSet_aux(dataset_name) {</td>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> partitions = Transpose(dfpm);</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return {</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sequences"): Eval("`dataset_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">species")</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#c7933e171033f4eac9d83419583cca5474f9266c"><strong>res/TemplateBatchFiles/libv3/tasks/estimators.bf</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">@@ -772,17 +772,6 @@ lfunction estimators.FitLF(data_filter, tree, model_map, initial_values, model_o</td>
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> can_do_restarts = null;</span></span>
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //Export (lfe</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> likelihoodFunction);</span></span>
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (lfe);</span></span>
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //GetString (lfe</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> likelihoodFunction</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>
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<pre style="margin: 0;">-<span id="LC780" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log (lfe);</span></span>
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<pre style="margin: 0;">-<span id="LC781" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //fprintf ("/Users/sergei/Desktop/busted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">txt"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> CLEAR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> lfe);</span></span>
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ToggleEnvVariable("VERBOSITY_LEVEL"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 10);</span></span>
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Has (run_options</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">search_grid")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"AssociativeList")) {</span></span>
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788
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> grid_results = mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeOnGrid (&likelihoodFunction</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> run_options </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">search_grid")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeOnGrid</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SimpleEvaluator"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeOnGrid</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ResultHandler");</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">@@ -1176,7 +1165,7 @@ lfunction estimators.FitCodonModel(codon_data, tree, generator, genetic_code, op</td>
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1176
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1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> component_tree = lf_components</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2 * i </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1177
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1166
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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ClearConstraints( * component_tree);</span></span>
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1178
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1167
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<pre style="margin: 0;"> <span id="LC1167" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> branch_map = (option</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">run_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partitioned_omega")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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1179
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<pre style="margin: 0;">-<span id="LC1179" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span></span></span>
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1180
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1169
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<pre style="margin: 0;"> <span id="LC1169" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> component_branches = BranchName( * component_tree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>
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1181
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1170
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<pre style="margin: 0;"> <span id="LC1170" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (j = 0; j </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> Columns(component_branches) </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1; j </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>
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1182
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1171
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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> /**</span></span>
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<li id="3945e6db8feb0e4ed58719b69ff3d8485bc45e87">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#3945e6db8feb0e4ed58719b69ff3d8485bc45e87"><strong>res/TemplateBatchFiles/libv3/tasks/trees.bf</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="383" 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">@@ -383,6 +383,8 @@ lfunction trees.KillZeroBranches (tree, estimates, branch_set, zero_internal) {</td>
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383
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((estimates</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">branch</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 1e</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">10) {</span></span>
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384
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> zero_internal </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> branch;</span></span>
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385
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> zero_internal </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> branch;</span></span>
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#02cbcb76e8ce1aa3e72d55e6696cda20813d57b6"><strong>src/core/batchlan.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">@@ -2656,7 +2656,7 @@ void _ElementaryCommand::ExecuteCase4 (_ExecutionList& chain) {</td>
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<pre style="margin: 0;"> <span id="LC2656" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC2657" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_ElementaryCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ExecuteCase5</span> <span class="p">(</span><span class="n" style="color: #333;">_ExecutionList</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">chain</span><span class="p">)</span> <span class="p">{</span></span>
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2658
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2658
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<pre style="margin: 0;"> <span id="LC2658" class="line" lang="cpp"> <span class="n" style="color: #333;">chain</span><span class="p">.</span><span class="n" style="color: #333;">currentCommand</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2659
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<pre style="margin: 0;">-<span id="LC2659" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">df</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2659" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">df</span><span class="p">;</span></span>
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2660
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2660
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<pre style="margin: 0;"> <span id="LC2660" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">fName</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">GetIthParameter</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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2661
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2661
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<pre style="margin: 0;"> <span id="LC2661" class="line" lang="cpp"> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ds</span><span class="p">;</span></span>
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2662
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2662
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<pre style="margin: 0;"> <span id="LC2662" class="line" lang="cpp"></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">@@ -2679,7 +2679,7 @@ void _ElementaryCommand::ExecuteCase5 (_ExecutionList& chain) {</td>
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2679
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<pre style="margin: 0;"> <span id="LC2679" class="line" lang="cpp"> <span class="p">}</span></span>
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2680
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<pre style="margin: 0;"> <span id="LC2680" class="line" lang="cpp"> <span class="n" style="color: #333;">SetStatusLine</span> <span class="p">(</span><span class="s" style="color: #d14;">"Loading Data"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2681" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2682" class="line" lang="cpp"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">do</span>File<span class="idiff right">Open</span></span> <span class="p">(</span><span class="n" style="color: #333;">fName</span><span class="p">.</span><span class="n" style="color: #333;">get_str</span><span class="p">(),</span><span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2682" class="line" lang="cpp"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">hy</span>File</span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">openFile</span></span> <span class="p">(</span><span class="n" style="color: #333;">fName</span><span class="p">.</span><span class="n" style="color: #333;">get_str</span><span class="p">(),</span><span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">nil</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2684" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// try reading this file as a string formula</span></span>
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<pre style="margin: 0;"> <span id="LC2685" class="line" lang="cpp"> <span class="n" style="color: #333;">fName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetStringFromFormula</span> <span class="p">((</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">parameters</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">),</span><span class="n" style="color: #333;">chain</span><span class="p">.</span><span class="n" style="color: #333;">nameSpacePrefix</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">@@ -2689,7 +2689,7 @@ void _ElementaryCommand::ExecuteCase5 (_ExecutionList& chain) {</td>
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<pre style="margin: 0;"> <span id="LC2689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2690" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2691" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC2692" class="line" lang="cpp"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">do</span>File<span class="idiff right">Open</span></span> <span class="p">(</span><span class="n" style="color: #333;">fName</span><span class="p">.</span><span class="n" style="color: #333;">get_str</span><span class="p">(),</span><span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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2692
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<pre style="margin: 0;">+<span id="LC2692" class="line" lang="cpp"> <span class="n" style="color: #333;">df</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">hy</span>File</span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">openFile</span></span> <span class="p">(</span><span class="n" style="color: #333;">fName</span><span class="p">.</span><span class="n" style="color: #333;">get_str</span><span class="p">(),</span><span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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2693
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2693
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<pre style="margin: 0;"> <span id="LC2693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">nil</span><span class="p">)</span> <span class="p">{</span></span>
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2694
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2694
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<pre style="margin: 0;"> <span id="LC2694" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">((</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Could not find source dataset file "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">((</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">parameters</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">))</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Enquote</span><span class="p">(</span><span class="sc" style="color: #d14;">'"'</span><span class="p">)</span></span>
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2695
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2695
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<pre style="margin: 0;"> <span id="LC2695" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" (resolved to '"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fName</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"')</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Path stack:</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">GetPathStack</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span><span class="p">)));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2697" 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="2697" 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">@@ -2697,7 +2697,10 @@ void _ElementaryCommand::ExecuteCase5 (_ExecutionList& chain) {</td>
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2697
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2697
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<pre style="margin: 0;"> <span id="LC2697" class="line" lang="cpp"> <span class="p">}</span></span>
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2698
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2698
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<pre style="margin: 0;"> <span id="LC2698" class="line" lang="cpp"> <span class="p">}</span></span>
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2699
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2699
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<pre style="margin: 0;"> <span id="LC2699" class="line" lang="cpp"> <span class="n" style="color: #333;">ds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ReadDataSetFile</span> <span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">nil</span><span class="p">,</span><span class="n" style="color: #333;">nil</span><span class="p">,</span><span class="n" style="color: #333;">chain</span><span class="p">.</span><span class="n" style="color: #333;">nameSpacePrefix</span><span class="o" style="font-weight: 600;">?</span><span class="n" style="color: #333;">chain</span><span class="p">.</span><span class="n" style="color: #333;">nameSpacePrefix</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetName</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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2700
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<pre style="margin: 0;">-<span id="LC2700" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span> <span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">);</span></span>
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2700
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<pre style="margin: 0;">+<span id="LC2700" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">)</span> <span class="p">{</span></span>
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2701
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<pre style="margin: 0;">+<span id="LC2701" class="line" lang="cpp"> <span class="n" style="color: #333;">df</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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2702
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<pre style="margin: 0;">+<span id="LC2702" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">df</span><span class="p">;</span></span>
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2703
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<pre style="margin: 0;">+<span id="LC2703" class="line" lang="cpp"> <span class="p">}</span></span>
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2701
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2704
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<pre style="margin: 0;"> <span id="LC2704" class="line" lang="cpp"> <span class="p">}</span></span>
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2702
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2705
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<pre style="margin: 0;"> <span id="LC2705" class="line" lang="cpp"> <span class="p">}</span></span>
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2703
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2706
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<pre style="margin: 0;"> <span id="LC2706" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5099" 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="5102" 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">@@ -5099,7 +5102,7 @@ void ReadBatchFile (_String& fName, _ExecutionList& target) {</td>
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5099
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5102
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<pre style="margin: 0;"> <span id="LC5102" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> FetchVar(LocateVarByName (optimizationPrecision))->SetValue(&precvalue);</span></span>
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5100
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5103
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<pre style="margin: 0;"> <span id="LC5103" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> #endif*/</span></span>
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5101
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5104
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<pre style="margin: 0;"> <span id="LC5104" class="line" lang="cpp"></span>
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5102
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<pre style="margin: 0;">-<span id="LC5102" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">FILE</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff">do</span>File<span class="idiff right">Open</span></span> <span class="p">(</span><span class="n" style="color: #333;">fName</span><span class="p">.</span><span class="n" style="color: #333;">get_str</span> <span class="p">(),</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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5105
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<pre style="margin: 0;">+<span id="LC5105" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">hyFile</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff">hy</span>File</span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff right">openFile</span></span> <span class="p">(</span><span class="n" style="color: #333;">fName</span><span class="p">.</span><span class="n" style="color: #333;">get_str</span> <span class="p">(),</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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5103
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5106
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<pre style="margin: 0;"> <span id="LC5106" class="line" lang="cpp"> <span class="n" style="color: #333;">SetStatusLine</span> <span class="p">(</span><span class="s" style="color: #d14;">"Parsing File"</span><span class="p">);</span></span>
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5104
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5107
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<pre style="margin: 0;"> <span id="LC5107" 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;">f</span><span class="p">)</span> <span class="p">{</span></span>
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5105
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5108
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<pre style="margin: 0;"> <span id="LC5108" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not read batch file '"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fName</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"'.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Path stack:</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">GetPathStack</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5112" 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="5115" 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">@@ -5112,8 +5115,9 @@ void ReadBatchFile (_String& fName, _ExecutionList& target) {</td>
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5112
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5115
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<pre style="margin: 0;"> <span id="LC5115" class="line" lang="cpp"> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">BuildList</span> <span class="p">(</span><span class="n" style="color: #333;">source_file</span><span class="p">);</span></span>
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5113
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5116
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<pre style="margin: 0;"> <span id="LC5116" class="line" lang="cpp"> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">sourceFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fName</span><span class="p">;</span></span>
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5114
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5117
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<pre style="margin: 0;"> <span id="LC5117" class="line" lang="cpp"> <span class="p">}</span></span>
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5115
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<pre style="margin: 0;">-<span id="LC5115" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">f</span></span><span class="p">);</span></span>
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5118
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<pre style="margin: 0;">+<span id="LC5118" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;"><span class="idiff left">-></span></span><span class="n" style="color: #333;">close</span><span class="p"><span class="idiff right">(</span>);</span></span>
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5116
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5119
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<pre style="margin: 0;"> <span id="LC5119" class="line" lang="cpp"> <span class="p">}</span></span>
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5120
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<pre style="margin: 0;">+<span id="LC5120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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5117
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5121
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<pre style="margin: 0;"> <span id="LC5121" class="line" lang="cpp"><span class="p">}</span></span>
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5118
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5122
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<pre style="margin: 0;"> <span id="LC5122" class="line" lang="cpp"></span>
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5119
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5123
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<pre style="margin: 0;"> <span id="LC5123" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#7474aa77ff4fbb7ca8b12091ad6d5e459fdc18c6"><strong>src/core/dataset.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1614" 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">@@ -1614,7 +1614,7 @@ void FilterRawString (_String& s, FileState* fs, _DataSet & ds) {</td>
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1614
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1614
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<pre style="margin: 0;"> <span id="LC1614" class="line" lang="cpp"></span>
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1615
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1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________________________________________________</span></span>
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1616
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1616
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<pre style="margin: 0;"> <span id="LC1616" class="line" lang="cpp"></span>
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1617
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<pre style="margin: 0;">-<span id="LC1617" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessTree</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1617" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessTree</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">hyFile</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1618" class="line" lang="cpp"> </span>
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1619
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<pre style="margin: 0;"> <span id="LC1619" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// TODO SLKP 20180921 this does extra work to read in the tree string multiple times;</span></span>
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<pre style="margin: 0;"> <span id="LC1620" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the solution is to have a proper buffer wrapper, and to</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">@@ -1622,7 +1622,7 @@ void ProcessTree (FileState *fState, FILE* f, _StringBuffer& CurrentLine) {</td>
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1622
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<pre style="margin: 0;"> <span id="LC1622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_MultilineBuffer</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="p">{</span></span>
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1623
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<pre style="margin: 0;"> <span id="LC1623" class="line" lang="cpp"> <span class="nl">public:</span></span>
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1624
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<pre style="margin: 0;"> <span id="LC1624" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC1625" class="line" lang="cpp"> <span class="n" style="color: #333;">_MultilineBuffer</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">current_line</span><span class="p">,</span> <span class="n" style="color: #333;">FileState</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="p">(</span><span class="n" style="color: #333;">current_line</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1625" class="line" lang="cpp"> <span class="n" style="color: #333;">_MultilineBuffer</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">current_line</span><span class="p">,</span> <span class="n" style="color: #333;">FileState</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fs</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="p">(</span><span class="n" style="color: #333;">current_line</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1626" class="line" lang="cpp"> <span class="n" style="color: #333;">file_state</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1627" class="line" lang="cpp"> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1628" class="line" lang="cpp"> <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">@@ -1642,7 +1642,7 @@ void ProcessTree (FileState *fState, FILE* f, _StringBuffer& CurrentLine) {</td>
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<pre style="margin: 0;"> <span id="LC1642" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1643" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="cpp"> <span class="n" style="color: #333;">FileState</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file_state</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1645" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1645" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="cpp"> </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">@@ -1809,7 +1809,7 @@ bool SkipLine (_StringBuffer& theLine, FileState* fS) {</td>
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<pre style="margin: 0;"> <span id="LC1809" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1810" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1811" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;">-<span id="LC1812" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextLine</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">upCase</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1812" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextLine</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hyFile</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">upCase</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1813" class="line" lang="cpp"> <span class="n" style="color: #333;">_StringBuffer</span> <span class="n" style="color: #333;">tempBuffer</span> <span class="p">(</span><span class="mi" style="color: #099;">1024L</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1814" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1815" class="line" lang="cpp"> <span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">currentFileLine</span> <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1817" 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">@@ -1817,7 +1817,7 @@ void ReadNextLine (FILE* fp, _StringBuffer *s, FileState* fs, bool, bool upCase)</td>
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<pre style="margin: 0;"> <span id="LC1817" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">lastc</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1818" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1819" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1820" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">getc_unlocked</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fp</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1820" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getc</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC1821" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1822" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pInSrc</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">?</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">char_at</span><span class="p">(</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pInSrc</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1823" class="line" lang="cpp"> <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">@@ -1825,12 +1825,12 @@ void ReadNextLine (FILE* fp, _StringBuffer *s, FileState* fs, bool, bool upCase)</td>
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<pre style="margin: 0;"> <span id="LC1825" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1826" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">fileType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// not NEXUS - do not skip [..]</span></span>
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1827
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1827
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<pre style="margin: 0;"> <span id="LC1827" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span></span>
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1828
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<pre style="margin: 0;">-<span id="LC1828" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">f<span class="idiff left">eof_unlocked</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fp</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">13</span> <span class="p">)</span> <span class="p">{</span></span>
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1828
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<pre style="margin: 0;">+<span id="LC1828" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">f<span class="idiff left">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">feof</span></span><span class="p"><span class="idiff right">(</span>)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">13</span> <span class="p">)</span> <span class="p">{</span></span>
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1829
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<pre style="margin: 0;"> <span id="LC1829" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lastc</span><span class="p">)</span> <span class="p">{</span></span>
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1830
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1830
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<pre style="margin: 0;"> <span id="LC1830" class="line" lang="cpp"> <span class="n" style="color: #333;">tempBuffer</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">lastc</span><span class="p">;</span></span>
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1831
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1831
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<pre style="margin: 0;"> <span id="LC1831" class="line" lang="cpp"> <span class="p">}</span></span>
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1832
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1832
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<pre style="margin: 0;"> <span id="LC1832" class="line" lang="cpp"> </span>
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1833
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<pre style="margin: 0;">-<span id="LC1833" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">getc_unlocked</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fp</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1833" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getc</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC1834" class="line" lang="cpp"> <span class="p">}</span></span>
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1835
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<pre style="margin: 0;"> <span id="LC1835" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1836
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1836
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<pre style="margin: 0;"> <span id="LC1836" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">13</span> <span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1843" 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="1843" 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">@@ -1843,7 +1843,7 @@ void ReadNextLine (FILE* fp, _StringBuffer *s, FileState* fs, bool, bool upCase)</td>
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1843
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<pre style="margin: 0;"> <span id="LC1843" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">lastc</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1844" class="line" lang="cpp"> <span class="p">}</span></span>
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1845
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<pre style="margin: 0;"> <span id="LC1845" class="line" lang="cpp"> </span>
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1846
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<pre style="margin: 0;">-<span id="LC1846" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(((</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">&&</span><span class="p"><span class="idiff left">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">feof_unlocked</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fp</span></span><span class="p"><span class="idiff right">)</span>))</span><span class="o" style="font-weight: 600;">||</span><span class="p">(</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pInSrc</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="p">())))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'\r'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1846" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(((</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">&&<span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">fp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">feof</span></span><span class="p"><span class="idiff right">(</span>))</span><span class="o" style="font-weight: 600;">||</span><span class="p">(</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pInSrc</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span> <span class="p">())))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'\r'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">!=</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1847" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lastc</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'['</span><span class="p">)</span> <span class="p">{</span></span>
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1848
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<pre style="margin: 0;"> <span id="LC1848" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isSkippingInNEXUS</span><span class="p">)</span> <span class="p">{</span></span>
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1849
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1849
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<pre style="margin: 0;"> <span id="LC1849" class="line" lang="cpp"> <span class="n" style="color: #333;">ReportWarning</span> <span class="p">(</span><span class="s" style="color: #d14;">"Nested comments in NEXUS really shouldn't be used."</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1862" 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">@@ -1862,9 +1862,9 @@ void ReadNextLine (FILE* fp, _StringBuffer *s, FileState* fs, bool, bool upCase)</td>
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1862
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<pre style="margin: 0;"> <span id="LC1862" class="line" lang="cpp"> </span>
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1863
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1863
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<pre style="margin: 0;"> <span id="LC1863" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span> <span class="p">{</span></span>
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1864
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1864
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<pre style="margin: 0;"> <span id="LC1864" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">upCase</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1865" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">fgetc</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">fp</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC1865" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">toupper</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">getc</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC1866" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1867" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">getc_unlocked</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fp</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1867" class="line" lang="cpp"> <span class="n" style="color: #333;">lastc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">getc</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC1868" class="line" lang="cpp"> <span class="p">}</span></span>
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1869
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<pre style="margin: 0;"> <span id="LC1869" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1870" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">upCase</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1883" 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="1883" 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">@@ -1883,7 +1883,7 @@ void ReadNextLine (FILE* fp, _StringBuffer *s, FileState* fs, bool, bool upCase)</td>
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<pre style="margin: 0;"> <span id="LC1883" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1884" class="line" lang="cpp"> <span class="n" style="color: #333;">tempBuffer</span><span class="p">.</span><span class="n" style="color: #333;">TrimSpace</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC1885" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC1886" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f<span class="idiff left">eof_unlocked</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">fp</span></span><span class="p">))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pInSrc</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">())</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1886" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f<span class="idiff left">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">feof</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">(</span>))</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pInSrc</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">fs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">())</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1887" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tempBuffer</span><span class="p">.</span><span class="n" style="color: #333;">empty</span> <span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1888" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1889" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1918" 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="1918" 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">@@ -1918,7 +1918,7 @@ void TrimPhylipLine (_String& CurrentLine, _DataSet& ds) {</td>
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1918
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<pre style="margin: 0;"> <span id="LC1918" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1919" class="line" lang="cpp"></span>
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1920
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<pre style="margin: 0;"> <span id="LC1920" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;">-<span id="LC1921" class="line" lang="cpp"><span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ReadDataSetFile</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">execBF</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">theS</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bfName</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">namespaceID</span><span class="p">,</span> <span class="n" style="color: #333;">_TranslationTable</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dT</span><span class="p">,</span> <span class="n" style="color: #333;">_ExecutionList</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ex</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1921" class="line" lang="cpp"><span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ReadDataSetFile</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">hyFile</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">execBF</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">theS</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">bfName</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">namespaceID</span><span class="p">,</span> <span class="n" style="color: #333;">_TranslationTable</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dT</span><span class="p">,</span> <span class="n" style="color: #333;">_ExecutionList</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ex</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1922" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1923" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">kNEXUS</span> <span class="p">(</span><span class="s" style="color: #d14;">"#NEXUS"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC1924" class="line" lang="cpp"> <span class="n" style="color: #333;">kDefSeqNamePrefix</span> <span class="p">(</span><span class="s" style="color: #d14;">"Species"</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">@@ -1928,7 +1928,8 @@ _DataSet* ReadDataSetFile (FILE*f, char execBF, _String* theS, _String* bfName,</td>
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<pre style="margin: 0;"> <span id="LC1928" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC1929" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1930" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC1931" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="n" style="color: #333;">flockfile</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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1931
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<pre style="margin: 0;">+<span id="LC1931" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (f) flockfile (f);</span></span>
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1932
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<pre style="margin: 0;">+<span id="LC1932" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lock</span><span class="p">();</span></span>
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1932
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="cpp"> </span>
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1933
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1934
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<pre style="margin: 0;"> <span id="LC1934" class="line" lang="cpp"> <span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EnvVariableSet</span><span class="p">(</span><span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">data_file_tree_string</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_Matrix</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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1934
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1935
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<pre style="margin: 0;"> <span id="LC1935" class="line" lang="cpp"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1971" 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="1972" 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">@@ -1971,13 +1972,13 @@ _DataSet* ReadDataSetFile (FILE*f, char execBF, _String* theS, _String* bfName,</td>
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1971
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1972
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<pre style="margin: 0;"> <span id="LC1972" class="line" lang="cpp"> <span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">pInSrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1972
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1973
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<pre style="margin: 0;"> <span id="LC1973" class="line" lang="cpp"> <span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">theNamespace</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">namespaceID</span><span class="p">;</span></span>
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1973
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1974
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<pre style="margin: 0;"> <span id="LC1974" class="line" lang="cpp"> </span>
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1974
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<pre style="margin: 0;">-<span id="LC1974" 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="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="n" style="color: #333;">theS</span><span class="p">)<span class="idiff right">)</span></span> <span class="p">{</span></span>
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1975
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<pre style="margin: 0;">+<span id="LC1975" 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="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">!</span></span><span class="n" style="color: #333;">theS</span><span class="p">)</span> <span class="p">{</span></span>
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1975
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1976
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<pre style="margin: 0;"> <span id="LC1976" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"ReadDataSetFile received null file AND string references. At least one must be specified"</span><span class="p">);</span></span>
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1976
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1977
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<pre style="margin: 0;"> <span id="LC1977" class="line" lang="cpp"> <span class="p">}</span></span>
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1977
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1978
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<pre style="margin: 0;"> <span id="LC1978" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// done initializing</span></span>
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1978
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1979
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<pre style="margin: 0;"> <span id="LC1979" class="line" lang="cpp"> </span>
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1979
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1980
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<pre style="margin: 0;"> <span id="LC1980" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>
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1980
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<pre style="margin: 0;">-<span id="LC1980" class="line" lang="cpp"> <span class="n" style="color: #333;">rewind</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">);</span></span>
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1981
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<pre style="margin: 0;">+<span id="LC1981" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">rewind</span> <span class="p">();</span></span>
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1981
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1982
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<pre style="margin: 0;"> <span id="LC1982" class="line" lang="cpp"> <span class="p">}</span></span>
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1982
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1983
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<pre style="margin: 0;"> <span id="LC1983" class="line" lang="cpp"> </span>
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1983
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1984
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<pre style="margin: 0;"> <span id="LC1984" class="line" lang="cpp"> <span class="n" style="color: #333;">_StringBuffer</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2029" 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="2030" 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">@@ -2029,7 +2030,7 @@ _DataSet* ReadDataSetFile (FILE*f, char execBF, _String* theS, _String* bfName,</td>
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2029
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2030
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<pre style="margin: 0;"> <span id="LC2030" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">fileType</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// PHYLIP</span></span>
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2030
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2031
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<pre style="margin: 0;"> <span id="LC2031" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">filePosition</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">0</span><span class="p">)</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">autoDetect</span><span class="p">))</span> <span class="p">{</span></span>
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2032
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<pre style="margin: 0;"> <span id="LC2032" class="line" lang="cpp"> <span class="n" style="color: #333;">filePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">?</span></span>
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<pre style="margin: 0;">-<span id="LC2032" class="line" lang="cpp"> <span class="n" style="color: #333;">ftell</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC2033" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-></span></span><span class="n" style="color: #333;">tell</span> <span class="p">()</span></span>
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2034
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<pre style="margin: 0;"> <span id="LC2034" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __WINDOZE__</span></span>
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2035
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<pre style="margin: 0;"> <span id="LC2035" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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2036
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<pre style="margin: 0;"> <span id="LC2036" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2086" 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="2087" 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">@@ -2086,7 +2087,7 @@ _DataSet* ReadDataSetFile (FILE*f, char execBF, _String* theS, _String* bfName,</td>
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2087
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<pre style="margin: 0;"> <span id="LC2087" class="line" lang="cpp"> <span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">autoDetect</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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2088
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<pre style="margin: 0;"> <span id="LC2088" class="line" lang="cpp"> </span>
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2089
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<pre style="margin: 0;"> <span id="LC2089" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC2089" class="line" lang="cpp"> <span class="n" style="color: #333;">fseek</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">filePosition</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2090" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-></span></span><span class="n" style="color: #333;">seek</span> <span class="p">(</span><span class="n" style="color: #333;">filePosition</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2091" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2092" class="line" lang="cpp"> <span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">pInSrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filePosition</span><span class="p">;</span></span>
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2093
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<pre style="margin: 0;"> <span id="LC2093" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2228" 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="2229" 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">@@ -2228,7 +2229,7 @@ _DataSet* ReadDataSetFile (FILE*f, char execBF, _String* theS, _String* bfName,</td>
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2229
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<pre style="margin: 0;"> <span id="LC2229" class="line" lang="cpp"> <span class="p">{</span></span>
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2230
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<pre style="margin: 0;"> <span id="LC2230" class="line" lang="cpp"> <span class="n" style="color: #333;">_TranslationTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">trialTable</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_TranslationTable</span> <span class="p">(</span><span class="n" style="color: #333;">hy_default_translation_table</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2231" class="line" lang="cpp"> <span class="n" style="color: #333;">trialTable</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">baseLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC2231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left">f</span>unlock<span class="idiff">file</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">f</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC2232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;">unlock</span><span class="p"><span class="idiff right">(</span>);</span></span>
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2232
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2233
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<pre style="margin: 0;"> <span id="LC2233" class="line" lang="cpp"> <span class="n" style="color: #333;">_DataSet</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">res2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ReadDataSetFile</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">execBF</span><span class="p">,</span> <span class="n" style="color: #333;">theS</span><span class="p">,</span> <span class="n" style="color: #333;">bfName</span><span class="p">,</span> <span class="n" style="color: #333;">namespaceID</span><span class="p">,</span> <span class="n" style="color: #333;">trialTable</span><span class="p">);</span></span>
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2233
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2234
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<pre style="margin: 0;"> <span id="LC2234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">res2</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetNoTypes</span><span class="p">())</span> <span class="p">{</span></span>
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2234
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2235
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<pre style="margin: 0;"> <span id="LC2235" class="line" lang="cpp"> <span class="n" style="color: #333;">DeleteObject</span> <span class="p">(</span><span class="n" style="color: #333;">result</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">@@ -2298,11 +2299,11 @@ _DataSet* ReadDataSetFile (FILE*f, char execBF, _String* theS, _String* bfName,</td>
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2298
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2299
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<pre style="margin: 0;"> <span id="LC2299" class="line" lang="cpp"> <span class="p">}</span></span>
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2299
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2300
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<pre style="margin: 0;"> <span id="LC2300" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">err</span><span class="p">)</span> <span class="p">{</span></span>
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2300
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2301
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<pre style="margin: 0;"> <span id="LC2301" class="line" lang="cpp"> <span class="n" style="color: #333;">DeleteObject</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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2301
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<pre style="margin: 0;">-<span id="LC2301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="n" style="color: #333;">funlock<span class="idiff left">file</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">f</span></span><span class="p">);</span></span>
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2302
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<pre style="margin: 0;">+<span id="LC2302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;"><span class="idiff left">-></span></span><span class="n" style="color: #333;">unlock</span><span class="p"><span class="idiff right">(</span>);</span></span>
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2302
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2303
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<pre style="margin: 0;"> <span id="LC2303" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="n" style="color: #333;">err</span><span class="p">);</span></span>
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2303
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2304
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<pre style="margin: 0;"> <span id="LC2304" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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2304
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2305
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<pre style="margin: 0;"> <span id="LC2305" class="line" lang="cpp"> <span class="p">}</span></span>
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2305
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<pre style="margin: 0;">-<span id="LC2305" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="n" style="color: #333;">funlock<span class="idiff left">file</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">f</span></span><span class="p">);</span></span>
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2306
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<pre style="margin: 0;">+<span id="LC2306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;"><span class="idiff left">-></span></span><span class="n" style="color: #333;">unlock</span><span class="p"><span class="idiff right">(</span>);</span></span>
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2307
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<pre style="margin: 0;"> <span id="LC2307" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2308" class="line" lang="cpp"><span class="p">}</span></span>
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2309
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<pre style="margin: 0;"> <span id="LC2309" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#a0fe81e4f5076dffb1bf945d1fc8f2b1bef8e630"><strong>src/core/dataset_filter.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">@@ -870,6 +870,20 @@ _List * _DataSetFilter::ComputePatternToSiteMap (void) const {</td>
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="cpp"><span class="p">}</span></span>
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_______________________________________________________________________</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"><span class="n" style="color: #333;">_SimpleList</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_DataSetFilter</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SitesForPattern</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pattern_id</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC878" 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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0UL</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">duplicateMap</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">duplicateMap</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">pattern_id</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_______________________________________________________________________</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#07aceb8d215a75908cea626d9c80bc2a7c06639c"><strong>src/core/global_things.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">@@ -54,6 +54,7 @@</td>
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<pre style="margin: 0;"> <span id="LC54" 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="LC55" 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="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <time.h></span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <float.h></span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <signal.h></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">@@ -121,7 +122,7 @@ namespace hy_global {</td>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringDatasetRefIndexError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Dataset index reference out of range"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringMatrixExportError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Export matrix called with a non-polynomial matrix argument"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringNullOperand</span> <span class="p">(</span><span class="s" style="color: #d14;">"Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.<span class="idiff left right">29</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.<span class="idiff left right">31</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">kNoneToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"None"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">kNullToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"null"</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">@@ -672,10 +673,20 @@ namespace hy_global {</td>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">str</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</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="LC675" class="line" lang="cpp"> <span class="n" style="color: #333;">fwrite</span> <span class="p">(</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">hy_message_log_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="cpp"> <span class="n" style="color: #333;">fwrite</span> <span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">.</span><span class="n" style="color: #333;">get_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">(),</span> <span class="n" style="color: #333;">hy_message_log_file</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="n" style="color: #333;">fwrite</span> <span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">.</span><span class="n" style="color: #333;">get_str</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">message</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">(),</span> <span class="n" style="color: #333;">hy_message_log_file</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="cpp"> <span class="n" style="color: #333;">fflush</span> <span class="p">(</span><span class="n" style="color: #333;">hy_message_log_file</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC678" 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="LC679" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReportWarningConsole</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">message</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">has_terminal_stdout</span><span class="p">)</span> <span class="p">{</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> <span class="n" style="color: #333;">NLToConsole</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"> <span class="n" style="color: #333;">BufferToConsole</span><span class="p">(</span><span class="s" style="color: #d14;">"***WARNING***</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="LC686" class="line" lang="cpp"> <span class="n" style="color: #333;">StringToConsole</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">NLToConsole</span><span class="p">();</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="p">}</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="p">}</span></span>
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690
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">HandleOrStoreApplicationError</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">error_string</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">message</span><span class="p">)</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">@@ -978,4 +989,128 @@ namespace hy_global {</td>
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978
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<pre style="margin: 0;"> <span id="LC989" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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990
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<pre style="margin: 0;"> <span id="LC990" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC991" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">openFile</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mode</span> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">error</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">buffer</span><span class="p">)</span> <span class="p">{</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">hyFile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">)</span> <span class="p">{</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fileReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span> <span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">);</span></span>
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998
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<pre style="margin: 0;">+<span id="LC998" 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;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fileReference</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">error</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not open file '"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file_path</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"' with mode '"</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"'."</span><span class="p">);</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="cpp"> <span class="p">}</span></span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="cpp"> <span class="p">}</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fileReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">doFileOpen</span><span class="p">(</span><span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">error</span><span class="p">);</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" 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;">f</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_fileReference</span> <span class="p">)</span> <span class="p">{</span></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="cpp"> <span class="p">}</span></span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp"> </span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="cpp"> <span class="p">}</span></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="cpp"></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">close</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">())</span> <span class="p">{</span></span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="cpp"> <span class="n" style="color: #333;">gzclose</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="cpp"> <span class="n" style="color: #333;">_fileReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="cpp"> <span class="p">}</span></span>
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1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="cpp"> <span class="p">}</span></span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="cpp"></span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lock</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1027" 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">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1028" 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">
1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1029" 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">
1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//gzclose (_fileReference);</span></span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1031" 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">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="cpp"> <span class="n" style="color: #333;">flockfile</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1032" 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">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cpp"> <span class="p">}</span></span>
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1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="cpp"> <span class="p">}</span></span>
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1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="1036" 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">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unlock</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1038" 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">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1039" 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">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//gzclose (_fileReference);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1041" 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">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cpp"> <span class="n" style="color: #333;">funlockfile</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1043" 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">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="cpp"> <span class="p">}</span></span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cpp"> <span class="p">}</span></span>
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1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="cpp"></span>
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1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">rewind</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">())</span> <span class="p">{</span></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="cpp"> <span class="n" style="color: #333;">gzrewind</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">rewind</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="cpp"> <span class="p">}</span></span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="cpp"> <span class="p">}</span></span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="cpp"></span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">seek</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">whence</span><span class="p">)</span> <span class="p">{</span></span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">())</span> <span class="p">{</span></span>
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1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="cpp"> <span class="n" style="color: #333;">gzseek</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">whence</span><span class="p">);</span></span>
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1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="cpp"> <span class="n" style="color: #333;">fseek</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">whence</span><span class="p">);</span></span>
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1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="cpp"> <span class="p">}</span></span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="cpp"> <span class="p">}</span></span>
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1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="cpp"> </span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="cpp"></span>
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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tell</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">())</span> <span class="p">{</span></span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gztell</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ftell</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="cpp"> <span class="p">}</span></span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="cpp"> <span class="p">}</span></span>
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1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">feof</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">())</span> <span class="p">{</span></span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzeof</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">feof_unlocked</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="cpp"> <span class="p">}</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="cpp"> <span class="p">}</span></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getc</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1094" 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">
1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">())</span> <span class="p">{</span></span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1096" 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">
1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzgetc</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1097" 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">
1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1098" 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">
1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">getc_unlocked</span> <span class="p">(</span><span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="cpp"> <span class="p">}</span></span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="cpp"> <span class="p">}</span></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="cpp"></span>
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1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">read</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">items</span><span class="p">)</span> <span class="p">{</span></span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">valid</span><span class="p">())</span> <span class="p">{</span></span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1108" 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">
1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gzfread</span> <span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">items</span><span class="p">,</span> <span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1110" 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">
1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fread</span> <span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">items</span><span class="p">,</span> <span class="n" style="color: #333;">_fileReference</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1111" 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">
1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1113" 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">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="cpp"><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">// namespace close</span></span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#d96642d31b69af6c250af904868c89a79c200f46"><strong>src/core/include/dataset.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">@@ -162,7 +162,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">DuplicateMap</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">theMap</span><span class="p">;</span> <span class="p">}</span></span>
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">friend</span> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_DataSetFilter</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">friend</span> <span class="n" style="color: #333;">_DataSet</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ReadDataSetFile</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">friend</span> <span class="n" style="color: #333;">_DataSet</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ReadDataSetFile</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_TranslationTable</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">_ExecutionList</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">friend</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">ProcessLine</span><span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">FileState</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fs</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ds</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">@@ -200,17 +200,17 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useHorizontalRep</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextLine</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">FileState</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">append</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextLine</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">FileState</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">append</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">upCase</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="LC205" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"><span class="n" style="color: #333;">_DataSet</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">ReadDataSetFile</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</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;">_String</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"><span class="n" style="color: #333;">_DataSet</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">ReadDataSetFile</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</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;">_String</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">,</span></span>
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">_TranslationTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hy_default_translation_table</span><span class="p">,</span></span>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">_ExecutionList</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">target</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">StoreADataSet</span><span class="p">(</span><span class="n" style="color: #333;">_DataSet</span> <span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNexusFile</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNexusFile</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="n" style="color: #333;">nexusBFBody</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#f096017b26d15cb3aebe7d7856046904f16536e5"><strong>src/core/include/dataset_filter.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">@@ -302,6 +302,12 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * have the same pattern in the original alignment</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SitesForPattern</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * return a list of sites matching a given pattern</span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">SOURCE_TYPE</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TARGET_TYPE</span><span class="p">></span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">PatternToSiteMapper</span><span class="p">(</span><span class="n" style="color: #333;">SOURCE_TYPE</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">TARGET_TYPE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">padup</span><span class="p">,</span> <span class="n" style="color: #333;">TARGET_TYPE</span> <span class="n" style="color: #333;">filler</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> </span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#390224bdc129deb2ba2cd939305e8b820a0eee6d"><strong>src/core/include/global_things.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">@@ -53,7 +53,11 @@</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <mpi.h></span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include <mpi.h></span></span>
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<pre style="margin: 0;">+<span id="LC57" 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="LC58" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include <zlib.h></span></span>
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<pre style="margin: 0;"> <span id="LC61" 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="LC62" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_Variable</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// forward decl</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">@@ -121,6 +125,30 @@ namespace hy_global {</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">get_platform_directory_char</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* pass-through structure for reading / writing from a file that may or may not be compressed */</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">hyFile</span> <span class="p">{</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"> <span class="nl">public:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFile</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">_fileReference</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;}</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">openFile</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file_path</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mode</span> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">128</span><span class="p">);</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">valid</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_fileReference</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;}</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">lock</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">unlock</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">rewind</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">seek</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">);</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">close</span> <span class="p">();</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">feof</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">read</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">items</span><span class="p">);</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">tell</span> <span class="p">();</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">getc</span> <span class="p">();</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __ZLIB__</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">gzFile</span> <span class="n" style="color: #333;">_fileReference</span><span class="p">;</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_fileReference</span><span class="p">;</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" 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="LC150" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> Open the file located at file_path using mode 'mode'</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </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">@@ -173,6 +201,14 @@ namespace hy_global {</td>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReportWarning</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">message</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//_______________________________________________________________________</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** Push waring message to console (high impact warnings)</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> @param message the diagnostic message to report</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ReportWarningConsole</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">message</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//_______________________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<li id="e0458243bd4e03f3eca3229e56d2bb31c81da1af">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#e0458243bd4e03f3eca3229e56d2bb31c81da1af"><strong>src/core/include/hy_string_buffer.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">@@ -42,7 +42,8 @@ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#pragma once</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "hy_strings.h"</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "global_things.h"</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">hy_global</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define HY_STRING_BUFFER_ALLOCATION_CHUNK 16UL</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define kAppendAnAssignmentToBufferPlain 0x00</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">@@ -178,6 +179,15 @@ public:</td>
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> - SLKP 20170920 initial implementation</span></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="n" style="color: #333;">_StringBuffer</span><span class="p">(</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * A constructor that read a possibly compressed file</span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @param file the source file</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Revision history</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> - SLKP 20210411 initial implementation</span></span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="n" style="color: #333;">_StringBuffer</span><span class="p">(</span><span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Default constructor initializer</span></span>
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<li id="2a8dd324ded753b0b3c559ac3950a2881ccd7a93">
<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#2a8dd324ded753b0b3c559ac3950a2881ccd7a93"><strong>src/core/likefunc.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">@@ -1572,7 +1572,7 @@ _Matrix* _LikelihoodFunction::ConstructCategoryMatrix (const _SimpleList& whi</td>
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1572
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1572
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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="cpp"> <span class="p">}</span></span>
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1573
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<pre style="margin: 0;"> <span id="LC1573" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// all sites</span></span>
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<pre style="margin: 0;"> <span id="LC1574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1575" class="line" lang="cpp"> <span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">BlockLength</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">i</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="cpp"> <span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">BlockLength</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">whichParts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC1576" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1577" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// only unique patterns for now</span></span>
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<pre style="margin: 0;"> <span id="LC1578" class="line" lang="cpp"></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">@@ -1920,6 +1920,7 @@ bool _LikelihoodFunction::PreCompute (void)</td>
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<pre style="margin: 0;"> <span id="LC1920" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">tp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cornholio</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Compute</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Value</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC1921" 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;">cornholio</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">IsValueInBounds</span><span class="p">(</span><span class="n" style="color: #333;">tp</span><span class="p">)){</span></span>
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<pre style="margin: 0;"> <span id="LC1922" class="line" lang="cpp"> <span class="n" style="color: #333;">ReportWarning</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Failing bound checks on "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cornholio</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" = "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">tp</span><span class="p">,</span> <span class="s" style="color: #d14;">"%25.16g"</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC1923" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//break;</span></span>
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<pre style="margin: 0;"> <span id="LC1924" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1925" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1926" class="line" lang="cpp"></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">@@ -3675,8 +3676,14 @@ void _LikelihoodFunction::SetupLFCaches (void) {</td>
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<pre style="margin: 0;"> <span id="LC3676" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">translation</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC3677" class="line" lang="cpp"> <span class="n" style="color: #333;">translation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theFilter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Translate2Frequencies</span> <span class="p">(</span><span class="n" style="color: #333;">aState</span><span class="p">,</span> <span class="n" style="color: #333;">translationCache</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC3678" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">translation</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC3679" class="line" lang="cpp"> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">total_weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3680" 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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0UL</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;">stateSpaceDim</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC3681" class="line" lang="cpp"> <span class="n" style="color: #333;">ambigs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Store</span><span class="p">(</span><span class="n" style="color: #333;">translationCache</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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3682
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<pre style="margin: 0;">+<span id="LC3682" class="line" lang="cpp"> <span class="n" style="color: #333;">total_weight</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">translationCache</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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3683
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<pre style="margin: 0;">+<span id="LC3683" class="line" lang="cpp"> <span class="p">}</span></span>
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3684
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<pre style="margin: 0;">+<span id="LC3684" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">CheckEqual</span><span class="p">(</span><span class="mf" style="color: #099;">0.</span><span class="p">,</span> <span class="n" style="color: #333;">total_weight</span><span class="p">))</span> <span class="p">{</span></span>
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3685
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<pre style="margin: 0;">+<span id="LC3685" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="n" style="color: #333;">pattern_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">theFilter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SitesForPattern</span><span class="p">(</span><span class="n" style="color: #333;">siteID</span><span class="p">);</span></span>
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3686
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<pre style="margin: 0;">+<span id="LC3686" class="line" lang="cpp"> <span class="n" style="color: #333;">HandleApplicationError</span><span class="p">(</span><span class="n" style="color: #333;">aState</span><span class="p">.</span><span class="n" style="color: #333;">Enquote</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" found at sites "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">_String</span> <span class="p">((</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">pattern_sites</span><span class="p">.</span><span class="n" style="color: #333;">toStr</span><span class="p">())</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" of sequence "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">theFilter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetSequenceName</span><span class="p">(</span><span class="n" style="color: #333;">leafID</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Enquote</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" maps to a null probability vector; this will result in an uncomputable likelihood function"</span><span class="p">);</span></span>
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3680
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3687
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<pre style="margin: 0;"> <span id="LC3687" class="line" lang="cpp"> <span class="p">}</span></span>
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3681
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3688
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<pre style="margin: 0;"> <span id="LC3688" class="line" lang="cpp"> <span class="n" style="color: #333;">translation</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">ambig_resolution_count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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3682
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3689
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<pre style="margin: 0;"> <span id="LC3689" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5611" 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">@@ -5611,11 +5618,16 @@ long _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle</td>
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5618
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<pre style="margin: 0;"> <span id="LC5618" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> (or involves a paremeter that has very little effect on the LF), recomputation could be within numerical error</span></span>
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5612
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5619
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<pre style="margin: 0;"> <span id="LC5619" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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5613
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5620
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<pre style="margin: 0;"> <span id="LC5620" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> **/</span></span>
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5614
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<pre style="margin: 0;">-<span id="LC5614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rightValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-1<span class="idiff left">2</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorTolerance</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">leftValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-1<span class="idiff right">2</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorTolerance</span><span class="p">)</span> <span class="p">{</span></span>
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5621
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<pre style="margin: 0;">+<span id="LC5621" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rightValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-1<span class="idiff left">0</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorTolerance</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">leftValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-1<span class="idiff right">0</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorTolerance</span><span class="p">)</span> <span class="p">{</span></span>
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5615
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5622
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<pre style="margin: 0;"> <span id="LC5622" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">],</span> <span class="n" style="color: #333;">buf2</span><span class="p">[</span><span class="mi" style="color: #099;">512</span><span class="p">];</span></span>
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5616
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5623
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<pre style="margin: 0;"> <span id="LC5623" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="mi" style="color: #099;">256</span><span class="p">,</span> <span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">ERROR: [_LikelihoodFunction::Bracket (index %ld) recomputed the value to midpoint: L(%g) = %g [@%g -> %g:@%g -> %g]]"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">,</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="n" style="color: #333;">leftValue</span><span class="p">,</span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">rightValue</span><span class="p">);</span></span>
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5617
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<td class="new_line diff-line-num" data-linenumber="5624" 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">
5624
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<pre style="margin: 0;"> <span id="LC5624" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buf2</span><span class="p">,</span> <span class="mi" style="color: #099;">512</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">[_LikelihoodFunction::Bracket (index %ld) BRACKET %s: %20.16g <= %20.16g >= %20.16g. steps, L=%g, R=%g, values %15.12g : %15.12g - %15.12g]"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">successful</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"SUCCESSFUL"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"FAILED"</span><span class="p">,</span> <span class="n" style="color: #333;">left</span><span class="p">,</span><span class="n" style="color: #333;">middle</span><span class="p">,</span><span class="n" style="color: #333;">right</span><span class="p">,</span> <span class="n" style="color: #333;">leftStep</span><span class="p">,</span> <span class="n" style="color: #333;">rightStep</span><span class="p">,</span> <span class="n" style="color: #333;">leftValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">rightValue</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span><span class="p">);</span></span>
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5618
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<pre style="margin: 0;">-<span id="LC5618" class="line" lang="cpp"> <span class="n" style="color: #333;">_TerminateAndDump</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">buf2</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Parameter name "</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">GetIthIndependentName</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"line optimization"</span><span class="p">));</span></span>
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5625
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<pre style="margin: 0;">+<span id="LC5625" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EnvVariableTrue</span><span class="p">(</span><span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tolerate_numerical_errors</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5626" 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">
5626
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<pre style="margin: 0;">+<span id="LC5626" class="line" lang="cpp"> <span class="n" style="color: #333;">ReportWarningConsole</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">buf2</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Parameter name "</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">GetIthIndependentName</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"line optimization"</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5627" 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">
5627
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<pre style="margin: 0;">+<span id="LC5627" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5628" 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">
5628
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<pre style="margin: 0;">+<span id="LC5628" class="line" lang="cpp"> <span class="n" style="color: #333;">_TerminateAndDump</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">buf2</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Parameter name "</span> <span class="o" style="font-weight: 600;">&</span> <span class="p">(</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">GetIthIndependentName</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"line optimization"</span><span class="p">));</span></span>
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5629
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<pre style="margin: 0;">+<span id="LC5629" class="line" lang="cpp"> <span class="p">}</span></span>
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5630
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<pre style="margin: 0;">+<span id="LC5630" class="line" lang="cpp"> </span>
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5619
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5631
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<pre style="margin: 0;"> <span id="LC5631" class="line" lang="cpp"> <span class="p">}</span></span>
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5620
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5632
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<pre style="margin: 0;"> <span id="LC5632" class="line" lang="cpp"> <span class="n" style="color: #333;">successful</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rightValue</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">middleValue</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">leftValue</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">middleValue</span><span class="p">;</span></span>
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5621
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5633
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<pre style="margin: 0;"> <span id="LC5633" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7062" 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="7074" 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">@@ -7062,10 +7074,14 @@ void _LikelihoodFunction::LocateTheBump (long index,hyFloat gPrecision, hyFlo</td>
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7062
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7074
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<pre style="margin: 0;"> <span id="LC7074" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="mi" style="color: #099;">256</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">[_LikelihoodFunction::LocateTheBump (index %ld) RESETTING THE VALUE (worse log likelihood obtained; current value %20.16g, best value %20.16g) ]</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">bestVal</span><span class="p">);</span></span>
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7063
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7075
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<pre style="margin: 0;"> <span id="LC7075" class="line" lang="cpp"> <span class="n" style="color: #333;">BufferToConsole</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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7064
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7076
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<pre style="margin: 0;"> <span id="LC7076" class="line" lang="cpp"> <span class="p">}</span></span>
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7065
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<td class="new_line diff-line-num old" data-linenumber="7077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7065" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">CheckEqual</span><span class="p">(</span><span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">bestVal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">middleValue</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-1<span class="idiff left right">2</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorTolerance</span><span class="p">)</span> <span class="p">{</span></span>
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7077
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<pre style="margin: 0;">+<span id="LC7077" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">CheckEqual</span><span class="p">(</span><span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">bestVal</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fabs</span> <span class="p">(</span><span class="n" style="color: #333;">middleValue</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1e-1<span class="idiff left right">0</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorTolerance</span><span class="p">)</span> <span class="p">{</span></span>
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7066
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7078
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<pre style="margin: 0;"> <span id="LC7078" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">256</span><span class="p">];</span></span>
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7067
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<pre style="margin: 0;">-<span id="LC7067" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="mi" style="color: #099;">256</span><span class="p">,</span> <span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">ERROR: [_LikelihoodFunction::LocateTheBump (index %ld) current value %20.16g (parameter = %20.16g), best value %20.16g (parameter = %20.16g)); delta = %20.16g, tolerance = %20.16g]</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333;">bestVal</span><span class="p">,</span> <span class="n" style="color: #333;">maxSoFar</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="mf" style="color: #099;">1e-12</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorTolerance</span><span class="p">);</span></span>
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7068
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<td class="new_line diff-line-num old" data-linenumber="7079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7068" class="line" lang="cpp"> <span class="n" style="color: #333;">_TerminateAndDump</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Parameter name "</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">GetIthIndependentName</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">));</span></span>
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7079
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<pre style="margin: 0;">+<span id="LC7079" class="line" lang="cpp"> <span class="n" style="color: #333;">snprintf</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="mi" style="color: #099;">256</span><span class="p">,</span> <span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">ERROR: [_LikelihoodFunction::LocateTheBump (index %ld) current value %20.16g (parameter = %20.16g), best value %20.16g (parameter = %20.16g)); delta = %20.16g, tolerance = %20.16g]</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">),</span> <span class="n" style="color: #333;">maxSoFar</span><span class="p">,</span> <span class="n" style="color: #333;">bestVal</span><span class="p">,</span> <span class="n" style="color: #333;">maxSoFar</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="mf" style="color: #099;">1e-10</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">errorTolerance</span><span class="p">);</span></span>
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7080
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<pre style="margin: 0;">+<span id="LC7080" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EnvVariableTrue</span><span class="p">(</span><span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tolerate_numerical_errors</span><span class="p">))</span> <span class="p">{</span></span>
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7081
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<pre style="margin: 0;">+<span id="LC7081" class="line" lang="cpp"> <span class="n" style="color: #333;">ReportWarningConsole</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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7082
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<pre style="margin: 0;">+<span id="LC7082" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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7083
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<pre style="margin: 0;">+<span id="LC7083" class="line" lang="cpp"> <span class="n" style="color: #333;">_TerminateAndDump</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Parameter name "</span> <span class="o" style="font-weight: 600;">&</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">GetIthIndependentName</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">));</span></span>
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7084
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<pre style="margin: 0;">+<span id="LC7084" class="line" lang="cpp"> <span class="p">}</span></span>
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7069
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7085
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<pre style="margin: 0;"> <span id="LC7085" class="line" lang="cpp"> <span class="p">}</span></span>
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7070
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7086
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<pre style="margin: 0;"> <span id="LC7086" class="line" lang="cpp"> <span class="n" style="color: #333;">SetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span><span class="n" style="color: #333;">bestVal</span><span class="p">);</span></span>
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7071
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7087
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<pre style="margin: 0;"> <span id="LC7087" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8762" 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="8778" 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">@@ -8762,10 +8778,7 @@ hyFloat _LikelihoodFunction::ComputeBlock (long index, hyFloat* siteRes, long c</td>
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8762
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8778
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<pre style="margin: 0;"> <span id="LC8778" class="line" lang="cpp"> </span>
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8763
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8779
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<pre style="margin: 0;"> <span id="LC8779" class="line" lang="cpp"> </span>
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8764
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8780
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<pre style="margin: 0;"> <span id="LC8780" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">EnvVariableTrue</span><span class="p">(</span><span class="n" style="color: #333;">hy_env</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">tolerate_numerical_errors</span><span class="p">))</span> <span class="p">{</span></span>
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8765
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<pre style="margin: 0;">-<span id="LC8765" class="line" lang="cpp"> <span class="n" style="color: #333;">NLToConsole</span><span class="p">();</span></span>
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8766
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<pre style="margin: 0;">-<span id="LC8766" class="line" lang="cpp"> <span class="n" style="color: #333;">BufferToConsole</span><span class="p">(</span><span class="s" style="color: #d14;">"***WARNING***</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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8767
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<pre style="margin: 0;">-<span id="LC8767" class="line" lang="cpp"> <span class="n" style="color: #333;">StringToConsole</span><span class="p">(</span><span class="n" style="color: #333;">err_msg</span><span class="p">);</span></span>
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8768
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<pre style="margin: 0;">-<span id="LC8768" class="line" lang="cpp"> <span class="n" style="color: #333;">NLToConsole</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC8781" class="line" lang="cpp"> <span class="n" style="color: #333;">ReportWarningConsole</span> <span class="p">(</span><span class="n" style="color: #333;">err_msg</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC8782" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC8783" class="line" lang="cpp"> <span class="n" style="color: #333;">_TerminateAndDump</span> <span class="p">(</span><span class="n" style="color: #333;">err_msg</span><span class="p">);</span></span>
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8784
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<pre style="margin: 0;"> <span id="LC8784" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">INFINITY</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#a07278be16446012117c4ede345bf6f66c7ec48e"><strong>src/core/nexus.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">@@ -69,15 +69,15 @@ void PadLine (FileState& fState, _DataSet& result);</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ISelector</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">SkipLine</span> <span class="p">(</span><span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">theLine</span><span class="p">,</span> <span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fS</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">TrimPhylipLine</span> <span class="p">(</span><span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ds</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusData</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusHYPHY</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusAssumptions</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusTaxa</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusTrees</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">FindNextNexusToken</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">SkipUntilNexusBlockEnd</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextNexusStatement</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextNexusEquate</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</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="LC72" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusData</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusHYPHY</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusAssumptions</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusTaxa</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusTrees</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">FindNextNexusToken</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">SkipUntilNexusBlockEnd</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextNexusStatement</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextNexusEquate</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</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="LC81" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">NexusParseEqualStatement</span> <span class="p">(</span><span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">error_conext</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="p">(</span><span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">.</span><span class="n" style="color: #333;">Cut</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" <=? "</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">buffer</span><span class="p">.</span><span class="n" style="color: #333;">Cut</span> <span class="p">(</span><span class="n" style="color: #333;">position</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">kStringEnd</span><span class="p">)).</span><span class="n" style="color: #333;">Enquote</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">@@ -85,7 +85,7 @@ static auto error_conext = [] (_String const& buffer, long position) -> const _</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">FindNextNexusToken</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">FindNextNexusToken</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>
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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;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">.</span><span class="n" style="color: #333;">FirstNonSpaceIndex</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">kStringDirectionForward</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">kNotFound</span><span class="p">)</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">@@ -102,7 +102,7 @@ bool FindNextNexusToken (FileState& fState, FILE* f, _StringBuffer& CurrentLi</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">SkipUntilNexusBlockEnd</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">SkipUntilNexusBlockEnd</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">endMark</span> <span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">.</span><span class="n" style="color: #333;">Find</span> <span class="p">(</span><span class="n" style="color: #333;">endMark</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">kStringEnd</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kNotFound</span><span class="p">)</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">@@ -143,7 +143,7 @@ void NexusParseEqualStatement (_StringBuffer& source)</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextNexusStatement</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">blank</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">stopOnSpace</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">stopOnComma</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">stopOnQuote</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">NLonly</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">preserveSpaces</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">preserveQuotes</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextNexusStatement</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">blank</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">stopOnSpace</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">stopOnComma</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">stopOnQuote</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">NLonly</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">preserveSpaces</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">preserveQuotes</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">insideLiteral</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">startedReading</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</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">@@ -229,7 +229,7 @@ bool ReadNextNexusStatement (FileState& fState, FILE* f, _StringBuffer& CurrentL</td>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextNexusEquate</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos2</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">blank</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">resetP</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">demandSemicolon</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNextNexusEquate</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos2</span><span class="p">,</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">blank</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">resetP</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">demandSemicolon</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blank</span><span class="p">.</span><span class="n" style="color: #333;">Find</span> <span class="p">(</span><span class="sc" style="color: #d14;">'='</span><span class="p">,</span><span class="n" style="color: #333;">pos2</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">blank</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</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">@@ -263,7 +263,7 @@ long ReadNextNexusEquate (FileState& fState, FILE* f, _StringBuffer& CurrentL</td>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusTaxa</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusTaxa</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">key1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"DIMENSIONS"</span><span class="p">,</span> <span class="n" style="color: #333;">key2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"NTAX"</span><span class="p">,</span> <span class="n" style="color: #333;">key3</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TAXLABELS"</span><span class="p">,</span> <span class="n" style="color: #333;">keyEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"END"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</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">@@ -344,7 +344,7 @@ void ProcessNexusTaxa (FileState& fState, long pos, FILE*f, _StringBuffer& Cu</td>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusAssumptions</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusAssumptions</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">key1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"CHARSET"</span><span class="p">,</span> <span class="n" style="color: #333;">keyEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"END"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</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">@@ -570,7 +570,7 @@ void ProcessNexusAssumptions (FileState& fState, long pos, FILE*f, _StringBuf</td>
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusTrees</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusTrees</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">key1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TRANSLATE"</span><span class="p">,</span> <span class="n" style="color: #333;">key2</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TREE"</span><span class="p">,</span> <span class="n" style="color: #333;">errMsg</span><span class="p">,</span> <span class="n" style="color: #333;">keyEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"END"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">readResult</span><span class="p">,</span> <span class="n" style="color: #333;">good</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="615" 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">@@ -615,7 +615,7 @@ void ProcessNexusTrees (FileState& fState, long pos, FILE*f, _StringBuffer& C</td>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">readResult</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;">feof</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">))</span><span class="o" style="font-weight: 600;">||</span><span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">pInSrc</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">feof</span><span class="p">())</span><span class="o" style="font-weight: 600;">||</span><span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">pInSrc</span><span class="p">)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="cpp"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</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">@@ -815,7 +815,7 @@ void ProcessNexusTrees (FileState& fState, long pos, FILE*f, _StringBuffer& C</td>
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusHYPHY</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusHYPHY</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">_String</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">endMark</span> <span class="p">(</span><span class="s" style="color: #d14;">"END;"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="cpp"> <span class="n" style="color: #333;">_StringBuffer</span> <span class="n" style="color: #333;">bfBody</span> <span class="p">(</span><span class="mi" style="color: #099;">128UL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="cpp"></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">@@ -863,7 +863,7 @@ void ProcessNexusHYPHY (FileState& fState, long pos, FILE*file, _StringBuffer</td>
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusData</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">ProcessNexusData</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">CurrentLine</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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867
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">key1</span> <span class="p">(</span><span class="s" style="color: #d14;">"DIMENSIONS"</span><span class="p">),</span> <span class="n" style="color: #333;">key11</span> <span class="p">(</span><span class="s" style="color: #d14;">"NTAX"</span><span class="p">),</span> <span class="n" style="color: #333;">key12</span> <span class="p">(</span><span class="s" style="color: #d14;">"NCHAR"</span><span class="p">),</span></span>
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868
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="cpp"> <span class="n" style="color: #333;">key2</span> <span class="p">(</span><span class="s" style="color: #d14;">"FORMAT"</span><span class="p">),</span><span class="n" style="color: #333;">key21</span> <span class="p">(</span><span class="s" style="color: #d14;">"DATATYPE"</span><span class="p">),</span> <span class="n" style="color: #333;">key22</span> <span class="p">(</span><span class="s" style="color: #d14;">"MISSING"</span><span class="p">),</span> <span class="n" style="color: #333;">key23</span> <span class="p">(</span><span class="s" style="color: #d14;">"GAP"</span><span class="p">),</span> <span class="n" style="color: #333;">key24</span> <span class="p">(</span><span class="s" style="color: #d14;">"SYMBOLS"</span><span class="p">),</span></span>
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869
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="cpp"> <span class="n" style="color: #333;">key25</span> <span class="p">(</span><span class="s" style="color: #d14;">"EQUATE"</span><span class="p">),</span> <span class="n" style="color: #333;">key26</span> <span class="p">(</span><span class="s" style="color: #d14;">"MATCHCHAR"</span><span class="p">),</span> <span class="n" style="color: #333;">key27</span> <span class="p">(</span><span class="s" style="color: #d14;">"NOLABELS"</span><span class="p">),</span> <span class="n" style="color: #333;">key28</span> <span class="p">(</span><span class="s" style="color: #d14;">"INTERLEAVE"</span><span class="p">),</span> <span class="n" style="color: #333;">key3</span> <span class="p">(</span><span class="s" style="color: #d14;">"MATRIX"</span><span class="p">),</span> <span class="n" style="color: #333;">keyEnd</span> <span class="p">(</span><span class="s" style="color: #d14;">"END"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1217" 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">@@ -1217,7 +1217,7 @@ bool ProcessNexusData (FileState& fState, long pos, FILE*f, _StringBuffer& Cu</td>
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// finished reading</span></span>
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="cpp"> <span class="p">}</span></span>
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1219
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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;">feof</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">f</span></span><span class="p">))</span><span class="o" style="font-weight: 600;">||</span><span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">pInSrc</span><span class="p">)))</span> <span class="p">{</span></span>
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1220
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">feof</span><span class="p">())</span><span class="o" style="font-weight: 600;">||</span><span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">&&</span><span class="p">(</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">theSource</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">pInSrc</span><span class="p">)))</span> <span class="p">{</span></span>
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1221
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="cpp"> <span class="p">}</span></span>
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1223
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<pre style="margin: 0;"> <span id="LC1223" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1258" 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">@@ -1258,7 +1258,7 @@ bool ProcessNexusData (FileState& fState, long pos, FILE*f, _StringBuffer& Cu</td>
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1258
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<pre style="margin: 0;"> <span id="LC1258" class="line" lang="cpp"></span>
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1259
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1259
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<pre style="margin: 0;"> <span id="LC1259" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_________________________________________________________</span></span>
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1260
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1260
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<pre style="margin: 0;"> <span id="LC1260" class="line" lang="cpp"></span>
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1261
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<pre style="margin: 0;">-<span id="LC1261" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNexusFile</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">FILE</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadNexusFile</span> <span class="p">(</span><span class="n" style="color: #333;">FileState</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fState</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">hyFile</span></span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span><span class="p">,</span> <span class="n" style="color: #333;">_DataSet</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="p">{</span></span>
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1262
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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">dataRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">lookForEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1263
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1263
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<pre style="margin: 0;"> <span id="LC1263" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">f</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">file_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fState</span><span class="p">.</span><span class="n" style="color: #333;">currentFileLine</span><span class="p">;</span></span>
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1264
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1264
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<pre style="margin: 0;"> <span id="LC1264" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#e6d7ca8f3c2b6fd6a56154efe97c9c135f9d663b"><strong>src/core/string_buffer.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" 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">@@ -210,6 +210,25 @@ _StringBuffer::~_StringBuffer (void ){</td>
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">s_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">allocated_ptr</span><span class="p">;</span></span>
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211
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">sa_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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212
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"><span class="p">}</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//=============================================================</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"><span class="n" style="color: #333;">_StringBuffer</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">_StringBuffer</span><span class="p">(</span><span class="n" style="color: #333;">hyFile</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">file</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">_String</span> <span class="p">()</span> <span class="p">{</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" 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="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">buffer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">65535</span><span class="p">;</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Initialize</span><span class="p">();</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buffer</span> <span class="p">[</span><span class="n" style="color: #333;">buffer_size</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1L</span><span class="p">];</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">items_read</span><span class="p">;</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">buffer_str</span> <span class="p">(</span><span class="n" style="color: #333;">buffer_size</span><span class="p">,</span> <span class="n" style="color: #333;">buffer</span><span class="p">);</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">items_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">read</span> <span class="p">(</span><span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="p">);</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">items_read</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">buffer_size</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">buffer_str</span><span class="p">;</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">items_read</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">buffer_size</span><span class="p">);</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">items_read</span><span class="p">)</span> <span class="p">{</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">buffer</span><span class="p">[</span><span class="n" style="color: #333;">items_read</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">buffer</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">==============================================================</span></span>
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215
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">Cloners and Copiers</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/0af13b84d7429690b83447c5ab385ea5b187e36b#bda7cb75d6978cc48706b966e994f4c167863cb4"><strong>tests/hbltests/UnitTests/HBLCommands/DataSet.bf</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">@@ -20,6 +20,7 @@ function runTest () {</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSet 2fas = ReadDataFile (PATH_TO_CURRENT_BF </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> '/</span><span class="nf" style="color: #900; font-weight: 600;">..</span><span class="c1" style="color: #998; font-style: italic;">/</span><span class="nf" style="color: #900; font-weight: 600;">..</span><span class="c1" style="color: #998; font-style: italic;">/data/2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fas');</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSet cd2Phylip = ReadDataFile(PATH_TO_CURRENT_BF </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> '/</span><span class="nf" style="color: #900; font-weight: 600;">..</span><span class="c1" style="color: #998; font-style: italic;">/</span><span class="nf" style="color: #900; font-weight: 600;">..</span><span class="c1" style="color: #998; font-style: italic;">/data/CD2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">phylip');</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> //</span><span class="nf" style="color: #900; font-weight: 600;">---------------------------------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> // ERROR HANDLING</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" 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="35" 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">@@ -34,7 +35,9 @@ function runTest () {</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> assert (runCommandWithSoftErrors ('DataSet list_ds = ReadFromString(T1);'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The format of the sequence file has not been recognized and may be invalid")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Failed error checking for trying to create a data set with ReadFromString(topology)");</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> assert (runCommandWithSoftErrors ('DataSet list_ds = ReadFromString(TT1);'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The format of the sequence file has not been recognized and may be invalid")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Failed error checking for trying to create a data set with ReadFromString(tree)");</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="brainfuck"></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> assert (runCommandWithSoftErrors ("DataSet thisIsntAValidFilePath = ReadDataFile('</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">/ThisFileDoesNotExist</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">txt');"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Could not find source dataset file")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Failed error checking for trying to create a data set with ReadDataFile with an invalid path");</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="brainfuck"></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> assert (runCommandWithSoftErrors ("DataSet thisFileIsntInAValidFormat = ReadDataFile(PATH_TO_CURRENT_BF </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> '/assert</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf');"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The format of the sequence file has not been recognized and may be invalid")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Failed error checking for trying to create a data set with ReadDataFile with a file in an invalid format");</span></span>
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39
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> assert (runCommandWithSoftErrors ("DataSet newickFile = ReadDataFile (PATH_TO_CURRENT_BF </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> '/</span><span class="nf" style="color: #900; font-weight: 600;">..</span><span class="c1" style="color: #998; font-style: italic;">/</span><span class="nf" style="color: #900; font-weight: 600;">..</span><span class="c1" style="color: #998; font-style: italic;">/data/CD2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">newick');"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The format of the sequence file has not been recognized and may be invalid")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Failed error checking for trying to create a data set with ReadDataFile with a file file containing a newick string but no sequences");</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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