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GitLab

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<h3>

Michael R. Crusoe 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/6884fa66cf5d542d45a116543c13c6757e02b6ef">6884fa66</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-02-25T17:40:09+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.29+dfsg</pre>

</li>

</ul>

<h4>28 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#595b42362bc80e51259da598ac8ff2dd32cd7358">

res/TemplateBatchFiles/GARD.bf

</a>

</li>

<li class="file-stats">

<a href="#e9da9a3aa17695c8e989fcc674d35432c64038e0">

res/TemplateBatchFiles/PairwiseRelativeRatio.bf

</a>

</li>

<li class="file-stats">

<a href="#cf5243a3058ebeab74574f8cd2c771cd63a43208">

res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf

</a>

</li>

<li class="file-stats">

<a href="#c079be28c5231888d711d5c41d1be180223dfce6">

res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf

</a>

</li>

<li class="file-stats">

<a href="#0843f8cd833e50a0ae1b16d6b9265232dd51e8b5">

res/TemplateBatchFiles/TemplateModels/GY94.ibf

</a>

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<li class="file-stats">

<a href="#a4592f091dc497086884a23526cefa41e6c904e3">

res/TemplateBatchFiles/TemplateModels/GY94.mdl

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<li class="file-stats">

<a href="#5162429bd3f362a69890c6b040d4be37e11a6308">

res/TemplateBatchFiles/files.lst

</a>

</li>

<li class="file-stats">

<a href="#c50a9ebb34fca832759d3d11698588f8851c99cb">

res/TemplateBatchFiles/libv3/UtilityFunctions.bf

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<li class="file-stats">

<a href="#04266769a57e3da898ac30696629599a2dbf70a6">

res/TemplateBatchFiles/libv3/convenience/regexp.bf

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<a href="#e7b72a8f9f424fe1e9e9e76f25522816189c14c9">

res/TemplateBatchFiles/libv3/tasks/alignments.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="#da9fe1b8aa482a95d2c6145ff61db7930bcd0fe8">

res/TemplateBatchFiles/readIndexFile.bf

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<li class="file-stats">

<a href="#9a5ae795d85e4d5f1568726c609e2499546cd590">

src/core/associative_list.cpp

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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="#984635b15ce26c0824ba85946c002feb3137c030">

src/core/batchlan2.cpp

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<li class="file-stats">

<a href="#cbedcf5fec686e5f563504b995c5d7d07fd8c6b2">

src/core/batchlanruntime.cpp

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<li class="file-stats">

<a href="#8f267f0287b6f2dfc1594ce4cfeb588fe8a2578c">

src/core/category.cpp

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<li class="file-stats">

<a href="#10496a7488dc0332386e6f734ef450e847cb8aac">

src/core/constant.cpp

</a>

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<li class="file-stats">

<a href="#d09b45303442d6299978fa8d0c8f3338d6a17886">

src/core/formula.cpp

</a>

</li>

<li class="file-stats">

<a href="#7f26a8678910b09a3bbef4b727e70c3ca29c2bd5">

src/core/global_object_lists.cpp

</a>

</li>

<li class="file-stats">

<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">

src/core/global_things.cpp

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<li class="file-stats">

<a href="#46380d67c22541ee76ad7fa2f39c30110df90a7c">

src/core/include/batchlan.h

</a>

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<li class="file-stats">

<a href="#40fc4f1e42852e6f2302e213cd9b3646abe98291">

src/core/include/formula.h

</a>

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<li class="file-stats">

<a href="#2a277e4b849d74ac4178f402409133631301633d">

src/core/include/global_object_lists.h

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<li class="file-stats">

<a href="#1f90bcae5572a43ed503911ecef65a7c99ec3d55">

src/core/include/variable.h

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<li class="file-stats">

<a href="#2a8dd324ded753b0b3c559ac3950a2881ccd7a93">

src/core/likefunc.cpp

</a>

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<li class="file-stats">

<a href="#795bd9642f0c76f4bba4eaba7f491566cf16e788">

src/core/operation.cpp

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<li class="file-stats">

<a href="#133fe28f0d337fcb69fd32fa3f4499c2e4c6ea50">

src/core/parser.cpp

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="595b42362bc80e51259da598ac8ff2dd32cd7358">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#595b42362bc80e51259da598ac8ff2dd32cd7358"><strong>res/TemplateBatchFiles/GARD.bf</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" 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="42" 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">@@ -42,7 +42,7 @@</td>

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<td class="old_line diff-line-num" data-linenumber="42" 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">

42

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<td class="new_line diff-line-num" data-linenumber="42" 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">

42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="43" 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">

43

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<td class="new_line diff-line-num" data-linenumber="43" 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">

43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/* 1a</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Initial Setup</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="44" 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">

44

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<td class="new_line diff-line-num" data-linenumber="44" 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="LC44" class="line" lang="brainfuck"><span class="nf" style="color: #900; font-weight: 600;">------------------------------------------------------------------------------</span><span class="c1" style="color: #998; font-style: italic;">*/</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="45" 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">

45

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<td class="new_line diff-line-num old" data-linenumber="45" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">RequireVersion ("2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">4</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">0</span>");</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="46" 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="45" 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">

45

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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="LC45" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">RequireVersion ("2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">5</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">29</span>");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="46" 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">

46

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<td class="new_line diff-line-num" data-linenumber="46" 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="LC46" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="47" 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">

47

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<td class="new_line diff-line-num" data-linenumber="47" 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="LC47" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary ("libv3/all</span><span class="nf" style="color: #900; font-weight: 600;">-</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;">bf");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="48" 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">

48

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<td class="new_line diff-line-num" data-linenumber="48" 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">

48

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary ("libv3/convenience/regexp</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" 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="75" 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">@@ -75,12 +75,15 @@ namespace terms.gard {</td>

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<td class="old_line diff-line-num" data-linenumber="75" 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">

75

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<td class="new_line diff-line-num" data-linenumber="75" 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="LC75" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    nucleotide = "nucleotide";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="76" 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="76" 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="LC76" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    protein    = "amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid";</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="77" 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="77" 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="LC77" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    codon      = "codon";</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    masterList = "masterList";</span></span>

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<pre style="margin: 0;"> <span id="LC79" 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="LC80" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC81" 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;">json = {   terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis: gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysisDescription</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="brainfuck"><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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">input: {}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<pre style="margin: 0;"> <span id="LC83" 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="LC84" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC85" 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;">SetEnvVariable ("OPTIMIZE_SUMMATION_ORDER_PARTITION"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 100); </span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// don't spend too much time optimizing column ordering</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/* 1b</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> User Input</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="brainfuck"><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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -164,7 +167,50 @@ function gard.model.withGDD  (options) {</td>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// Where to save the json</span></span>

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<pre style="margin: 0;"> <span id="LC168" 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;">defaultJsonFilePath = (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;">GARD</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json');</span></span>

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<pre style="margin: 0;"> <span id="LC169" 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;"> "Write the resulting JSON to this file (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;"> 'GARD</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json')"</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;">defaultJsonFilePath);</span></span>

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<pre style="margin: 0;">-<span id="LC167" 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;">jsonFileLocation = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUserForFilePath ("Save the resulting JSON file to");</span></span>

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<pre style="margin: 0;">+<span id="LC170" 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;">jsonFileLocation = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReadFromOrCreate ("Save the resulting JSON file to"</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;">json);</span></span>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="brainfuck"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="172" 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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<pre style="margin: 0;">+<span id="LC172" 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;">json = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">jsonFileLocation </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;">value"</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="LC173" 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;">jsonFileLocation = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">jsonFileLocation </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>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("mode"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Run mode (Normal or Faster)"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Normal");</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="brainfuck"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="177" 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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<pre style="margin: 0;">+<span id="LC177" 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;">fastRunMode = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SelectAnOption  ({"Normal" : "Default optimization and convergence settings"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="178" 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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<pre style="margin: 0;">+<span id="LC178" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                        "Faster" :  "Reduce individual optimization precision and relax convergence settings"}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="179" 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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<pre style="margin: 0;">+<span id="LC179" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                        "Run type") == "Faster";</span></span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="brainfuck"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="181" 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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<pre style="margin: 0;">+<span id="LC181" class="line" lang="brainfuck"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="182" 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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<pre style="margin: 0;">+<span id="LC182" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// Setup master list of evaluated models</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="183" 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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<pre style="margin: 0;">+<span id="LC183" 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;">masterList = {};</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="184" 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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<pre style="margin: 0;">+<span id="LC184" 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;">masterList:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="185" 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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<pre style="margin: 0;">+<span id="LC185" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    "model string": "model fitness (cAIC score)"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="186" 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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<pre style="margin: 0;">+<span id="LC186" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    model string is in the format: "{\n{bp1} \n{bp2} </span><span class="nf" style="color: #900; font-weight: 600;">...</span><span class="c1" style="color: #998; font-style: italic;">\n}"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    model fitness is either infinity (if not evaluated) or the numeric cAIC score</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">**/</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="brainfuck"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="190" 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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<pre style="margin: 0;">+<span id="LC190" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="168" 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="191" 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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<pre style="margin: 0;">+<span id="LC191" 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;">startWithBP = 0;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="192" 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">

192

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="brainfuck"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="193" 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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<pre style="margin: 0;">+<span id="LC193" 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 (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">masterList</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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<pre style="margin: 0;">+<span id="LC194" 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 ("</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="168" 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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<pre style="margin: 0;">+<span id="LC196" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">### Found partial run results in `gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">jsonFileLocation`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> </span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="197" 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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<pre style="margin: 0;">+<span id="LC197" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">Will resume search from the end of the previous run</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="198" 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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<pre style="margin: 0;">+<span id="LC198" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    ");</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="201" 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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<pre style="margin: 0;">+<span id="LC201" 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;">startWithBP = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">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 class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="168" 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="202" 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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<pre style="margin: 0;">+<span id="LC202" 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;">masterList = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</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;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">masterList</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="168" 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="203" 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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<pre style="margin: 0;">+<span id="LC203" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}  else {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="168" 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="204" 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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<pre style="margin: 0;">+<span id="LC204" 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 (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "breakpointData"</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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<pre style="margin: 0;">+<span id="LC205" 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 ("</span></span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    ### Found previous run results in `gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">jsonFileLocation`</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="LC208" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    Run terminating without overwriting previous results</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC210" 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="LC211" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        return 0;</span></span>

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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 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="LC216" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="197" 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">@@ -197,15 +243,6 @@ for (_pattern_; in; alignments.Extract_site_patterns ("gard.filter")) {</td>

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<pre style="margin: 0;"> <span id="LC243" 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="LC244" 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="LC245" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC200" 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="LC201" 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 (alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Extract_site_patterns ("gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_pattern_"</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="LC202" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (_pattern_</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;">is_constant</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">==FALSE) {</span></span>

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<pre style="margin: 0;">-<span id="LC203" 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 (_pattern_</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;">sites</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '_key_'</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>

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<pre style="margin: 0;">-<span id="LC204" 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="LC205" 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;">variableSiteMap </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;">siteMultiplier*_value_ </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;">siteShift);</span></span>

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<pre style="margin: 0;">-<span id="LC206" 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="LC207" 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="LC208" 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="LC246" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC247" 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;">variableSiteMap = Transpose (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DictToArray (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">variableSiteMap)) % 0; // sort by 1st column</span></span>

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<pre style="margin: 0;"> <span id="LC248" 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;">variableSites = Rows (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">variableSiteMap);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" 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="296" 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">@@ -259,21 +296,22 @@ io.ReportProgressMessageMD("GARD", "baseline-fit", "* " + selection.io.report_fi</td>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="brainfuck"><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="LC297" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// Setup mpi variableSiteMap</span></span>

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<pre style="margin: 0;"> <span id="LC298" 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;">createLikelihoodFunctionForExport ("gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">exportedModel"</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;">model);</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (fastRunMode) {</span></span>

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<pre style="margin: 0;">+<span id="LC301" 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;">SetEnvVariable ("OPTIMIZATION_PRECISION"</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">1); </span></span>

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<pre style="margin: 0;">+<span id="LC302" 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="LC303" 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;">SetEnvVariable ("OPTIMIZATION_PRECISION"</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">001);     </span></span>

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<pre style="margin: 0;">+<span id="LC304" 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="LC305" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC307" 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;">queue = mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">CreateQueue (</span></span>

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<pre style="margin: 0;"> <span id="LC308" 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="LC309" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            "LikelihoodFunctions" : {{"gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">exportedModel"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            "Headers" : {{"libv3/all</span><span class="nf" style="color: #900; font-weight: 600;">-</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;">bf"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="311" 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="LC266" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            "Variables" : {{"gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globalParameterCount"</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;">numSites"</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;">alignment"</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;">variableSiteMap"</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;">dataType"</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon"}}</span></span>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            "Variables" : {{"gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">globalParameterCount"</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;">numSites"</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;">alignment"</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;">variableSiteMap"</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;">dataType"</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">gard</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 class="idiff left">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">"OPTIMIZE_SUMMATION_ORDER_PARTITION"</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"> "OPTIMIZATION_PRECISION"</span>}}</span></span>

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<pre style="margin: 0;"> <span id="LC312" 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="LC313" 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="LC314" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// Setup master list of evaluated models</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>

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<pre style="margin: 0;">-<span id="LC271" 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;">masterList = {};</span></span>

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<pre style="margin: 0;">-<span id="LC272" 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;">masterList:</span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    "model string": "model fitness (cAIC score)"</span></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    model string is in the format: "{\n{bp1} \n{bp2} </span><span class="nf" style="color: #900; font-weight: 600;">...</span><span class="c1" style="color: #998; font-style: italic;">\n}"</span></span>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    model fitness is either infinity (if not evaluated) or the numeric cAIC score</span></span>

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<pre style="margin: 0;">-<span id="LC276" 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="LC315" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC316" 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;">masterList </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;"> = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_cAIC;</span></span>

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<pre style="margin: 0;"> <span id="LC317" 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;">bestOverall_cAIC_soFar = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_cAIC;</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">@@ -298,56 +336,63 @@ gard.json['baselineScore'] = gard.baseline_cAIC;</td>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="brainfuck"><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="LC337" 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('GARD'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'single</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">breakpoint'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'Performing an exhaustive single breakpoint analysis');</span></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">namespace gard {</span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // 2a1</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Loop over every valid single break point</span></span>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    singleBreakPointBest_cAIC = ^"math</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Infinity";</span></span>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">startWithBP </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 0) {</span></span>

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<pre style="margin: 0;">+<span id="LC341" 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('GARD'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'single</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">breakpoint'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'Single breakpoint analysis already completed</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="LC342" 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;">improvements = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"improvements"</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="LC343" 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="LC344" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    namespace gard {</span></span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    <span class="idiff left">for (breakPointIndex = 0; breakPointIndex </span></span><span class="nb" style="color: #0086b3;"><span class="idiff"><</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">variableSites </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"> 1;</span> break<span class="idiff">P</span>oint<span class="idiff">Index </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">= 1) {</span></span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        si<span class="idiff left">teIndex = variableSiteMap </span></span><span class="p"><span class="idiff">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff">breakPointIndex</span></span><span class="p"><span class="idiff right">]</span></span><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="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    <span class="idiff left">    // 2a1</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"> Loop over every valid single</span> break<span class="idiff right"> p</span>oint</span></span>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        si<span class="idiff left">ngleBreakPointBest_cAIC = ^"math</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">Infinity"</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (singleBreakPointBest_cAIC </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> baseline_cAIC) {</span></span>

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<pre style="margin: 0;">-<span id="LC310" 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;">ReportProgressBar ("GARD"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Breakpoint " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">  Format (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">breakPointIndex</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 10</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> " of " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (variableSites</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1) </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 cAIC = " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (singleBreakPointBest_cAIC</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 4) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">delta = " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (baseline_cAIC </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> singleBreakPointBest_cAIC</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 4) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> with breakpoint at site " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (singleBreakPointBestLocation</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 10</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0));</span></span>

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<pre style="margin: 0;">-<span id="LC311" 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="LC312" 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;">ReportProgressBar ("GARD"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Breakpoint " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">  Format (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">breakPointIndex</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 10</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> " of " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (variableSites</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1) </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 cAIC = " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (baseline_cAIC</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 4) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " with no breakpoints</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="LC313" 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="LC349" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (breakPointIndex = 0; breakPointIndex </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">variableSites </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1; breakPointIndex </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="LC350" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            siteIndex = variableSiteMap </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">breakPointIndex</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="LC351" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (singleBreakPointBest_cAIC </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> baseline_cAIC) {</span></span>

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<pre style="margin: 0;">+<span id="LC353" 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;">ReportProgressBar ("GARD"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Breakpoint " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">  Format (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">breakPointIndex</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 10</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> " of " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (variableSites</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1) </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 cAIC = " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (singleBreakPointBest_cAIC</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 4) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">delta = " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (baseline_cAIC </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> singleBreakPointBest_cAIC</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 4) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> with breakpoint at site " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (singleBreakPointBestLocation</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 10</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 0));</span></span>

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<pre style="margin: 0;">+<span id="LC354" 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="LC355" 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;">ReportProgressBar ("GARD"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Breakpoint " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">  Format (1</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">breakPointIndex</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 10</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> " of " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (variableSites</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1) </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 cAIC = " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Format (baseline_cAIC</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 4) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " with no breakpoints</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="LC356" 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="LC357" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="316" 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">

316

</td>

<td class="new_line diff-line-num old" data-linenumber="359" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC316" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">validatePartititon ({{siteIndex}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> minPartitionSize</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> numSites) == FALSE)  {</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="317" 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">

317

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<td class="new_line diff-line-num old" data-linenumber="359" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC317" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            continue;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="318" 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">

318

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<td class="new_line diff-line-num old" data-linenumber="359" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC318" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="319" 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="359" 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">

359

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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="LC359" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        <span class="idiff left right">    </span>if (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">validatePartititon ({{siteIndex}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> minPartitionSize</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> numSites) == FALSE)  {</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="319" 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="360" 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">

360

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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="LC360" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            <span class="idiff left right">    </span>continue;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="319" 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="361" 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">

361

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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="LC361" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        <span class="idiff left right">    </span>}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="319" 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">

319

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<td class="new_line diff-line-num" data-linenumber="362" 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">

362

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC362" class="line" lang="brainfuck"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="320" 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">

320

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<td class="new_line diff-line-num old" data-linenumber="363" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC320" class="line" lang="brainfuck"><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;">QueueJob (queue</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;">obtainModel_cAIC"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"0" : {{siteIndex__}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="321" 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">

321

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<td class="new_line diff-line-num old" data-linenumber="363" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC321" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                     "1" : model</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="322" 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">

322

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<td class="new_line diff-line-num old" data-linenumber="363" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                     "2" : baseLikelihoodInfo}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="323" 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">

323

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<td class="new_line diff-line-num old" data-linenumber="363" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC323" 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;">storeSingleBreakPointModelResults");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="324" 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="363" 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">

363

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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="LC363" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        <span class="idiff left right">    </span>mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">QueueJob (queue</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;">obtainModel_cAIC"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"0" : {{siteIndex__}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="324" 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="364" 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">

364

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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="LC364" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                     <span class="idiff left right">    </span>"1" : model</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="324" 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="365" 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">

365

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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="LC365" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                     <span class="idiff left right">    </span>"2" : baseLikelihoodInfo}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="324" 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="366" 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">

366

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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="LC366" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                     <span class="idiff left right">    </span>"gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">storeSingleBreakPointModelResults");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="324" 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">

324

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<td class="new_line diff-line-num" data-linenumber="367" 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">

367

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC367" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                     </span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="325" 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">

325

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<td class="new_line diff-line-num" data-linenumber="368" 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">

368

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC368" class="line" lang="brainfuck"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="326" 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">

326

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="327" 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="369" 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">

369

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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="LC369" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">    </span>    }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="327" 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">

327

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<td class="new_line diff-line-num" data-linenumber="370" 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">

370

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC370" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="328" 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">

328

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<td class="new_line diff-line-num old" data-linenumber="371" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC328" class="line" lang="brainfuck"><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;">QueueComplete (queue);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="329" 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">

329

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<td class="new_line diff-line-num old" data-linenumber="371" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC329" 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;">ClearProgressBar();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="330" 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="371" 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">

371

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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="LC371" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">    </span>    mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">QueueComplete (queue);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="330" 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="372" 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">

372

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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="LC372" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">    </span>    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ClearProgressBar();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="330" 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">

330

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<td class="new_line diff-line-num" data-linenumber="373" 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">

373

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC373" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="331" 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">

331

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<td class="new_line diff-line-num old" data-linenumber="374" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC331" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // 2a2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Report the status of the sinlge break point analysis</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="332" 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">

332

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<td class="new_line diff-line-num old" data-linenumber="374" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC332" 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('GARD'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'single</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">breakpoint'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'Done with single breakpoint analysis</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">');</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="333" 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">

333

</td>

<td class="new_line diff-line-num old" data-linenumber="374" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC333" 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('GARD'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'single</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">breakpoint'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ("   Best sinlge break point location: " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> singleBreakPointBestLocation));</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="334" 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">

334

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<td class="new_line diff-line-num old" data-linenumber="374" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC334" 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('GARD'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'single</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">breakpoint'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ("   c</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">AIC  = " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> singleBreakPointBest_cAIC));</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="335" 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">

335

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<td class="new_line diff-line-num old" data-linenumber="374" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="336" 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="374" 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">

374

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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="LC374" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">    </span>    // 2a2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Report the status of the sinlge break point analysis</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="336" 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="375" 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">

375

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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="LC375" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">    </span>    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD('GARD'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'single</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">breakpoint'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'Done with single breakpoint analysis</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">');</span></span>

</pre>

</td>

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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="336" 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="376" 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">

376

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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="LC376" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">    </span>    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD('GARD'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'single</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">breakpoint'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ("   Best sinlge break point location: " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> singleBreakPointBestLocation));</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">    </span>    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD('GARD'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'single</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">breakpoint'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ("   c</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">AIC  = " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> singleBreakPointBest_cAIC));</span></span>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">    </span>}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// 2a3</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Evaluate if the best single breakpoint is the overall best model</span></span>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">singleBreakPointBest_cAIC </span><span class="nb" style="color: #0086b3;"><</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;">bestOverall_cAIC_soFar) {</span></span>

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<pre style="margin: 0;">-<span id="LC339" 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;">bestOverall_cAIC_soFar = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">singleBreakPointBest_cAIC;</span></span>

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<pre style="margin: 0;">-<span id="LC340" 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;">bestOverallModelSoFar = {{gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">singleBreakPointBestLocation}};</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC341" 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;">improvements = {'0': {</span></span>

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                "deltaAICc": gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_cAIC </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;">bestOverall_cAIC_soFar</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                "breakpoints": gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bestOverallModelSoFar</span></span>

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<pre style="margin: 0;">-<span id="LC344" 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="LC345" 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="LC346" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">} else {</span></span>

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<td class="new_line diff-line-num old" data-linenumber="380" 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="LC347" 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;">bestOverallModelSoFar = null;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="348" 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="380" 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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<pre style="margin: 0;">+<span id="LC380" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // 2a3</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Evaluate if the best single breakpoint is the overall best model</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="348" 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="381" 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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<pre style="margin: 0;">+<span id="LC381" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">singleBreakPointBest_cAIC </span><span class="nb" style="color: #0086b3;"><</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;">bestOverall_cAIC_soFar) {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC382" 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;">bestOverall_cAIC_soFar = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">singleBreakPointBest_cAIC;</span></span>

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<pre style="margin: 0;">+<span id="LC383" 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;">bestOverallModelSoFar = {{gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">singleBreakPointBestLocation}};</span></span>

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<td class="new_line diff-line-num new" data-linenumber="384" 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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<pre style="margin: 0;">+<span id="LC384" 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;">improvements = {'0': {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="385" 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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<pre style="margin: 0;">+<span id="LC385" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "deltaAICc": gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_cAIC </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;">bestOverall_cAIC_soFar</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">                                    "breakpoints": gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bestOverallModelSoFar</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;">                                  }</span></span>

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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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<td class="new_line diff-line-num new" data-linenumber="389" 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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<pre style="margin: 0;">+<span id="LC389" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    } else {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="390" 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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<pre style="margin: 0;">+<span id="LC390" 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;">bestOverallModelSoFar = null;</span></span>

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<pre style="margin: 0;">+<span id="LC391" 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="LC392" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC393" 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;">concludeAnalysis(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bestOverallModelSoFar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> TRUE);</span></span>

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<pre style="margin: 0;"> <span id="LC394" 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="LC395" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC350" 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;">concludeAnalysis(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bestOverallModelSoFar);</span></span>

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/* 2b</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Evaluation of multiple break points with genetic algorithm</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="355" 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">@@ -355,6 +400,7 @@ gard.concludeAnalysis(gard.bestOverallModelSoFar);</td>

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<pre style="margin: 0;"> <span id="LC400" 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('GARD'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'multi</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">breakpoint'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 'Performing multi breakpoint analysis using a genetic algorithm');</span></span>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">namespace gard {</span></span>

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // GA</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1: Setup global parameters</span></span>

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    populationSize = 32; // the GARD paper used: (numberOfMpiNodes*2 </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 2) with 17 mpi nodes</span></span>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if(populationSize </span><span class="nb" style="color: #0086b3;"><</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;">NodeCount() </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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -364,15 +410,35 @@ namespace gard {</td>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    rateOfMutationsTharAreSmallShifts = 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">8; // some mutations are a new random break point; some are small shifts of the break point to an adjacent location</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    maxFailedAttemptsToMakeNewModel = 7;</span></span>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    cAIC_diversityThreshold   = 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">01;</span></span>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    cAIC_improvementThreshold = 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">01; // I think this was basically 0 in the gard paper</span></span>

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    maxGenerationsAllowedWithNoNewModelsAdded = 2; // TODO: Not in the GARD paper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> use 10?</span></span>

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    maxGenerationsAllowedAtStagnant_cAIC = 100; // TODO: this is set to 100 in the GARD paper</span></span>

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<pre style="margin: 0;">+<span id="LC413" 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="LC414" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (fastRunMode) {</span></span>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        maxGenerationsAllowedAtStagnant_cAIC = Min (populationSize</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 40);</span></span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        cAIC_improvementThreshold = 2;</span></span>

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<pre style="margin: 0;">+<span id="LC417" 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="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        maxGenerationsAllowedAtStagnant_cAIC = 100;</span></span>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        cAIC_improvementThreshold = 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">01;</span></span>

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<pre style="margin: 0;">+<span id="LC420" 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="LC421" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num new" data-linenumber="422" 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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<pre style="margin: 0;">+<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    maxGenerationsAllowedWithNoNewModelsAdded = maxGenerationsAllowedAtStagnant_cAIC $ 4; // TODO: Not in the GARD paper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> use 10?</span></span>

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<pre style="margin: 0;">+<span id="LC423" 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="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // GA</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">2: Loop over increasing number of break points</span></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    addingBreakPointsImproves_cAIC = TRUE;</span></span>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    numberOfBreakPointsBeingEvaluated = 1;</span></span>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (startWithBP </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 0) {</span></span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        numberOfBreakPointsBeingEvaluated = startWithBP;</span></span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC429" 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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<td class="new_line diff-line-num new" data-linenumber="430" 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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<pre style="margin: 0;">+<span id="LC430" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC432" 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="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC434" 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="LC435" 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="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        numberOfBreakPointsBeingEvaluated = 1;</span></span>

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<pre style="margin: 0;">+<span id="LC437" 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="LC438" 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="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    while(addingBreakPointsImproves_cAIC) {</span></span>

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<td class="new_line diff-line-num old" data-linenumber="440" 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="LC375" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        // GA</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">a Setup for n number of break points</span></span>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        //#profile START;</span></span>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       // GA</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">a Setup for n number of break points</span></span>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        numberOfBreakPointsBeingEvaluated</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="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        generationsAtCurrentBest_cAIC = 0;</span></span>

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<pre style="margin: 0;"> <span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        generationsNoNewModelsAdded = 0;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="477" 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="543" 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">@@ -477,7 +543,9 @@ namespace gard {</td>

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        } else {</span></span>

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<td class="new_line diff-line-num" data-linenumber="544" 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="LC544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            addingBreakPointsImproves_cAIC = FALSE;</span></span>

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="new_line diff-line-num old" data-linenumber="546" 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="LC480" 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;">concludeAnalysis(bestOverallModelSoFar);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="481" 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="546" 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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<pre style="margin: 0;">+<span id="LC546" 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;">concludeAnalysis(bestOverallModelSoFar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> addingBreakPointsImproves_cAIC);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="547" 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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<pre style="margin: 0;">+<span id="LC547" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        //#profile _hyphy_profile_dump;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="548" 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">

548

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<pre style="margin: 0;">+<span id="LC548" 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;">FinishAndPrintProfile (_hyphy_profile_dump);</span></span>

</pre>

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481

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<td class="new_line diff-line-num" data-linenumber="549" 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">

549

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="482" 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">

482

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<td class="new_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

550

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="483" 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">

483

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<td class="new_line diff-line-num" data-linenumber="551" 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">

551

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="508" 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="576" 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">@@ -508,7 +576,7 @@ namespace gard {</td>

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<td class="old_line diff-line-num" data-linenumber="508" 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">

508

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<td class="new_line diff-line-num" data-linenumber="576" 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="LC576" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="509" 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">

509

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<td class="new_line diff-line-num" data-linenumber="577" 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">

577

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<pre style="margin: 0;"> <span id="LC577" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="510" 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">

510

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<td class="new_line diff-line-num" data-linenumber="578" 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">

578

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<pre style="margin: 0;"> <span id="LC578" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fitPartitionedModel (breakPoints</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;"> initialValues</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> saveToFile</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> constrainToOneTopology) {</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="511" 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">

511

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<td class="new_line diff-line-num old" data-linenumber="579" 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="LC511" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="512" 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="579" 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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<pre style="margin: 0;">+<span id="LC579" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    //#profile START;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="512" 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">

512

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<td class="new_line diff-line-num" data-linenumber="580" 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">

580

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<pre style="margin: 0;"> <span id="LC580" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="513" 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">

513

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<td class="new_line diff-line-num" data-linenumber="581" 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">

581

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    currentIndex = 0;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="514" 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">

514

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<td class="new_line diff-line-num" data-linenumber="582" 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">

582

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    currentStart = 0;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="583" 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="651" 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">@@ -583,6 +651,9 @@ lfunction gard.fitPartitionedModel (breakPoints, model, initialValues, saveToFil</td>

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<td class="old_line diff-line-num" data-linenumber="583" 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">

583

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<td class="new_line diff-line-num" data-linenumber="651" 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">

651

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    DeleteObject (likelihoodFunction</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> :shallow);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="584" 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">

584

</td>

<td class="new_line diff-line-num" data-linenumber="652" 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">

652

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="585" 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">

585

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<td class="new_line diff-line-num" data-linenumber="653" 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">

653

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    res</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="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;">= df </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (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="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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">empirical"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="586" 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="654" 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">

654

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="586" 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="655" 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">

655

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<pre style="margin: 0;">+<span id="LC655" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    //#profile _fit_dump;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC656" 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;">FinishAndPrintProfile (_fit_dump); </span></span>

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586

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return res;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="brainfuck"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="659" 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="LC659" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="653" 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="724" 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">@@ -653,12 +724,19 @@ lfunction gard.modelIsNotInMasterList(masterList, breakPoints) {</td>

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<pre style="margin: 0;"> <span id="LC724" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    //return utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">KeyExists(masterList</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;"> breakPoints) == FALSE;</span></span>

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654

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<td class="new_line diff-line-num" data-linenumber="725" 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="LC725" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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655

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<td class="new_line diff-line-num" data-linenumber="726" 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="LC726" class="line" lang="brainfuck"></span>

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656

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<td class="new_line diff-line-num old" data-linenumber="727" 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="LC656" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">concludeAnalysis(bestOverallModel) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="657" 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="727" 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">

727

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<pre style="margin: 0;">+<span id="LC727" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">concludeAnalysis(bestOverallModel</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> writeMaster) {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="657" 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="728" 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">

728

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<pre style="margin: 0;">+<span id="LC728" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="729" 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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<pre style="margin: 0;">+<span id="LC729" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="old_line diff-line-num new" data-linenumber="657" 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="730" 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">

730

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<pre style="margin: 0;">+<span id="LC730" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (writeMaster) {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="657" 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="731" 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">

731

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<pre style="margin: 0;">+<span id="LC731" 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;">json)</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;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">masterList</span><span class="p">]</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;">masterList;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="657" 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="732" 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">

732

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<pre style="margin: 0;">+<span id="LC732" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    } else {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="657" 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="733" 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">

733

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<pre style="margin: 0;">+<span id="LC733" 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;">json) </span><span class="nf" style="color: #900; font-weight: 600;">-</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;">gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">masterList;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="657" 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="734" 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">

734

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<pre style="margin: 0;">+<span id="LC734" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre>

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657

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<td class="new_line diff-line-num" data-linenumber="735" 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">

735

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<pre style="margin: 0;"> <span id="LC735" 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;">json)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">'timeElapsed'</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = Time(1) </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;">startTime;</span></span>

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<td class="old_line diff-line-num" data-linenumber="658" 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">

658

</td>

<td class="new_line diff-line-num" data-linenumber="736" 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">

736

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<pre style="margin: 0;"> <span id="LC736" 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;">json)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">'siteBreakPointSupport'</span><span class="p">]</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;">getSiteBreakPointSupport(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">masterList</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;">bestOverall_cAIC_soFar);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="659" 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">

659

</td>

<td class="new_line diff-line-num" data-linenumber="737" 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">

737

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<pre style="margin: 0;"> <span id="LC737" 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;">json)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">'singleTreeAICc'</span><span class="p">]</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;">getSingleTree_cAIC(bestOverallModel);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="660" 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">

660

</td>

<td class="new_line diff-line-num" data-linenumber="738" 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">

738

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<pre style="margin: 0;"> <span id="LC738" 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;">json)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">'totalModelCount'</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = Abs(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">masterList);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="661" 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">

661

</td>

<td class="new_line diff-line-num old" data-linenumber="739" 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">

</td>

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<pre style="margin: 0;">-<span id="LC661" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="662" 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="739" 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">

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;">    (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">'bestModelAICc'</span><span class="p">]</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;">bestOverall_cAIC_soFar;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="662" 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">

662

</td>

<td class="new_line diff-line-num" data-linenumber="740" 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">

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;">    gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">setBestModelTreeInfoToJson(bestOverallModel);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="663" 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">

663

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<td class="new_line diff-line-num" data-linenumber="741" 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">

741

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC741" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="664" 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">

664

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<td class="new_line diff-line-num" data-linenumber="742" 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">

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;">    if(Abs((gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">'trees'</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;"> 1) {</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="721" 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="799" 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">@@ -721,38 +799,27 @@ lfunction gard.getSingleTree_cAIC(bestOverallModel) {</td>

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<td class="old_line diff-line-num" data-linenumber="721" 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">

721

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<td class="new_line diff-line-num" data-linenumber="799" 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">

799

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC799" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="722" 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">

722

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<td class="new_line diff-line-num" data-linenumber="800" 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">

800

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC800" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="723" 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">

723

</td>

<td class="new_line diff-line-num" data-linenumber="801" 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">

801

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC801" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getSiteBreakPointSupport(modelMasterList</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> best_cAIC_score) {</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="724" 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">

724

</td>

<td class="new_line diff-line-num old" data-linenumber="802" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC724" 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;">masterListModels = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Keys(modelMasterList);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="725" 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">

725

</td>

<td class="new_line diff-line-num old" data-linenumber="802" 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="LC725" 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;">masterList_cAIC_values = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Values(modelMasterList);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="726" 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">

726

</td>

<td class="new_line diff-line-num old" data-linenumber="802" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC726" 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;">numberOfModels = Columns(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">masterList_cAIC_values);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="727" 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">

727

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<td class="new_line diff-line-num old" data-linenumber="802" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC727" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="728" 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">

728

</td>

<td class="new_line diff-line-num old" data-linenumber="802" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC728" 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;">siteAkaikeWeights = {};</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="729" 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">

729

</td>

<td class="new_line diff-line-num old" data-linenumber="802" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC729" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for(modelIndex=0; modelIndex</span><span class="nb" style="color: #0086b3;"><</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;">numberOfModels; modelIndex=modelIndex</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1) {</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="730" 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">

730

</td>

<td class="new_line diff-line-num old" data-linenumber="802" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC730" 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;">cAIC_delta = best_cAIC_score </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;">masterList_cAIC_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">modelIndex</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="731" 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">

731

</td>

<td class="new_line diff-line-num old" data-linenumber="802" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC731" 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;">akaikeWeight = Exp(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">cAIC_delta * 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="732" 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">

732

</td>

<td class="new_line diff-line-num" data-linenumber="802" 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">

802

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC802" class="line" lang="brainfuck"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="733" 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">

733

</td>

<td class="new_line diff-line-num old" data-linenumber="803" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC733" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if( Abs(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">masterListModels</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">modelIndex</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;"> 3) {</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="734" 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">

734

</td>

<td class="new_line diff-line-num old" data-linenumber="803" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC734" 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;">breakPointMatrix = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Helper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">convertMatrixStringToMatrix(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">masterListModels</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">modelIndex</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="735" 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">

735

</td>

<td class="new_line diff-line-num old" data-linenumber="803" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC735" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        } else {</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="736" 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">

736

</td>

<td class="new_line diff-line-num old" data-linenumber="803" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC736" 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;">breakPointMatrix = 0;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="737" 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">

737

</td>

<td class="new_line diff-line-num old" data-linenumber="803" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC737" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="738" 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">

738

</td>

<td class="new_line diff-line-num old" data-linenumber="803" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC738" 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;">numberOfBreakPoints = Columns(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">breakPointMatrix);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="739" 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">

739

</td>

<td class="new_line diff-line-num old" data-linenumber="803" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC739" class="line" lang="brainfuck"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="740" 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">

740

</td>

<td class="new_line diff-line-num old" data-linenumber="803" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC740" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for(breakPointIndex=0; breakPointIndex</span><span class="nb" style="color: #0086b3;"><</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;">numberOfBreakPoints; breakPointIndex=breakPointIndex</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1) {</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="741" 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">

741

</td>

<td class="new_line diff-line-num old" data-linenumber="803" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC741" 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;">siteAkaikeWeights</span><span class="p">[</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;">breakPointMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">breakPointIndex</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;">= gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">akaikeWeight;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="742" 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="803" 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">

803

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC803" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    bp_support = {};</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="742" 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="804" 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">

804

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC804" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    total_weight = 0;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="742" 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="805" 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">

805

</td>

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<pre style="margin: 0;">+<span id="LC805" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (model</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> score; in; modelMasterList) {</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="806" 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">

806

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<pre style="margin: 0;">+<span id="LC806" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        aicw = Exp ((best_cAIC_score</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">score)*0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="742" 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="807" 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">

807

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<pre style="margin: 0;">+<span id="LC807" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (aicw </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 0) {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="742" 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="808" 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">

808

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<pre style="margin: 0;">+<span id="LC808" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            total_weight </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= aicw;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="742" 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="809" 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">

809

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<pre style="margin: 0;">+<span id="LC809" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            bps = Eval (model);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="742" 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="810" 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">

810

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<pre style="margin: 0;">+<span id="LC810" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            for (bp; in; bps) {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="742" 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="811" 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">

811

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<pre style="margin: 0;">+<span id="LC811" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                bp_support</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">bp</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;">= aicw;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="742" 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="812" 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">

812

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<pre style="margin: 0;">+<span id="LC812" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="742" 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">

742

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<td class="new_line diff-line-num" data-linenumber="813" 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">

813

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<pre style="margin: 0;"> <span id="LC813" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="743" 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">

743

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<td class="new_line diff-line-num" data-linenumber="814" 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">

814

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<pre style="margin: 0;"> <span id="LC814" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="744" 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">

744

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<td class="new_line diff-line-num old" data-linenumber="815" 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="LC744" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="745" 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">

745

</td>

<td class="new_line diff-line-num old" data-linenumber="815" 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="LC745" 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;">akaikeWeightScallingFactor = 1 / (Max(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">siteAkaikeWeights)</span><span class="p">[</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;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="746" 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">

746

</td>

<td class="new_line diff-line-num old" data-linenumber="815" 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="LC746" 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;">normalizedSiteAkaikeWeights = {};</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="747" 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">

747

</td>

<td class="new_line diff-line-num old" data-linenumber="815" 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="LC747" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="748" 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">

748

</td>

<td class="new_line diff-line-num old" data-linenumber="815" 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="LC748" 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;">potentialBreakPointList = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Keys(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">siteAkaikeWeights);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="749" 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">

749

</td>

<td class="new_line diff-line-num old" data-linenumber="815" 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="LC749" 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;">numberOfPotentialBreakPoints = Abs(gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">siteAkaikeWeights);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="750" 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">

750

</td>

<td class="new_line diff-line-num old" data-linenumber="815" 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="LC750" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for(breakPointIndex=0; breakPointIndex</span><span class="nb" style="color: #0086b3;"><</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;">numberOfPotentialBreakPoints; breakPointIndex</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) {</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="751" 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">

751

</td>

<td class="new_line diff-line-num old" data-linenumber="815" 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="LC751" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        siteIndex = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">potentialBreakPointList</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">breakPointIndex</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="815" 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="LC752" 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;">normalizedSiteAkaikeWeights</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">siteIndex</span><span class="p">]</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;">siteAkaikeWeights</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">siteIndex</span><span class="p">]</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;">akaikeWeightScallingFactor;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="753" 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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<pre style="margin: 0;">+<span id="LC815" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="new_line diff-line-num new" data-linenumber="816" 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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<pre style="margin: 0;">+<span id="LC816" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    normalized_support = {};</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC817" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (bp</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> support; in; bp_support) {</span></span>

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<pre style="margin: 0;">+<span id="LC818" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        normalized_support</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">bp</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = support / total_weight;</span></span>

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<pre style="margin: 0;"> <span id="LC819" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

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<td class="old_line diff-line-num old" data-linenumber="754" 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="LC754" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC755" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">normalizedSiteAkaikeWeights;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="756" 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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<pre style="margin: 0;">+<span id="LC820" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    DeleteObject (bp_support);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="756" 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="821" 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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<pre style="margin: 0;">+<span id="LC821" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return normalized_support;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC822" 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="LC823" 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="LC824" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC825" class="line" lang="brainfuck"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="779" 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="846" 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">@@ -779,7 +846,7 @@ lfunction gard.GA.initializeModels (numberOfBreakPoints, populationSize, numberO</td>

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<pre style="margin: 0;"> <span id="LC846" 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="LC847" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            breakPoints </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">breakpoint</span><span class="nf" style="color: #900; font-weight: 600;">.</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;"> = (^"gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">variableSiteMap") </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">Random(0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> numberOfPotentialBreakPoints)$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="LC848" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            breakPoints = gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Helper</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sortedMatrix(breakPoints);</span></span>

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782

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<td class="new_line diff-line-num old" data-linenumber="849" 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="LC782" class="line" lang="brainfuck"></span>

</pre>

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</td>

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849

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<pre style="margin: 0;">+<span id="LC849" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

</pre>

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783

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<td class="new_line diff-line-num" data-linenumber="850" 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">

850

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<pre style="margin: 0;"> <span id="LC850" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        } while (gard</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">validatePartititon (breakPoints</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;">minPartitionSize"</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;">numSites") == FALSE);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="784" 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">

784

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<td class="new_line diff-line-num" data-linenumber="851" 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">

851

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<pre style="margin: 0;"> <span id="LC851" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="785" 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">

785

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<td class="new_line diff-line-num" data-linenumber="852" 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">

852

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<pre style="margin: 0;"> <span id="LC852" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        initializedModels</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">breakPoints</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ^"math</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Infinity";</span></span>

</pre>

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<br>

</li>

<li id="e9da9a3aa17695c8e989fcc674d35432c64038e0">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#e9da9a3aa17695c8e989fcc674d35432c64038e0"><strong>res/TemplateBatchFiles/PairwiseRelativeRatio.bf</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" 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="38" 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">@@ -38,8 +38,7 @@ referenceSpecCount = ds.species;</td>

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38

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38

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="39" 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">

39

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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;">treeRead = 0;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="40" 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">

40

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40

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="brainfuck"></span>

</pre>

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41

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<td class="new_line diff-line-num old" data-linenumber="41" 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="LC41" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (IS_TREE_PRESENT_IN_DATA)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="42" 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">

42

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<td class="new_line diff-line-num old" data-linenumber="41" 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="LC42" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="43" 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="41" 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">

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;">if (IS_TREE_PRESENT_IN_DATA) {</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="43" 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">

43

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<td class="new_line diff-line-num" data-linenumber="42" 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">

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;"> treeString = DATAFILE_TREE;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="44" 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">

44

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<td class="new_line diff-line-num" data-linenumber="43" 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">

43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> treeRead = 1;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="45" 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">

45

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<td class="new_line diff-line-num" data-linenumber="44" 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">

44

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="65" 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="64" 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">@@ -65,36 +64,29 @@ for (counter = 1; counter<fileCount; counter = counter+1) {</td>

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65

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<td class="new_line diff-line-num" data-linenumber="64" 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="LC64" class="line" lang="brainfuck"></span>

</pre>

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66

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<pre style="margin: 0;"> <span id="LC65" 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;">"\n\n** All data files were read successfully **\n\n");</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="68" 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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<td class="new_line diff-line-num old" data-linenumber="67" 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="LC68" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (dataType)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="67" 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="LC69" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="70" 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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<td class="new_line diff-line-num old" data-linenumber="67" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC70" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (codeTables)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="71" 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">

71

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<td class="new_line diff-line-num old" data-linenumber="67" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC71" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="72" 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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<td class="new_line diff-line-num old" data-linenumber="67" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC72" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         dummy = ApplyGeneticCodeTable (codeTableMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="73" 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="67" 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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<pre style="margin: 0;">+<span id="LC67" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (dataType) {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="73" 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="68" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC68" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (codeTables) {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="73" 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="69" 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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<pre style="margin: 0;">+<span id="LC69" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         ApplyGeneticCodeTable (codeTableMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="73" 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="70" 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="LC70" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         ModelMatrixDimension = 0;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="74" 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="71" 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="LC71" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="75" 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="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSetFilter filteredData = CreateFilter (ds</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3</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;">GeneticCodeExclusions);</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="73" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC76" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="77" 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">

77

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<td class="new_line diff-line-num old" data-linenumber="73" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC77" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">else</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="78" 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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<td class="new_line diff-line-num old" data-linenumber="73" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC78" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="79" 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="73" 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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<pre style="margin: 0;">+<span id="LC73" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">} else {</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="79" 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="74" 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">

74

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC74" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> DataSetFilter filteredData = CreateFilter (ds</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="80" 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="75" 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">

75

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC75" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="76" 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">

76

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC76" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="77" 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">

77

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC77" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="83" 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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<td class="new_line diff-line-num old" data-linenumber="78" 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="LC83" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (treeRead)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="84" 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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<td class="new_line diff-line-num old" data-linenumber="78" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC84" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="85" 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="78" 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">

78

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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="LC78" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (treeRead) {</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="85" 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">

85

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<td class="new_line diff-line-num" data-linenumber="79" 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">

79

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC79" 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;"> "\n\nA tree was found in the data file:\n"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">treeString</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n\nWould you like to use it:(Y/N)?");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="86" 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">

86

</td>

<td class="new_line diff-line-num" data-linenumber="80" 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">

80

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC80" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fscanf (stdin</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "String"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> response);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="87" 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">

87

</td>

<td class="new_line diff-line-num old" data-linenumber="81" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC87" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((response=="n")||(response=="N"))</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="88" 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">

88

</td>

<td class="new_line diff-line-num old" data-linenumber="81" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC88" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> {</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="89" 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="81" 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">

81

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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="LC81" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((response=="n")||(response=="N")) {</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="89" 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">

89

</td>

<td class="new_line diff-line-num" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC82" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         treeRead = 0;</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="90" 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">

90

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<td class="new_line diff-line-num" data-linenumber="83" 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">

83

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC83" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="91" 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">

91

</td>

<td class="new_line diff-line-num" data-linenumber="84" 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">

84

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC84" 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;"> "\n\n");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="92" 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">

92

</td>

<td class="new_line diff-line-num" data-linenumber="85" 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">

85

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC85" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="93" 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">

93

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<td class="new_line diff-line-num" data-linenumber="86" 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">

86

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC86" class="line" lang="brainfuck"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="94" 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">

94

</td>

<td class="new_line diff-line-num old" data-linenumber="87" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC94" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (!treeRead)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="95" 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">

95

</td>

<td class="new_line diff-line-num old" data-linenumber="87" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC95" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="96" 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="87" 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">

87

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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="LC87" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (!treeRead) {</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="96" 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">

96

</td>

<td class="new_line diff-line-num" data-linenumber="88" 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">

88

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC88" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> SetDialogPrompt ("Please select a tree file for the data:");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="97" 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">

97

</td>

<td class="new_line diff-line-num old" data-linenumber="89" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC97" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fscanf (PROMPT_FOR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "String"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> treeString);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="98" 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="89" 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">

89

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC89" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fscanf (PROMPT_FOR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left">REWIND</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"> </span>"String"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> treeString);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="98" 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">

98

</td>

<td class="new_line diff-line-num" data-linenumber="90" 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">

90

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC90" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="99" 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">

99

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<td class="new_line diff-line-num" data-linenumber="91" 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">

91

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">SelectTemplateModel(filteredData);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" 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">@@ -104,30 +96,20 @@ global  RelRatio;</td>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relationString = ":=RelRatio*";</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">#include "selectModelParameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf";</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="LC99" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">SetDialogPrompt ("Save full results to:");</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">modelParameterCount = Rows("LAST_MODEL_PARAMETER_LIST");</span></span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fprintf (PROMPT_FOR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">CLEAR_FILE);</span></span>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="114" 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="LC102" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">tabulatedFileName = LAST_FILE_PATH;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">singleFileResults = {fileCount</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="LC118" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC104" 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;">"\n\n***** RUNNING SINGLE FILE ANALYSES *****\n\n");</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="brainfuck"></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;">fullParameterCount = 0;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num old" data-linenumber="107" 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="LC123" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/*MESSAGE_LOGGING = 0;*/</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="124" 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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<td class="new_line diff-line-num old" data-linenumber="107" 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="LC124" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="125" 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="LC125" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">OPTIMIZATION_PRECISION = OPTIMIZATION_PRECISION/10;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="126" 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="LC126" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="127" 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="LC107" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">timer = Time(0);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="128" 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="LC108" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="129" 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="LC109" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (counter = 1; counter</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= fileCount; counter </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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<td class="old_line diff-line-num" data-linenumber="130" 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="LC110" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        HarvestFrequencies (vectorOfFrequencies</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">filteredData</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1</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="LC111" 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="LC112" 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="LC113" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (FREQUENCY_SENSITIVE) {</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                modelMatrix = 0;</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="115" 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="LC115" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (USE_POSITION_SPECIFIC_FREQS) {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" 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="126" 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">@@ -144,34 +126,9 @@ for (counter = 1; counter<= fileCount; counter += 1) {</td>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="old_line diff-line-num" data-linenumber="145" 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="LC127" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="old_line diff-line-num" data-linenumber="146" 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="128" 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="LC128" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        Tree firstFileTree = treeString;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="147" 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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<td class="new_line diff-line-num old" data-linenumber="129" 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="LC147" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="148" 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="129" 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="LC129" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        LikelihoodFunction lf = (filteredData</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">firstFileTree);</span></span>

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<td class="old_line diff-line-num" data-linenumber="149" 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="LC130" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        Optimize (res</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">lf);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        DeleteObject (lf);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="152" 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="LC131" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="153" 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="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (counter</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">fileCount) {</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="154" 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="LC154" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                DeleteObject (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> :shallow);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="155" 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="LC155" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="156" 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="LC156" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                DataSet ds = ReadDataFile (stringMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="157" 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="LC157" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (dataType)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC158" 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="LC159" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        if (codeTables)</span></span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        {</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="161" 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="LC161" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                dummy = ApplyGeneticCodeTable (codeTableMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="162" 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="LC162" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                ModelMatrixDimension = 0;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="163" 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="LC163" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="164" 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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<td class="new_line diff-line-num old" data-linenumber="132" 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="LC164" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        DataSetFilter filteredData = CreateFilter (ds</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3</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;">GeneticCodeExclusions);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="165" 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="LC165" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="166" 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="LC166" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                else</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="167" 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="LC167" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                {</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="168" 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="LC168" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        DataSetFilter filteredData = CreateFilter (ds</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC169" 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="LC170" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC171" 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="LC172" 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="LC173" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                fullParameterCount = res</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;">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="LC174" 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="LC132" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        singleFileResults </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</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;"> = res</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;">0</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="LC133" 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;">"\nFile "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">stringMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</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="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">" : ln</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">likelihood = "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">res</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;">0</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="LC134" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (counter==1)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="204" 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="161" 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">@@ -204,6 +161,27 @@ for (counter = 1; counter<= fileCount; counter += 1) {</td>

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<pre style="margin: 0;"> <span id="LC161" 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="LC162" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                fprintf (tabulatedFileName</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;">res</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">counter3</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="LC163" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="new_line diff-line-num new" data-linenumber="164" 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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<pre style="margin: 0;">+<span id="LC164" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        DeleteObject (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> :shallow);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="165" 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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<pre style="margin: 0;">+<span id="LC165" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (counter</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">fileCount) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="166" 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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<pre style="margin: 0;">+<span id="LC166" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                DataSet ds = ReadDataFile (stringMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="167" 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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<pre style="margin: 0;">+<span id="LC167" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (dataType)</span></span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                {</span></span>

</pre>

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169

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        if (codeTables)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="170" 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">

170

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        {</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="171" 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">

171

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                ApplyGeneticCodeTable (codeTableMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="172" 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">

172

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                ModelMatrixDimension = 0;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        }</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="174" 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">

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        DataSetFilter filteredData = CreateFilter (ds</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3</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;">GeneticCodeExclusions);</span></span>

</pre>

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175

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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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="176" 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">

176

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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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="177" 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">

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;">                {</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="178" 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">

178

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        DataSetFilter filteredData = CreateFilter (ds</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="179" 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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<pre style="margin: 0;">+<span id="LC179" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="180" 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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<pre style="margin: 0;">+<span id="LC180" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="181" 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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<pre style="margin: 0;">+<span id="LC181" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        else</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="182" 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">

182

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        {</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="183" 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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<pre style="margin: 0;">+<span id="LC183" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                fullParameterCount = res</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;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="184" 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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<pre style="margin: 0;">+<span id="LC184" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="185" 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">

185

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="186" 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">

186

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="209" 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">

209

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<td class="new_line diff-line-num" data-linenumber="187" 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">

187

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/*OPTIMIZATION_PRECISION = OPTIMIZATION_PRECISION*10;*/</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -222,17 +200,17 @@ fprintf(stdout,"\n\n In the summary table below");</td>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC201" 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;">"\n\n (*)   corresponds to the </span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">05 significance level\n (**)  corresponds to the </span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">01 significance level\n (***) corresponds to the </span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">001 significance level</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">\n\n");</span></span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">separator = "</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="LC226" 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;">separator</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n| File 1 | File 2 |      LRT     |    P</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">Value   |\n"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">separator);</span></span>

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<pre style="margin: 0;">+<span id="LC203" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">separator = "</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;">";</span></span>

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<pre style="margin: 0;">+<span id="LC204" 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;">separator</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n| File 1 | File 2 |      LRT     |   <span class="idiff left">Rel</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">Ratio  |   </span> P</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">Value   |\n"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">separator);</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (counter = 0; counter</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> fileCount; counter = <span class="idiff left">counter</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff right">+</span></span><span class="c1" style="color: #998; font-style: italic;">1) {</span></span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (counter = 0; counter</span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> fileCount; counter </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;">= 1) {</span></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    DataSet ds = ReadDataFile (stringMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</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="LC208" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (dataType)</span></span>

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<pre style="margin: 0;"> <span id="LC210" 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="LC211" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (codeTables)</span></span>

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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="LC235" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        <span class="idiff left right">dummy = </span>ApplyGeneticCodeTable (codeTableMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</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="LC213" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        ApplyGeneticCodeTable (codeTableMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</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="LC214" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        ModelMatrixDimension = 0;</span></span>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

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<td class="old_line diff-line-num" data-linenumber="238" 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="216" 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="LC216" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                DataSetFilter filteredData = CreateFilter (ds</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3</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;">GeneticCodeExclusions);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="269" 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="247" 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">@@ -269,7 +247,7 @@ for (counter = 0; counter< fileCount; counter = counter+1) {</td>

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<pre style="margin: 0;"> <span id="LC247" 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="LC248" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        if (codeTables)</span></span>

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<pre style="margin: 0;"> <span id="LC249" 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="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                <span class="idiff left right">dummy = </span>ApplyGeneticCodeTable (codeTableMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter2</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="LC250" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                ApplyGeneticCodeTable (codeTableMatrix</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter2</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="LC251" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                ModelMatrixDimension = 0;</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        }</span></span>

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<td class="old_line diff-line-num" data-linenumber="275" 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="253" 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="LC253" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        DataSetFilter filteredData2 = CreateFilter (ds2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3</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;">GeneticCodeExclusions);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="297" 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="275" 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">@@ -297,53 +275,49 @@ for (counter = 0; counter< fileCount; counter = counter+1) {</td>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                Model RRmodel2 = (modelMatrix2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">vectorOfFrequencies2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">MULTIPLY_BY_FREQS);</span></span>

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<pre style="margin: 0;"> <span id="LC276" 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="LC277" 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="LC278" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                Tree secondFileTree = treeString;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                ReplicateConstraint (constraintString</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">secondFileTree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">firstFileTree);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="brainfuck"></span>

</pre>

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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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<pre style="margin: 0;"> <span id="LC284" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                LikelihoodFunction lfConstrained = (filteredData2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">secondFileTree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">filteredData</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">firstFileTree);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                Optimize (res1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">lfConstrained);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="309" 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="LC287" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                LRT = 2*(singleFileResults</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">singleFileResults</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">counter2</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">res1</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;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="288" 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="LC288" class="line" lang="brainfuck"></span>

</pre>

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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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="311" 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="290" 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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<pre style="margin: 0;">+<span id="LC290" 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;"> lfConstrained);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="311" 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="291" 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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<pre style="margin: 0;">+<span id="LC291" 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;"> lfE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="292" 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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<pre style="margin: 0;">+<span id="LC292" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        */</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="293" 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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<pre style="margin: 0;">+<span id="LC293" class="line" lang="brainfuck"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="294" 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="LC294" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                degFDiff = 2*fullParameterCount</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">res1</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;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="brainfuck"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="296" 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="LC313" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (LRT</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">0)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="315" 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="296" 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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<pre style="margin: 0;">+<span id="LC296" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (LRT</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">0) {</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="315" 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="297" 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="LC297" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        pValue = 1</span><span class="nf" style="color: #900; font-weight: 600;">.</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;">CChi2(LRT</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">degFDiff);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                else</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                else {</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="319" 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="LC300" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        pValue = 1;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="320" 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="LC301" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        fprintf (MESSAGE_LOG</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\nA negative LRT statistic encoutered</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> You may want to increase the optimization precision settings to resolve numerical apporximation errors");</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="322" 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="303" 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="LC303" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="323" 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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<td class="new_line diff-line-num old" data-linenumber="304" 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="LC323" 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;">" | "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Format (LRT</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">5)</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;"> Format (pValue</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">" |");</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="324" 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="304" 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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<pre style="margin: 0;">+<span id="LC304" 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;">" | "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Format (LRT</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">5)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">" | <span class="idiff left">"</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">Format (RelRatio</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">12</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">5)</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">" | </span>"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Format (pValue</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">12</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">8)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">" |");</span></span>

</pre>

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<td class="new_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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<pre style="margin: 0;"> <span id="LC305" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (pValue</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;">05)</span></span>

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326

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                {</span></span>

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<td class="old_line diff-line-num old" data-linenumber="327" 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">

327

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<td class="new_line diff-line-num old" data-linenumber="306" 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="LC327" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        if (pValue</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;">01)</span></span>

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328

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        {</span></span>

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<td class="old_line diff-line-num old" data-linenumber="329" 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">

329

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<td class="new_line diff-line-num old" data-linenumber="306" 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="LC329" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                if (pValue</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;">001)</span></span>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="331" 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="306" 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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<pre style="margin: 0;">+<span id="LC306" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (pValue</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;">05) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="331" 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="307" 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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<pre style="margin: 0;">+<span id="LC307" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        if (pValue</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;">01) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="331" 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="308" 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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<pre style="margin: 0;">+<span id="LC308" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                if (pValue</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;">001) {</span></span>

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309

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<pre style="margin: 0;"> <span id="LC309" 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;">" (***) ");</span></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                }</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="311" 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="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                else</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="311" 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="LC334" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                {</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="311" 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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<pre style="margin: 0;">+<span id="LC311" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                else {</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="312" 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="LC312" 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;">" (**) ");</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="313" 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="LC313" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="337" 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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<td class="new_line diff-line-num old" data-linenumber="314" 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="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="338" 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">

338

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<td class="new_line diff-line-num old" data-linenumber="314" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        else</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="339" 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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<td class="new_line diff-line-num old" data-linenumber="314" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC339" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        {</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" 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="LC315" 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;">" (*) ");</span></span>

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<pre style="margin: 0;"> <span id="LC316" 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="LC317" 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="LC318" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if ((counter==0)&&(counter2==1))</span></span>

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<pre style="margin: 0;">-<span id="LC345" 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="LC346" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        fprintf (tabulatedFileName</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n\nRelative Ratio Tests\n\nFile 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">File 2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Ln</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">Likelihood</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LRT</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">pValue");</span></span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if ((counter==0)&&(counter2==1)) {</span></span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        fprintf (tabulatedFileName</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n\nRelative Ratio Tests\n\nFile 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">File 2</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Ln</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">Likelihood</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LRT</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">RelRatio</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">pValue");</span></span>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        dataDimension = Columns(res1);</span></span>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        for (counter3 = 0; counter3 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> dataDimension; counter3=counter3</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="LC323" 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">@@ -352,12 +326,13 @@ for (counter = 0; counter< fileCount; counter = counter+1) {</td>

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<pre style="margin: 0;"> <span id="LC326" 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="LC327" 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="LC328" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                fprintf (tabulatedFileName</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Format(counter</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">0)</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;">Format(counter2</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">0)</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;">res1</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;">0</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;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LRT</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;">pValue);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="356" 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">

356

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<td class="new_line diff-line-num old" data-linenumber="329" 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="LC356" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                for (counter3 = 0; counter3 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> dataDimension; counter3=counter3</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="357" 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">

357

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<td class="new_line diff-line-num old" data-linenumber="329" 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="LC357" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="358" 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="329" 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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<pre style="margin: 0;">+<span id="LC329" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                fprintf (tabulatedFileName</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">Format(counter</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">0)</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;">Format(counter2</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">0)</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;">res1</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;">0</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;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LRT</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;">RelRation</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;">pValue);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="358" 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="330" 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">

330

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                for (counter3 = 0; counter3 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> dataDimension; counter3=counter3</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">1) {</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="358" 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">

358

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<td class="new_line diff-line-num" data-linenumber="331" 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">

331

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<pre style="margin: 0;"> <span id="LC331" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        fprintf (tabulatedFileName</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;">res1</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">counter3</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="359" 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">

359

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<td class="new_line diff-line-num" data-linenumber="332" 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">

332

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="360" 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="333" 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">

333

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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="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                DeleteObject (lfConstrained</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> :shallow);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="360" 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">

360

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<td class="new_line diff-line-num" data-linenumber="334" 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">

334

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="361" 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="335" 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">

335

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="361" 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">

361

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<td class="new_line diff-line-num" data-linenumber="336" 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">

336

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="362" 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">

362

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<td class="new_line diff-line-num" data-linenumber="337" 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">

337

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="363" 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">

363

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<td class="new_line diff-line-num" data-linenumber="338" 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">

338

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<pre style="margin: 0;"> <span id="LC338" 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;">"\n"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">separator</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"\n");</span></span>

</pre>

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</li>

<li id="cf5243a3058ebeab74574f8cd2c771cd63a43208">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#cf5243a3058ebeab74574f8cd2c771cd63a43208"><strong>res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="920" 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="920" 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">@@ -920,6 +920,9 @@ function relax.FitMainTestPair () {</td>

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920

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<pre style="margin: 0;"> <span id="LC920" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        } else {</span></span>

</pre>

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921

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921

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<pre style="margin: 0;"> <span id="LC921" class="line" lang="brainfuck"><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;">SetRange (model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalParameter (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_object_map </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test"</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;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k)</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k_range1);</span></span>

</pre>

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922

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922

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<pre style="margin: 0;"> <span id="LC922" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        }</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="923" 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="923" 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">

923

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<pre style="margin: 0;">+<span id="LC923" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="923" 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="924" 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">

924

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<pre style="margin: 0;">+<span id="LC924" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        //assert (__SIGTRAP__);</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="925" 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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<pre style="margin: 0;">+<span id="LC925" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                </span></span>

</pre>

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923

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<td class="new_line diff-line-num" data-linenumber="926" 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">

926

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<pre style="margin: 0;"> <span id="LC926" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</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;">take2 =  estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FitLF (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_names</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">trees</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> { "0" : relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_map}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

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924

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<td class="new_line diff-line-num" data-linenumber="927" 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">

927

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<pre style="margin: 0;"> <span id="LC927" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                                                                                                   relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</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>

</pre>

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925

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<td class="new_line diff-line-num" data-linenumber="928" 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">

928

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<pre style="margin: 0;"> <span id="LC928" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                                                                                                   relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_object_map</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="927" 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="930" 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">@@ -927,6 +930,7 @@ function relax.FitMainTestPair () {</td>

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927

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<td class="new_line diff-line-num" data-linenumber="930" 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">

930

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<pre style="margin: 0;"> <span id="LC930" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                                                                                                   );</span></span>

</pre>

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928

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931

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<pre style="margin: 0;"> <span id="LC931" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="929" 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">

929

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<td class="new_line diff-line-num" data-linenumber="932" 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">

932

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<pre style="margin: 0;"> <span id="LC932" class="line" lang="brainfuck"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="930" 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="933" 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">

933

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<pre style="margin: 0;">+<span id="LC933" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

</pre>

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930

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<td class="new_line diff-line-num" data-linenumber="934" 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">

934

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<pre style="margin: 0;"> <span id="LC934" class="line" lang="brainfuck"></span>

</pre>

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931

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<td class="new_line diff-line-num" data-linenumber="935" 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">

935

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<pre style="margin: 0;"> <span id="LC935" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</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;">take2 </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;">log_likelihood</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;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</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;">log_likelihood</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="932" 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">

932

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<td class="new_line diff-line-num" data-linenumber="936" 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">

936

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<pre style="margin: 0;"> <span id="LC936" class="line" lang="brainfuck"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="947" 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="951" 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">@@ -947,6 +951,7 @@ function relax.FitMainTestPair () {</td>

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<td class="old_line diff-line-num" data-linenumber="947" 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">

947

</td>

<td class="new_line diff-line-num" data-linenumber="951" 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">

951

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<pre style="margin: 0;"> <span id="LC951" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit = relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</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;">take2;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="948" 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">

948

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<td class="new_line diff-line-num" data-linenumber="952" 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">

952

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<pre style="margin: 0;"> <span id="LC952" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="949" 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">

949

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<td class="new_line diff-line-num" data-linenumber="953" 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">

953

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<pre style="margin: 0;"> <span id="LC953" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="950" 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="954" 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">

954

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<pre style="margin: 0;">+<span id="LC954" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            DeleteObject (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</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;">take2);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="950" 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">

950

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<td class="new_line diff-line-num" data-linenumber="955" 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">

955

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<pre style="margin: 0;"> <span id="LC955" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="951" 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">

951

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<td class="new_line diff-line-num" data-linenumber="956" 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">

956

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<pre style="margin: 0;"> <span id="LC956" class="line" lang="brainfuck"><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;">SetRange (model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalParameter (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_object_map </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test"</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;"> terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k)</span><span class="nf" style="color: #900; font-weight: 600;">,</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;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k_range);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="952" 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">

952

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<td class="new_line diff-line-num" data-linenumber="957" 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">

957

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<pre style="margin: 0;"> <span id="LC957" class="line" lang="brainfuck"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="995" 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="1000" 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">@@ -995,8 +1000,7 @@ function relax.FitMainTestPair () {</td>

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<td class="old_line diff-line-num" data-linenumber="995" 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">

995

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<td class="new_line diff-line-num" data-linenumber="1000" 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">

1000

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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="996" 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">

996

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<td class="new_line diff-line-num" data-linenumber="1001" 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">

1001

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<pre style="margin: 0;"> <span id="LC1001" 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 ("RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "null"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Fitting the null (K := 1) model");</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="997" 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">

997

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<td class="new_line diff-line-num" data-linenumber="1002" 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">

1002

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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="998" 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">

998

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<td class="new_line diff-line-num old" data-linenumber="1003" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC998" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="999" 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">

999

</td>

<td class="new_line diff-line-num old" data-linenumber="1003" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC999" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1000" 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="1003" 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">

1003

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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre>

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1000

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<td class="new_line diff-line-num" data-linenumber="1004" 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">

1004

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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       for (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k = 1; relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">numbers_of_tested_groups; relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1001" 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">

1001

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<td class="new_line diff-line-num" data-linenumber="1005" 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">

1005

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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">               relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_nmsp = relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_namespaces</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k </span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1002" 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">

1002

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<td class="new_line diff-line-num" data-linenumber="1006" 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">

1006

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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">               if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 1) {</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1006" 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="1010" 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">@@ -1006,7 +1010,6 @@ function relax.FitMainTestPair () {</td>

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<td class="old_line diff-line-num" data-linenumber="1006" 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">

1006

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<td class="new_line diff-line-num" data-linenumber="1010" 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">

1010

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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">               }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1007" 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">

1007

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<td class="new_line diff-line-num" data-linenumber="1011" 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">

1011

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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1008" 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">

1008

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<td class="new_line diff-line-num" data-linenumber="1012" 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">

1012

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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1009" 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">

1009

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<td class="new_line diff-line-num old" data-linenumber="1013" 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="LC1009" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1010" 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">

1010

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<td class="new_line diff-line-num" data-linenumber="1013" 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">

1013

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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">null_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FitExistingLF (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</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;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_object_map);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1011" 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">

1011

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<td class="new_line diff-line-num" data-linenumber="1014" 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">

1014

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<pre style="margin: 0;"> <span id="LC1014" 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 ("RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "null"</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;"> selection</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;">report_fit (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">null_model</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;"> 9</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_data_info</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;">sample_size</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1012" 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">

1012

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<td class="new_line diff-line-num" data-linenumber="1015" 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">

1015

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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LRT = math</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DoLRT (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">null_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</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;">log_likelihood</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</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;">log_likelihood</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">numbers_of_tested_groups</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>

</pre>

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<br>

</li>

<li id="c079be28c5231888d711d5c41d1be180223dfce6">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#c079be28c5231888d711d5c41d1be180223dfce6"><strong>res/TemplateBatchFiles/SelectionAnalyses/modules/shared-load-file.bf</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_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="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">@@ -103,8 +103,10 @@ function load_file (prefix) {</td>

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103

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103

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<pre style="margin: 0;"> <span id="LC103" 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;">SetEnvVariable(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;">trees</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data_for_neighbor_joining")</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                           codon_data_info</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;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">datafilter")</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="LC105" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    partitions_and_trees = trees</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadAnnotatedTreeTopology</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">match_partitions (codon_data_info</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;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partitions")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> name_mapping);</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC110" 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;">SetEnvVariable(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;">trees</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data_for_neighbor_joining")</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="LC111" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        /**  this will return a dictionary of partition strings and trees; one set per partition</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> as in</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">@@ -155,7 +157,8 @@ function load_file (prefix) {</td>

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<pre style="margin: 0;"> <span id="LC157" 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="LC158" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        selected_branches = selection</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;">defineBranchSets(partitions_and_trees);</span></span>

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<pre style="margin: 0;"> <span id="LC159" 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="LC158" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC160" 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="LC161" 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="LC162" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // Place in own attribute called `tested`</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     selection</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;">json_store_key_value_pair (json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> None</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tested")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> selected_branches);</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="brainfuck"></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="219" 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">@@ -216,8 +219,10 @@ function load_file (prefix) {</td>

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<pre style="margin: 0;"> <span id="LC219" 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="LC220" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function store_tree_information () {</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;">    // Place in own attribute called `tested`</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // Place in own attribute called `tested`</span></span>

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<pre style="margin: 0;">+<span id="LC224" 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="LC225" 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="LC226" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     selection</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;">json_store_key_value_pair (json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> None</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">tested")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> selected_branches);</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        /**  this will return a dictionary of selected branches; one set per partition</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> like in</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">@@ -255,6 +260,7 @@ function store_tree_information () {</td>

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<pre style="margin: 0;"> <span id="LC260" 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="LC261" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    selection</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;">json_store_key_value_pair (json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> None</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partitions")</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                         filter_specification);</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     trees = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Map (partitions_and_trees</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_partition_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '_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;">tree</span><span class="p">]</span><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">@@ -263,11 +269,31 @@ function store_tree_information () {</td>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     filter_names = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Map (filter_specification</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_partition_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '_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;">name</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="LC270" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     /* Store original name mapping */</span></span>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     for (partition_index = 0; partition_index </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> partition_count; partition_index </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="LC267" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        selection</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;">json_store_branch_attribute(json</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;">original_name")</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">node_label")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> display_orders</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;">original_name")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                         partition_index</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                         name_mapping);</span></span>

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<pre style="margin: 0;">+<span id="LC272" 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="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     if (None != name_mapping) {</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         name_mapping_upper_case = {};</span></span>

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<pre style="margin: 0;">+<span id="LC275" 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;">n; in; name_mapping) {</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">             name_mapping_upper_case</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i&&1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = n;</span></span>

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<pre style="margin: 0;">+<span id="LC277" 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="LC278" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         for (partition_index = 0; partition_index </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> partition_count; partition_index </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="LC280" 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="LC281" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            local_name_mapping = {};</span></span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            for (l</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> label; in; (trees</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;">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;">trees</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partitioned")</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="LC283" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (label == ^"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;">leaf") {</span></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    if (name_mapping / l) {</span></span>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        local_name_mapping </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">l</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = name_mapping </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">l</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="LC286" 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="LC287" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        local_name_mapping </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">l</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = name_mapping_upper_case </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">l</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC288" 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="LC289" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC291" 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="LC292" 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="LC293" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            selection</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;">json_store_branch_attribute(json</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;">original_name")</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">node_label")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> display_orders</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;">original_name")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                             partition_index</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                             local_name_mapping);</span></span>

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<pre style="margin: 0;">+<span id="LC296" 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="LC297" 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="LC298" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="brainfuck"></span>

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<br>

</li>

<li id="0843f8cd833e50a0ae1b16d6b9265232dd51e8b5">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#0843f8cd833e50a0ae1b16d6b9265232dd51e8b5"><strong>res/TemplateBatchFiles/TemplateModels/GY94.ibf</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">/* defines a sparse transition probabilities matrix </span>

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> now we'll go through the matrix and assign the elements based on syn/non-syn status*/</span>

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">function PopulateModelMatrix (ModelMatrixName&, EFV)</span>

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5

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">{</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">function PopulateModelMatrix (ModelMatrixName&, EFV) {</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">      ModelMatrixName = {ModelMatrixDimension,ModelMatrixDimension}; </span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>

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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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">      hshift = 0;</span>

</pre>

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<br>

</li>

<li id="a4592f091dc497086884a23526cefa41e6c904e3">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#a4592f091dc497086884a23526cefa41e6c904e3"><strong>res/TemplateBatchFiles/TemplateModels/GY94.mdl</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,8 +18,7 @@</td>

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18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">ModelMatrixDimension = 0;</span>

</pre>

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<td class="old_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">

20

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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="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="21" 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">

21

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<td class="new_line diff-line-num old" data-linenumber="21" 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="LC21" class="line" lang="plaintext">if (!ModelMatrixDimension)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="22" 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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<td class="new_line diff-line-num old" data-linenumber="21" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">{</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="23" 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="21" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">if (!ModelMatrixDimension) {</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="23" 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">

23

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<td class="new_line diff-line-num" data-linenumber="22" 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="LC22" class="line" lang="plaintext">     ModelMatrixDimension = 64;</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="24" 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="23" 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="LC23" class="line" lang="plaintext">     for (h = 0 ;h<64; h=h+1)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="25" 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="24" 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="LC24" class="line" lang="plaintext">     {</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" 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="29" 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">@@ -30,8 +29,7 @@ if (!ModelMatrixDimension)</td>

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<td class="old_line diff-line-num" data-linenumber="30" 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="29" 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="LC29" class="line" lang="plaintext">     }</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="31" 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="30" 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="LC30" class="line" lang="plaintext">}</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="32" 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="31" 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="LC31" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="33" 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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<td class="new_line diff-line-num old" data-linenumber="32" 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="LC33" class="line" lang="plaintext">function BuildCodonFrequencies (obsF)</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="34" 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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<td class="new_line diff-line-num old" data-linenumber="32" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">{</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="35" 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="32" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">function BuildCodonFrequencies (obsF) {</span>

</pre>

</td>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" data-linenumber="33" 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="LC33" class="line" lang="plaintext">     PIStop = 1.0;</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="36" 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="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">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">     result = {ModelMatrixDimension,1};</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="37" 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="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">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">     hshift = 0;</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" 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="85" 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">@@ -87,14 +85,9 @@ if (modelType>0)</td>

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<td class="old_line diff-line-num" data-linenumber="87" 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="85" 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="LC85" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="88" 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="86" 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="LC86" class="line" lang="plaintext">#include "GY94.ibf";</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="89" 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="87" 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="LC87" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="90" 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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<td class="new_line diff-line-num old" data-linenumber="88" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="91" 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="LC88" class="line" lang="plaintext">GY94 = 0;</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="92" 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">

92

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<td class="new_line diff-line-num old" data-linenumber="89" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="93" 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">

93

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<td class="new_line diff-line-num" data-linenumber="89" 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="LC89" class="line" lang="plaintext">vectorOfFrequencies = BuildCodonFrequencies (observedFreq);</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="94" 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">

94

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<td class="new_line diff-line-num old" data-linenumber="90" 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="LC94" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="95" 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">

95

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<td class="new_line diff-line-num" data-linenumber="90" 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">

90

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">MULTIPLY_BY_FREQS = PopulateModelMatrix ("GY94", observedFreq);</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="96" 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">

96

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<td class="new_line diff-line-num old" data-linenumber="91" 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="LC96" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="97" 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">

97

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91

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">FREQUENCY_SENSITIVE = 1;</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="92" 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="LC98" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="99" 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="LC92" class="line" lang="plaintext">Model GY94model = (GY94,vectorOfFrequencies,1);</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="93" 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="LC93" class="line" lang="plaintext"></span></pre>

</td>

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<br>

</li>

<li id="5162429bd3f362a69890c6b040d4be37e11a6308">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#5162429bd3f362a69890c6b040d4be37e11a6308"><strong>res/TemplateBatchFiles/files.lst</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" 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="108" 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">@@ -108,4 +108,4 @@</td>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="109" 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="LC109" class="line" lang="plaintext">"","Perform relative ratio tests.","!Relative Ratio";</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="110" 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="110" 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="LC110" class="line" lang="plaintext">"RRT","Use relative ratio test on 2 datasets and a variety of standard models","RelativeRatio.bf";</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="111" 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">

111

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<td class="new_line diff-line-num old" data-linenumber="111" 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="LC111" class="line" lang="plaintext">"PRRTI","Given a list of files (and optinally genetic code tables), perform relative ratio tests on all possible pair of the data files.","PairwiseRelativeRatio.bf";</span></pre>

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<td class="old_line diff-line-num new" data-linenumber="112" 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="111" 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">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">"PRRTI","Given a list of files (and opti<span class="idiff left right">o</span>nally genetic code tables), perform relative ratio tests on all possible pair of the data files.","PairwiseRelativeRatio.bf";</span></pre>

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</li>

<li id="c50a9ebb34fca832759d3d11698588f8851c99cb">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#c50a9ebb34fca832759d3d11698588f8851c99cb"><strong>res/TemplateBatchFiles/libv3/UtilityFunctions.bf</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1074" 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="1074" 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">@@ -1074,3 +1074,10 @@ function utility.FinishAndPrintProfile (_hyphy_profile_dump) {</td>

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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1076" 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="1076" 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="LC1076" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1077" 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="1077" 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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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">TrapAllErrors (command) {</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1078" 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">

1078

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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="LC1078" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1077" 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="1079" 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">

1079

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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="LC1079" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    LAST_HBL_EXECUTION_ERROR = "";</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1077" 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="1080" 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">

1080

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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    ExecuteCommands ("SetParameter(HBL_EXECUTION_ERROR_HANDLING</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> command);</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1081" 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">

1081

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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return LAST_HBL_EXECUTION_ERROR;</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="1082" 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">

1082

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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="1083" 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">

1083

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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="brainfuck"></span></pre>

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</li>

<li id="04266769a57e3da898ac30696629599a2dbf70a6">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#04266769a57e3da898ac30696629599a2dbf70a6"><strong>res/TemplateBatchFiles/libv3/convenience/regexp.bf</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" 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="115" 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">@@ -115,7 +115,7 @@ lfunction regexp.PartitionByRegularExpressions(strings, rex) {</td>

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115

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115

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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116

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="117" 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">

117

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117

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="118" 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">

118

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="119" 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="118" 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">

118

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="119" 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">

119

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<td class="new_line diff-line-num" data-linenumber="119" 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">

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return result;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="120" 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">

120

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<td class="new_line diff-line-num" data-linenumber="120" 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">

120

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="121" 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">

121

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<td class="new_line diff-line-num" data-linenumber="121" 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">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="brainfuck"></span>

</pre>

</td>

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<br>

</li>

<li id="e7b72a8f9f424fe1e9e9e76f25522816189c14c9">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#e7b72a8f9f424fe1e9e9e76f25522816189c14c9"><strong>res/TemplateBatchFiles/libv3/tasks/alignments.bf</strong></a>

<hr>

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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="828" 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="828" 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">@@ -828,26 +828,6 @@ lfunction alignments.Extract_site_patterns (data_filter) {</td>

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828

</td>

<td class="new_line diff-line-num" data-linenumber="828" 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">

828

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<pre style="margin: 0;"> <span id="LC828" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre>

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829

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<td class="new_line diff-line-num" data-linenumber="829" 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">

829

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC829" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="830" 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">

830

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<td class="new_line diff-line-num" data-linenumber="830" 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">

830

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC830" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="831" 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">

831

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<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC831" class="line" lang="brainfuck"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="832" 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">

832

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC832" 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 (pattern_list</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_site_index_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_pattern_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="833" 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">

833

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

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<pre style="margin: 0;">-<span id="LC833" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        '</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="834" 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">

834

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC834" 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;">EnsureKey (`&site_info`</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _pattern_);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="835" 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">

835

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

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<pre style="margin: 0;">-<span id="LC835" 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;">EnsureKey (`&site_info`</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pattern_</span><span class="p">]</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;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites"));</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="836" 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">

836

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC836" class="line" lang="brainfuck"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="837" 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">

837

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

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<pre style="margin: 0;">-<span id="LC837" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        (`&site_info`</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pattern_</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;">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;">sites")</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;"> _site_index_</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>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="838" 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">

838

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC838" class="line" lang="brainfuck"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="839" 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">

839

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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="LC839" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (Abs ((`&site_info`</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pattern_</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;">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;">sites")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) == 1) {</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="840" 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">

840

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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="LC840" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            // first time we see this site</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="841" 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">

841

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

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<pre style="margin: 0;">-<span id="LC841" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            GetDataInfo (`&site_characters`</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> `data_filter`</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 class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _pattern_);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="842" 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">

842

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC842" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            `&site_characters` = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Filter (`&site_characters`</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="843" 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">

843

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC843" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                 "_value_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="844" 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">

844

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC844" 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 class="c1" style="color: #998; font-style: italic;">_value_</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">0)");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="845" 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">

845

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC845" class="line" lang="brainfuck"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="846" 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">

846

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC846" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            (`&site_info`</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pattern_</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;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">is_constant"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = Abs (`&site_characters`) </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= 1;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="847" 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">

847

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<td class="new_line diff-line-num old" data-linenumber="831" 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">

</td>

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<pre style="margin: 0;">-<span id="LC847" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="848" 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">

848

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<td class="new_line diff-line-num old" data-linenumber="831" 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="LC848" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="849" 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">

849

</td>

<td class="new_line diff-line-num old" data-linenumber="831" 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="LC849" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        '</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="850" 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">

850

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<td class="new_line diff-line-num old" data-linenumber="831" 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="LC850" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    );*/</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="851" 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">

851

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831

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<pre style="margin: 0;"> <span id="LC831" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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852

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832

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<pre style="margin: 0;"> <span id="LC832" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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853

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833

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<pre style="margin: 0;"> <span id="LC833" class="line" lang="brainfuck"></span>

</pre>

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<br>

</li>

<li id="3945e6db8feb0e4ed58719b69ff3d8485bc45e87">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#3945e6db8feb0e4ed58719b69ff3d8485bc45e87"><strong>res/TemplateBatchFiles/libv3/tasks/trees.bf</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" 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="154" 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">@@ -154,6 +154,7 @@ lfunction trees.GetTreeString(look_for_newick_tree) {</td>

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154

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="155" 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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155

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="156" 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="LC156" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (regexp</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Find(treeString</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "^#NEXUS")) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="157" 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="157" 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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<pre style="margin: 0;">+<span id="LC157" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

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<td class="old_line diff-line-num" data-linenumber="157" 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="158" 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="LC158" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                ExecuteCommands(treeString);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="159" 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="160" 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="LC160" 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;">GetEnvVariable("IS_TREE_PRESENT_IN_DATA")) {</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" 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="208" 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">@@ -207,8 +208,6 @@ lfunction trees.GetTreeString(look_for_newick_tree) {</td>

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<td class="old_line diff-line-num" data-linenumber="207" 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="208" 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="LC208" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="208" 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="209" 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="LC209" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="brainfuck"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC211" 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="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;">        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;">file"): look_for_newick_tree</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="254" 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">@@ -255,6 +254,7 @@ lfunction trees.LoadAnnotatedTopology(look_for_newick_tree) {</td>

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<pre style="margin: 0;"> <span id="LC254" 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="LC255" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction trees</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LoadAnnotatedTopologyAndMap(look_for_newick_tree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> mapping) {</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    reverse = {};</span></span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (k</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">v; in; mapping) {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="447" 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="447" 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">@@ -447,6 +447,7 @@ lfunction trees.ExtractTreeInfoFromTopology(topology_object) {</td>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="brainfuck"></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    branch_lengths = BranchLength(^topology_object</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="LC449" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    branch_names   = BranchName(^topology_object</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="LC450" 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="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    branch_count   = Max (2</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 (branch_names) </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="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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452

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453

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<br>

</li>

<li id="da9fe1b8aa482a95d2c6145ff61db7930bcd0fe8">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#da9fe1b8aa482a95d2c6145ff61db7930bcd0fe8"><strong>res/TemplateBatchFiles/readIndexFile.bf</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,8 +5,7 @@ fscanf                         (PROMPT_FOR_FILE,"Lines",inLines);</td>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="brainfuck"></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">

6

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">counter   = Columns (inLines);</span></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="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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="brainfuck"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="8" 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">

8

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<td class="new_line diff-line-num old" data-linenumber="8" 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="LC8" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (skipCodeSelectionStep)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="9" 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">

9

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<td class="new_line diff-line-num old" data-linenumber="8" 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="LC9" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="10" 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="8" 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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (skipCodeSelectionStep) {</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="10" 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">

10

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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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  stringMatrix    = {counter$2</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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<td class="old_line diff-line-num" data-linenumber="11" 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">

11

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<td class="new_line diff-line-num" data-linenumber="10" 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> codeTableMatrix = {counter$2</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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<td class="old_line diff-line-num" data-linenumber="12" 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">

12

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<td class="new_line diff-line-num" data-linenumber="11" 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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> counter  = 0;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,7 +16,6 @@ if (skipCodeSelectionStep)</td>

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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">

17

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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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<pre style="margin: 0;"> <span id="LC16" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         stringMatrix    </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k$2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = inLines</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre>

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18

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<td class="new_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">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>

</pre>

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<td class="old_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">

19

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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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<pre style="margin: 0;"> <span id="LC18" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="20" 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">

20

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<td class="new_line diff-line-num old" data-linenumber="19" 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="LC20" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">else</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="21" 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">

21

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<td class="new_line diff-line-num old" data-linenumber="19" 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="LC21" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="22" 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="19" 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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">else {</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="22" 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">

22

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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">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> stringMatrix = Transpose (inLines);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="23" 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">

23

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<td class="new_line diff-line-num" data-linenumber="21" 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">

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;">}</span></span></pre>

</td>

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</li>

<li id="9a5ae795d85e4d5f1568726c609e2499546cd590">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#9a5ae795d85e4d5f1568726c609e2499546cd590"><strong>src/core/associative_list.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">@@ -88,6 +88,9 @@ BaseRef _AssociativeList::makeDynamic (void) const {</td>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">newAL</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool _debug_memory_leak = false;</span></span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC94" 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="LC95" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">_AssociativeList</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ParseStringRepresentation</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;">serialized_form</span><span class="p">,</span> <span class="n" style="color: #333;">_FormulaParsingContext</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fpc</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="104" 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">@@ -104,8 +107,10 @@ bool _AssociativeList::ParseStringRepresentation (_String& serialized_form, _For</td>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp">            <span class="n" style="color: #333;">_ElementaryCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ExtractConditions</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;">splitKeys</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">key_value_pair</span><span class="p">,</span> <span class="sc" style="color: #d14;">':'</span> <span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">key_value_pair</span><span class="p">.</span><span class="n" style="color: #333;">countitems</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2UL</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp">                </span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//_debug_memory_leak = true;</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp">                <span class="n" style="color: #333;">_String</span>  <span class="n" style="color: #333;">key</span>        <span class="p">(</span><span class="n" style="color: #333;">compute_keys_values</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">ProcessLiteralArgument</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;">key_value_pair</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span><span class="n" style="color: #333;">theP</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</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;">key_value_pair</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">));</span></span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp">              </span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//_debug_memory_leak = false;</span></span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp">                </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="109" 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">

109

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<td class="new_line diff-line-num" data-linenumber="114" 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="LC114" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="110" 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">

110

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<td class="new_line diff-line-num" data-linenumber="115" 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">

115

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp">                  <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</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;">key_value_pair</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="111" 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">

111

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<td class="new_line diff-line-num" data-linenumber="116" 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">

116

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp">                <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="02cbcb76e8ce1aa3e72d55e6696cda20813d57b6">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#02cbcb76e8ce1aa3e72d55e6696cda20813d57b6"><strong>src/core/batchlan.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1068" 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="1068" 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">@@ -1068,9 +1068,7 @@ void    _ExecutionList::ReportAnExecutionError (_String errMsg, bool doCurrentCo</td>

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1068

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1068

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<pre style="margin: 0;"> <span id="LC1068" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1069" 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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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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1070" 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">

1070

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<td class="new_line diff-line-num" data-linenumber="1070" 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="LC1070" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span>    <span class="n" style="color: #333;">_ExecutionList</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">StartProfile</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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1071" 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">

1071

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<td class="new_line diff-line-num old" data-linenumber="1071" 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="LC1071" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">profileCounter</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1072" 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">

1072

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<td class="new_line diff-line-num old" data-linenumber="1071" 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="LC1072" class="line" lang="cpp">        <span class="n" style="color: #333;">DeleteObject</span> <span class="p">(</span><span class="n" style="color: #333;">profileCounter</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1073" 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">

1073

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<td class="new_line diff-line-num old" data-linenumber="1071" 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="LC1073" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1074" 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="1071" 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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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="cpp">    <span class="n" style="color: #333;">DeleteObject</span> <span class="p">(</span><span class="n" style="color: #333;">profileCounter</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1074" 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">

1074

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<td class="new_line diff-line-num" data-linenumber="1072" 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">

1072

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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="cpp">    <span class="n" style="color: #333;">profileCounter</span><span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_Matrix</span> <span class="p">(</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1075" 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">

1075

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<td class="new_line diff-line-num" data-linenumber="1073" 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">

1073

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<pre style="margin: 0;"> <span id="LC1073" class="line" lang="cpp">    <span class="n" style="color: #333;">doProfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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1076

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<td class="new_line diff-line-num" data-linenumber="1074" 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">

1074

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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1283" 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="1281" 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">@@ -1283,7 +1281,7 @@ _StringBuffer const       _ExecutionList::GenerateHelpMessage(_AVLList * scanned</td>

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1283

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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">this_command</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">HY_HBL_COMMAND_FORMULA</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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1284

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<td class="new_line diff-line-num" data-linenumber="1282" 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="LC1282" class="line" lang="cpp">                <span class="n" style="color: #333;">_List</span>      <span class="n" style="color: #333;">hbl_functions</span><span class="p">;</span></span>

</pre>

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1285

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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="cpp">                <span class="n" style="color: #333;">_AVLListX</span> <span class="n" style="color: #333;">other_functions</span> <span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hbl_functions</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC1286" class="line" lang="cpp">                <span class="n" style="color: #333;">this_command</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">BuildListOfDependancies</span><span class="p">(</span><span class="n" style="color: #333;">other_functions</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><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>

</pre>

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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp">                <span class="n" style="color: #333;">this_command</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">BuildListOfDependancies</span><span class="p">(</span><span class="n" style="color: #333;">other_functions</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><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 class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">true</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1285" class="line" lang="cpp">                </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1288" 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="LC1286" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">AVLListXIteratorKeyValue</span> <span class="n" style="color: #333;">function_iterator</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">AVLListXIterator</span> <span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">other_functions</span><span class="p">))</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="cpp">                    <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">function_name</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;">other_functions</span><span class="p">.</span><span class="n" style="color: #333;">Retrieve</span> <span class="p">(</span><span class="n" style="color: #333;">function_iterator</span><span class="p">.</span><span class="n" style="color: #333;">get_index</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3269" 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="3267" 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">@@ -3269,7 +3267,7 @@ void      _ElementaryCommand::ExecuteCase52 (_ExecutionList& chain) {</td>

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<pre style="margin: 0;"> <span id="LC3267" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3268" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3269" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3272" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3273" 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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<pre style="margin: 0;">+<span id="LC3270" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//extern bool _debug_memory_leak;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3271" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3272" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3275" 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="3273" 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">

3273

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<pre style="margin: 0;"> <span id="LC3273" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3362" 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="3360" 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">@@ -3362,12 +3360,24 @@ bool      _ElementaryCommand::Execute    (_ExecutionList& chain) {</td>

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3362

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<pre style="margin: 0;"> <span id="LC3360" class="line" lang="cpp">                <span class="n" style="color: #333;">indepA</span><span class="p">.</span><span class="n" style="color: #333;">ReorderList</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3363" 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="LC3361" class="line" lang="cpp">                <span class="n" style="color: #333;">depA</span><span class="p">.</span><span class="n" style="color: #333;">ReorderList</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3364" 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">

3364

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<pre style="margin: 0;"> <span id="LC3362" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3365" 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="LC3365" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3363" class="line" lang="cpp">            </span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3364" 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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<pre style="margin: 0;">+<span id="LC3364" class="line" lang="cpp"> </span>

</pre>

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<pre style="margin: 0;"> <span id="LC3365" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//indep.Sort();</span></span>

</pre>

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3367

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3366

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<pre style="margin: 0;"> <span id="LC3366" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//dep.Sort();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3368" 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">

3368

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3367

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<pre style="margin: 0;"> <span id="LC3367" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3369" 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">

3369

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<td class="new_line diff-line-num" data-linenumber="3368" 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">

3368

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<pre style="margin: 0;"> <span id="LC3368" class="line" lang="cpp">            <span class="n" style="color: #333;">holder</span><span class="p">.</span><span class="n" style="color: #333;">Union</span> <span class="p">(</span><span class="n" style="color: #333;">indep</span><span class="p">,</span><span class="n" style="color: #333;">dep</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3370" 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">

3370

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3369

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<pre style="margin: 0;"> <span id="LC3369" class="line" lang="cpp">            <span class="n" style="color: #333;">leftOverVars</span><span class="p">.</span><span class="n" style="color: #333;">Sort</span> <span class="p">();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3370" 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">

3370

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<pre style="margin: 0;">+<span id="LC3370" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3371" 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">

3371

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<pre style="margin: 0;">+<span id="LC3371" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            BufferToConsole("\nIndependents+nDependendts\n");</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3372" 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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<pre style="margin: 0;">+<span id="LC3372" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            ObjectToConsole(&holder); NLToConsole();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3373" 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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<pre style="margin: 0;">+<span id="LC3373" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            BufferToConsole("\nLeftover\n");</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3374" 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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<pre style="margin: 0;">+<span id="LC3374" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            ObjectToConsole(&leftOverVars); NLToConsole();</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3375" 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">

3375

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<pre style="margin: 0;">+<span id="LC3375" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            */</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3371" 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="3376" 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">

3376

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<pre style="margin: 0;">+<span id="LC3376" class="line" lang="cpp">            </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3371" 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="3377" 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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<pre style="margin: 0;">+<span id="LC3377" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/*leftOverVars.Each ([](long v, unsigned long) -> void {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3371" 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="3378" 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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<pre style="margin: 0;">+<span id="LC3378" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                StringToConsole(*LocateVar(v)->GetName()); NLToConsole();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3371" 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="3379" 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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<pre style="margin: 0;">+<span id="LC3379" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            });*/</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3371" 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="3380" 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">

3380

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<pre style="margin: 0;">+<span id="LC3380" class="line" lang="cpp">            </span>

</pre>

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3371

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<td class="new_line diff-line-num" data-linenumber="3381" 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">

3381

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<pre style="margin: 0;"> <span id="LC3381" class="line" lang="cpp">            <span class="n" style="color: #333;">indep</span><span class="p">.</span><span class="n" style="color: #333;">Subtract</span> <span class="p">(</span><span class="n" style="color: #333;">leftOverVars</span><span class="p">,</span><span class="n" style="color: #333;">holder</span><span class="p">);</span></span>

</pre>

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3372

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<td class="new_line diff-line-num" data-linenumber="3382" 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">

3382

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3382" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="3383" 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="LC3383" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/* the bit with freeSlots is here b/c</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3458" 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="3468" 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">@@ -3458,6 +3468,10 @@ bool      _ElementaryCommand::Execute    (_ExecutionList& chain) {</td>

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<pre style="margin: 0;"> <span id="LC3468" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3459" 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="3469" 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="LC3469" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3460" 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="3470" 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="LC3470" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//printf ("Return compiled %d\n", ((_Formula*)simpleParameters(1))->GetList().lLength);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3461" 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="3471" 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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<pre style="margin: 0;">+<span id="LC3471" class="line" lang="cpp">              <span class="c1" style="color: #998; font-style: italic;">//if (_debug_memory_leak) {</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3461" 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="3472" 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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<pre style="margin: 0;">+<span id="LC3472" class="line" lang="cpp">              <span class="c1" style="color: #998; font-style: italic;">//    BufferToConsole("In return while parsing AssociateList string repr\n");</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3473" 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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<pre style="margin: 0;">+<span id="LC3473" class="line" lang="cpp">              <span class="c1" style="color: #998; font-style: italic;">//}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3461" 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="3474" 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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<pre style="margin: 0;">+<span id="LC3474" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3461" 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="3475" 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="LC3475" class="line" lang="cpp">            <span class="n" style="color: #333;">ret_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">simpleParameters</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;">Compute</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;">nil</span><span class="p">,</span><span class="n" style="color: #333;">HY_ANY_OBJECT</span><span class="p">,</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3462" 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">

3462

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<td class="new_line diff-line-num" data-linenumber="3476" 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="LC3476" class="line" lang="cpp">          <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3463" 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">

3463

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<td class="new_line diff-line-num" data-linenumber="3477" 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">

3477

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<pre style="margin: 0;"> <span id="LC3477" class="line" lang="cpp"></span>

</pre>

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<br>

</li>

<li id="984635b15ce26c0824ba85946c002feb3137c030">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#984635b15ce26c0824ba85946c002feb3137c030"><strong>src/core/batchlan2.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="795" 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="795" 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">@@ -795,7 +795,7 @@ void      _ElementaryCommand::ExecuteCase58 (_ExecutionList& chain)</td>

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795

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<td class="new_line diff-line-num" data-linenumber="795" 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="LC795" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="796" 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="796" 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="LC796" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="797" 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">

797

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<td class="new_line diff-line-num" data-linenumber="797" 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="LC797" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="798" 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">

798

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<td class="new_line diff-line-num old" data-linenumber="798" 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="LC798" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">kStart</span> <span class="p">(</span><span class="s" style="color: #d14;">"START"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="799" 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="798" 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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<pre style="margin: 0;">+<span id="LC798" class="line" lang="cpp">   <span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">kStart</span> <span class="p">(</span><span class="s" style="color: #d14;">"START"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="799" 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="799" 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="LC799" class="line" lang="cpp">                  <span class="n" style="color: #333;">kPause</span> <span class="p">(</span><span class="s" style="color: #d14;">"PAUSE"</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC800" class="line" lang="cpp">                  <span class="n" style="color: #333;">kResume</span> <span class="p">(</span><span class="s" style="color: #d14;">"RESUME"</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="801" 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">

801

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<td class="new_line diff-line-num" data-linenumber="801" 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">

801

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<pre style="margin: 0;"> <span id="LC801" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1179" 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="1179" 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">@@ -1179,7 +1179,7 @@ _String const _HYHBLTypeToText (long type) {</td>

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1179

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1179

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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>

</pre>

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1180

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1180

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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1181" 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">

1181

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1181

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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1182" 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">

1182

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<td class="new_line diff-line-num old" data-linenumber="1182" 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="LC1182" 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;">ScanStringExpressionForHBLFunctions</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;">expression</span><span class="p">,</span> <span class="n" style="color: #333;">_ExecutionList</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p">,</span> <span class="n" style="color: #333;">_AVLListX</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span><span class="idiff left right"> </span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1182" 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;">ScanStringExpressionForHBLFunctions</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;">expression</span><span class="p">,</span> <span class="n" style="color: #333;">_ExecutionList</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p">,</span> <span class="n" style="color: #333;">_AVLListX</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">help_mode</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="cpp">  </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1184" 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">

1184

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<td class="new_line diff-line-num" data-linenumber="1184" 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">

1184

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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="cpp">  <span class="n" style="color: #333;">_Formula</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">f2</span><span class="p">;</span></span>

</pre>

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1185

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<td class="new_line diff-line-num" data-linenumber="1185" 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">

1185

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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1190" 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="1190" 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">@@ -1190,8 +1190,8 @@ void _ElementaryCommand::ScanStringExpressionForHBLFunctions (_String* expressio</td>

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1190

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<td class="new_line diff-line-num" data-linenumber="1190" 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">

1190

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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">long</span>     <span class="n" style="color: #333;">parseCode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Parse</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">expression</span><span class="p">,</span><span class="n" style="color: #333;">fpc</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">f2</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1191" 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">

1191

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<td class="new_line diff-line-num" data-linenumber="1191" 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">

1191

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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="cpp">  </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1192" 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">

1192

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<td class="new_line diff-line-num" data-linenumber="1192" 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">

1192

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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parseCode</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">HY_FORMULA_FAILED</span> <span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1193" 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">

1193

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<td class="new_line diff-line-num old" data-linenumber="1193" 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="LC1193" class="line" lang="cpp">    <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">ScanFormulaForHBLFunctions</span> <span class="p">(</span><span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="n" style="color: #333;">recursive</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1194" 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">

1194

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<td class="new_line diff-line-num old" data-linenumber="1193" 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="LC1194" class="line" lang="cpp">    <span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">ScanFormulaForHBLFunctions</span><span class="p">(</span><span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="n" style="color: #333;">recursive</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1195" 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="1193" 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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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="cpp">    <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">ScanFormulaForHBLFunctions</span> <span class="p">(</span><span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="n" style="color: #333;">recursive</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff right">help_mode</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1195" 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="1194" 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">

1194

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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="cpp">    <span class="n" style="color: #333;">f2</span><span class="p">.</span><span class="n" style="color: #333;">ScanFormulaForHBLFunctions</span><span class="p">(</span><span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="n" style="color: #333;">recursive</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff right">help_mode</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1195" 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">

1195

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<td class="new_line diff-line-num" data-linenumber="1195" 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">

1195

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<pre style="margin: 0;"> <span id="LC1195" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1196" 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">

1196

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<td class="new_line diff-line-num" data-linenumber="1196" 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">

1196

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<pre style="margin: 0;"> <span id="LC1196" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1197" 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">

1197

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<td class="new_line diff-line-num" data-linenumber="1197" 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">

1197

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<pre style="margin: 0;"> <span id="LC1197" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1199" 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="1199" 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">@@ -1199,7 +1199,7 @@ void _ElementaryCommand::ScanStringExpressionForHBLFunctions (_String* expressio</td>

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1199

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<td class="new_line diff-line-num" data-linenumber="1199" 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">

1199

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<pre style="margin: 0;"> <span id="LC1199" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1200" 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">

1200

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<td class="new_line diff-line-num" data-linenumber="1200" 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="LC1200" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1201" 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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1201

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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1202" 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">

1202

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<td class="new_line diff-line-num old" data-linenumber="1202" 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="LC1202" 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;">BuildListOfDependancies</span>    <span class="p">(</span><span class="n" style="color: #333;">_AVLListX</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p">,</span> <span class="n" style="color: #333;">_ExecutionList</span> <span class="k" style="font-weight: 600;">const</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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1203" 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="1202" 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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<pre style="margin: 0;">+<span id="LC1202" 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;">BuildListOfDependancies</span>    <span class="p">(</span><span class="n" style="color: #333;">_AVLListX</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p">,</span> <span class="n" style="color: #333;">_ExecutionList</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">chain</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">help_mode</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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1203

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<td class="new_line diff-line-num" data-linenumber="1203" 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">

1203

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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="cpp">  </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1204" 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">

1204

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<td class="new_line diff-line-num" data-linenumber="1204" 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">

1204

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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">code</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1205" 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">

1205

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<td class="new_line diff-line-num" data-linenumber="1205" 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">

1205

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<pre style="margin: 0;"> <span id="LC1205" class="line" lang="cpp">      </span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1208" 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="1208" 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">@@ -1208,7 +1208,7 @@ void      _ElementaryCommand::BuildListOfDependancies    (_AVLListX & collection</td>

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<td class="old_line diff-line-num" data-linenumber="1208" 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">

1208

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<td class="new_line diff-line-num" data-linenumber="1208" 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">

1208

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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">14</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1209" 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">

1209

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<td class="new_line diff-line-num" data-linenumber="1209" 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">

1209

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1209" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1210" 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">

1210

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<td class="new_line diff-line-num" data-linenumber="1210" 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">

1210

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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1211" 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="LC1211" class="line" lang="cpp">        <span class="n" style="color: #333;">ScanStringExpressionForHBLFunctions</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;">0</span><span class="p">),</span> <span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="n" style="color: #333;">recursive</span><span class="p">,</span> <span class="n" style="color: #333;">collection</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="cpp">        <span class="n" style="color: #333;">ScanStringExpressionForHBLFunctions</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;">0</span><span class="p">),</span> <span class="n" style="color: #333;">chain</span><span class="p">,</span> <span class="n" style="color: #333;">recursive</span><span class="p">,</span> <span class="n" style="color: #333;">collection</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">help_mode</span></span><span class="p">);</span></span>

</pre>

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1212

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1212

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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="cpp">      <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

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1214

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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="cpp">    <span class="p">}</span></span>

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<br>

</li>

<li id="cbedcf5fec686e5f563504b995c5d7d07fd8c6b2">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#cbedcf5fec686e5f563504b995c5d7d07fd8c6b2"><strong>src/core/batchlanruntime.cpp</strong></a>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include      "function_templates.h"</span></span>

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55

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num new" data-linenumber="56" 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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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include      <signal.h></span></span>

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56

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57

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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;">#ifndef __HYPHY_NO_SQLITE__</span></span>

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58

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59

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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 "sqlite3.h"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1515" 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="1516" 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">@@ -1515,7 +1516,7 @@ bool      _ElementaryCommand::HandleReplicateConstraint (_ExecutionList& current</td>

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1515

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1516

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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="cpp">                    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1516" 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">

1516

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<td class="new_line diff-line-num" data-linenumber="1517" 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">

1517

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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="cpp">                <span class="p">};</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="1518" 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="LC1518" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1518" 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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<td class="new_line diff-line-num old" data-linenumber="1519" 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="LC1518" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reference_iteratee</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">HasLocals</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// stuff to do</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1519" 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="1519" 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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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reference_iteratee</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">HasLocals</span><span class="p">()</span><span class="idiff left"> </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">!</span></span><span class="n" style="color: #333;"><span class="idiff">traversers</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">reference_argument</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">IsAtRoot</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// stuff to do</span></span>

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1519

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1520

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<pre style="margin: 0;"> <span id="LC1520" class="line" lang="cpp">                    <span class="n" style="color: #333;">_List</span> <span class="n" style="color: #333;">parameter_sets</span><span class="p">,</span></span>

</pre>

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1520

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1521

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<pre style="margin: 0;"> <span id="LC1521" class="line" lang="cpp">                          <span class="n" style="color: #333;">matched_subexpressions</span><span class="p">;</span></span>

</pre>

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1521

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<td class="new_line diff-line-num" data-linenumber="1522" 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">

1522

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<pre style="margin: 0;"> <span id="LC1522" 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;">i</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;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">template_parameter_count</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2079" 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="2080" 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">@@ -2079,9 +2080,16 @@ bool      _ElementaryCommand::HandleGetURL(_ExecutionList& current_program){</td>

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2079

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2080

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<pre style="margin: 0;"> <span id="LC2080" class="line" lang="cpp"></span>

</pre>

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2080

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<td class="new_line diff-line-num" data-linenumber="2081" 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">

2081

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<pre style="margin: 0;"> <span id="LC2081" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span>      <span class="n" style="color: #333;">_ElementaryCommand</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">HandleAssert</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;">current_program</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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2081

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<td class="new_line diff-line-num" data-linenumber="2082" 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">

2082

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<pre style="margin: 0;"> <span id="LC2082" class="line" lang="cpp">  <span class="n" style="color: #333;">current_program</span><span class="p">.</span><span class="n" style="color: #333;">advance</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2082" 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="2083" 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">

2083

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<pre style="margin: 0;">+<span id="LC2083" 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;">kBreakpointTrap</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"__SIGTRAP__"</span><span class="p">);</span></span>

</pre>

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2082

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<td class="new_line diff-line-num" data-linenumber="2084" 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">

2084

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<pre style="margin: 0;"> <span id="LC2084" class="line" lang="cpp"></span>

</pre>

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2083

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<td class="new_line diff-line-num" data-linenumber="2085" 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">

2085

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<pre style="margin: 0;"> <span id="LC2085" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2084" 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">

2084

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<td class="new_line diff-line-num" 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">

2086

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<pre style="margin: 0;"> <span id="LC2086" class="line" lang="cpp">    <span class="n" style="color: #333;">_Formula</span> <span class="n" style="color: #333;">parsed_expression</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2085" 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="2087" 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">

2087

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<pre style="margin: 0;">+<span id="LC2087" class="line" lang="cpp">      </span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2085" 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="2088" 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">

2088

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<pre style="margin: 0;">+<span id="LC2088" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">kBreakpointTrap</span> <span class="o" style="font-weight: 600;">==</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;">0</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2089" 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">

2089

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<pre style="margin: 0;">+<span id="LC2089" class="line" lang="cpp">      <span class="n" style="color: #333;">raise</span><span class="p">(</span><span class="n" style="color: #333;">SIGTRAP</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2090" 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">

2090

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<pre style="margin: 0;">+<span id="LC2090" 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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2085" 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="2091" 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">

2091

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<pre style="margin: 0;">+<span id="LC2091" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2085" 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="2092" 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">

2092

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<pre style="margin: 0;">+<span id="LC2092" class="line" lang="cpp">      </span>

</pre>

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2085

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<td class="new_line diff-line-num" data-linenumber="2093" 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">

2093

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<pre style="margin: 0;"> <span id="LC2093" class="line" lang="cpp">    <span class="n" style="color: #333;">_CheckExpressionForCorrectness</span> <span class="p">(</span><span class="n" style="color: #333;">parsed_expression</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;">0UL</span><span class="p">),</span> <span class="n" style="color: #333;">current_program</span><span class="p">,</span> <span class="n" style="color: #333;">NUMBER</span><span class="p">);</span></span>

</pre>

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2086

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2094

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<pre style="margin: 0;"> <span id="LC2094" 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;">parsed_expression</span><span class="p">.</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 class="mf" style="color: #099;">0.0</span><span class="p">))</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// assertion failed</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" data-linenumber="2095" 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="LC2095" class="line" lang="cpp">      <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">soft_assertions</span> <span class="o" style="font-weight: 600;">=</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;">assertion_behavior</span><span class="p">);</span></span>

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<br>

</li>

<li id="8f267f0287b6f2dfc1594ce4cfeb588fe8a2578c">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#8f267f0287b6f2dfc1594ce4cfeb588fe8a2578c"><strong>src/core/category.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="177" 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="177" 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">@@ -177,7 +177,7 @@ void _CategoryVariable::Construct (_List& parameters, _VariableContainer *theP)</td>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp">                    <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">CheckEqual</span> <span class="p">(</span><span class="n" style="color: #333;">iSplitter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetMaxX</span><span class="p">(),</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>

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<td class="old_line diff-line-num" data-linenumber="178" 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="LC178" class="line" lang="cpp">                    <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">theName</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">splitterName</span> <span class="o" style="font-weight: 600;">||</span></span>

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<td class="old_line diff-line-num" data-linenumber="179" 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">

179

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp">                    <span class="p">(</span><span class="n" style="color: #333;">intervals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iSplitter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetNumberOfIntervals</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="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="180" 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">

180

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<td class="new_line diff-line-num old" data-linenumber="180" 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="LC180" class="line" lang="cpp">                <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span><span class="n" style="color: #333;">errorMsg</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;">"Category variables which specify interval splitting options must be supported on [0,1], and not result in circular depend<span class="idiff left right">a</span>nce"</span><span class="p">));</span></span>

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<td class="old_line diff-line-num new" data-linenumber="181" 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="180" 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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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp">                <span class="n" style="color: #333;">HandleApplicationError</span> <span class="p">(</span><span class="n" style="color: #333;">errorMsg</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;">"Category variables which specify interval splitting options must be supported on [0,1], and not result in circular depend<span class="idiff left right">e</span>nce"</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="181" 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">

181

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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182

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182

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp">            <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="183" 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">

183

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183

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="475" 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="475" 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">@@ -475,7 +475,7 @@ void _CategoryVariable::Construct (_List& parameters, _VariableContainer *theP)</td>

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<td class="old_line diff-line-num" data-linenumber="475" 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">

475

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="476" 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">

476

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476

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="478" 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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<td class="new_line diff-line-num old" data-linenumber="478" 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="LC478" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// disallow category -> category depend<span class="idiff left right">a</span>nce</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="479" 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="478" 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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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// disallow category -> category depend<span class="idiff left right">e</span>nce</span></span>

</pre>

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479

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<pre style="margin: 0;"> <span id="LC479" 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;">long</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">scannedVarsList</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">;</span> <span class="n" style="color: #333;">i</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="LC480" class="line" lang="cpp">        <span class="n" style="color: #333;">_Variable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">curVar</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_Variable</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">variablePtrs</span> <span class="p">(</span><span class="n" style="color: #333;">scannedVarsList</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">curVar</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">IsCategory</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="489" 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="489" 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">@@ -489,7 +489,7 @@ void _CategoryVariable::Construct (_List& parameters, _VariableContainer *theP)</td>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="cpp">    <span class="n" style="color: #333;">hiddenMarkovModel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HY_NO_MODEL</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC490" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="cpp">    <span class="n" style="color: #333;">parameterList</span><span class="p">.</span><span class="n" style="color: #333;">Duplicate</span>  <span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">scannedVarsList</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// finally go thru all the variables and put them where they belong in depend<span class="idiff left right">a</span>nce containers</span></span>

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// finally go thru all the variables and put them where they belong in depend<span class="idiff left right">e</span>nce containers</span></span>

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="494" 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="LC494" class="line" lang="cpp">    <span class="n" style="color: #333;">_SimpleList</span>     <span class="n" style="color: #333;">exclude</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"></span>

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<li id="10496a7488dc0332386e6f734ef450e847cb8aac">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#10496a7488dc0332386e6f734ef450e847cb8aac"><strong>src/core/constant.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="724" 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="724" 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">@@ -724,6 +724,7 @@ HBLObjectRef _Constant::Time (HBLObjectRef cache) {</td>

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<pre style="margin: 0;"> <span id="LC724" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//return     result;</span></span>

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<pre style="margin: 0;"> <span id="LC725" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC728" 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="LC729" class="line" lang="cpp"><span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">_Constant</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Less</span> <span class="p">(</span><span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">theObj</span><span class="p">,</span> <span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">cache</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC730" class="line" lang="cpp">   <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_check_type_and_compute</span> <span class="p">(</span><span class="n" style="color: #333;">theObj</span><span class="p">,</span> <span class="p">[]</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">hyFloat</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">b</span><span class="p">;},</span> <span class="n" style="color: #333;">cache</span><span class="p">);</span></span>

</pre>

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<br>

</li>

<li id="d09b45303442d6299978fa8d0c8f3338d6a17886">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#d09b45303442d6299978fa8d0c8f3338d6a17886"><strong>src/core/formula.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2494" 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="2494" 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">@@ -2494,7 +2494,7 @@ bool _Formula::HasChanged (bool ingoreCats) {</td>

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<pre style="margin: 0;"> <span id="LC2494" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2495" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//__________________________________________________________________________________</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2496" 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="LC2496" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2497" 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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<td class="new_line diff-line-num old" data-linenumber="2497" 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="LC2497" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ScanFormulaForHBLFunctions</span> <span class="p">(</span><span class="n" style="color: #333;">_AVLListX</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2498" 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="2497" 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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<pre style="margin: 0;">+<span id="LC2497" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ScanFormulaForHBLFunctions</span> <span class="p">(</span><span class="n" style="color: #333;">_AVLListX</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">simplify</span></span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC2498" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2499" 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="LC2499" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2500" 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="LC2500" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">handle_function_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="n" style="color: #333;">recursive</span><span class="p">]</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">hbl_id</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2514" 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="2514" 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">@@ -2514,7 +2514,9 @@ void _Formula::ScanFormulaForHBLFunctions (_AVLListX& collection , bool recursiv</td>

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2514

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<td class="new_line diff-line-num" data-linenumber="2514" 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="LC2514" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2515" 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="2515" 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="LC2515" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theTree</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2516" 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="2516" 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="LC2516" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2517" 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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<td class="new_line diff-line-num old" data-linenumber="2517" 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="LC2517" class="line" lang="cpp">    <span class="n" style="color: #333;">InternalSimplify</span><span class="p">(</span><span class="n" style="color: #333;">theTree</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2518" 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="2517" 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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<pre style="margin: 0;">+<span id="LC2517" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">simplify</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2518" 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="2518" 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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<pre style="margin: 0;">+<span id="LC2518" class="line" lang="cpp">        <span class="n" style="color: #333;">InternalSimplify</span><span class="p">(</span><span class="n" style="color: #333;">theTree</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2519" class="line" lang="cpp">    <span class="p">}</span></span>

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2518

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<pre style="margin: 0;"> <span id="LC2520" class="line" lang="cpp">    <span class="n" style="color: #333;">node_iterator</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ni</span> <span class="p">(</span><span class="n" style="color: #333;">theTree</span><span class="p">,</span> <span class="n" style="color: #333;">_HY_TREE_TRAVERSAL_PREORDER</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC2521" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC2522" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">long</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ni</span><span class="p">.</span><span class="n" style="color: #333;">Next</span><span class="p">())</span> <span class="p">{</span></span>

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<br>

</li>

<li id="7f26a8678910b09a3bbef4b727e70c3ca29c2bd5">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#7f26a8678910b09a3bbef4b727e70c3ca29c2bd5"><strong>src/core/global_object_lists.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="121" 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="121" 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">@@ -121,7 +121,7 @@ namespace hyphy_global_objects {</td>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//lf->Rebuild();</span></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp">               <span class="cm" style="color: #998; font-style: italic;">/* 20170328 SLKP: this COULD MODIFY the 'listeners' object, hence the buffering */</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp">          <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">event_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kNotificationTypeDelete</span><span class="p">)</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;">hy_global</span><span class="o" style="font-weight: 600;">::</span><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;">"Attempted to delete a data set filter "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">GetFilterName</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="n" style="color: #333;">Enquote</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" which is <span class="idiff left">still being </span>referenced by <span class="idiff right">a</span> likelihood function "</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;">hy_global</span><span class="o" style="font-weight: 600;">::</span><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;">"Attempted to delete a data set filter "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">GetFilterName</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="n" style="color: #333;">Enquote</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">" which is referenced by <span class="idiff left">the</span> likelihood function "</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff">  </span><span class="n" style="color: #333;"><span class="idiff">GetObjectNameByType</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">HY_BL_LIKELIHOOD_FUNCTION</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">FindLikeFuncIndex</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lf</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">false</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">Enquote</span></span><span class="p"><span class="idiff right">()</span>);</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp">          <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC127" 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="824" 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="824" 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">@@ -824,6 +824,11 @@ namespace hyphy_global_objects {</td>

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<pre style="margin: 0;"> <span id="LC824" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC825" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC826" class="line" lang="cpp">    </span>

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</td>

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<pre style="margin: 0;">+<span id="LC827" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="827" 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="828" 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">

828

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<pre style="margin: 0;">+<span id="LC828" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">long</span>    <span class="n" style="color: #333;">FindLikeFuncIndex</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">lfp</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="827" 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="829" 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">

829

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<pre style="margin: 0;">+<span id="LC829" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">likeFuncList</span><span class="p">.</span><span class="n" style="color: #333;">_SimpleList</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Find</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;">lfp</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="827" 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="830" 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">

830

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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="827" 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="831" 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">

831

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<pre style="margin: 0;">+<span id="LC831" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="827" 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">

827

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832

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<pre style="margin: 0;"> <span id="LC832" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="828" 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">

828

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<td class="new_line diff-line-num" data-linenumber="833" 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">

833

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<pre style="margin: 0;"> <span id="LC833" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">long</span>    <span class="n" style="color: #333;">FindSCFGName</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;">s</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="834" 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">

834

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<pre style="margin: 0;"> <span id="LC834" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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</li>

<li id="07aceb8d215a75908cea626d9c80bc2a7c06639c">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#07aceb8d215a75908cea626d9c80bc2a7c06639c"><strong>src/core/global_things.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="121" 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="121" 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">@@ -121,7 +121,7 @@ namespace hy_global {</td>

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121

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<pre style="margin: 0;"> <span id="LC121" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="122" 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">

122

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<pre style="margin: 0;"> <span id="LC122" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="123" 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="123" 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="LC123" 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>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="124" 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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<td class="new_line diff-line-num old" data-linenumber="124" 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="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;">"2.5.2<span class="idiff left right">8</span>"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="125" 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="124" 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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<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;">"2.5.2<span class="idiff left right">9</span>"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="125" 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="125" 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="LC125" class="line" lang="cpp">    </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="126" 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="126" 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="LC126" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="127" 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="127" 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="LC127" 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>

</pre>

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<br>

</li>

<li id="46380d67c22541ee76ad7fa2f39c30110df90a7c">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#46380d67c22541ee76ad7fa2f39c30110df90a7c"><strong>src/core/include/batchlan.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="386" 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="386" 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">@@ -386,7 +386,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span>              <span class="n" style="color: #333;">DecompileFormulae</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="LC388" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span>              <span class="n" style="color: #333;">BuildListOfDependancies</span>  <span class="p">(</span><span class="n" style="color: #333;">_AVLListX</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p">,</span> <span class="n" style="color: #333;">_ExecutionList</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">chain</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span>              <span class="n" style="color: #333;">BuildListOfDependancies</span>  <span class="p">(</span><span class="n" style="color: #333;">_AVLListX</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p">,</span> <span class="n" style="color: #333;">_ExecutionList</span> <span class="k" style="font-weight: 600;">const</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">chain</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">help_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"><span class="nl">protected:</span></span>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp">  </span>

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<pre style="margin: 0;">-<span id="LC408" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span>    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ScanStringExpressionForHBLFunctions</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;">_ExecutionList</span> <span class="k" style="font-weight: 600;">const</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="n" style="color: #333;">_AVLListX</span><span class="o" style="font-weight: 600;">&</span> <span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span>    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ScanStringExpressionForHBLFunctions</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;">_ExecutionList</span> <span class="k" style="font-weight: 600;">const</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="n" style="color: #333;">_AVLListX</span><span class="o" style="font-weight: 600;">&</span> <span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">help_mode</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp">    <span class="n" style="color: #333;">_String</span>  <span class="o" style="font-weight: 600;">*</span>   <span class="n" style="color: #333;">GetIthParameter</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;">i</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">range_check</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</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="LC411" class="line" lang="cpp">        <span class="n" style="color: #333;">BaseRef</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">GetItemRangeCheck</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>

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<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#40fc4f1e42852e6f2302e213cd9b3646abe98291"><strong>src/core/include/formula.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">@@ -247,7 +247,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span>      <span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">*</span>        <span class="n" style="color: #333;">PatchFormulasTogether</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">op1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">op2</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="n" style="color: #333;">op_code</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span>      <span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">*</span>        <span class="n" style="color: #333;">PatchFormulasTogether</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">op1</span><span class="p">,</span> <span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">op2</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="n" style="color: #333;">op_code</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span>        <span class="n" style="color: #333;">ScanFormulaForHBLFunctions</span> <span class="p">(</span><span class="n" style="color: #333;">_AVLListX</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span>        <span class="n" style="color: #333;">ScanFormulaForHBLFunctions</span> <span class="p">(</span><span class="n" style="color: #333;">_AVLListX</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">collection</span> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">recursive</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">simplify</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">true</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/** A compute and forget utility function.</span></span>

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<li id="2a277e4b849d74ac4178f402409133631301633d">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#2a277e4b849d74ac4178f402409133631301633d"><strong>src/core/include/global_object_lists.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">@@ -298,6 +298,7 @@ namespace hyphy_global_objects {</td>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// added by afyp, March 18, 2007</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">long</span>      <span class="n" style="color: #333;">FindLikeFuncName</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="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="LC301" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">long</span>      <span class="n" style="color: #333;">FindLikeFuncIndex</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">long</span>      <span class="n" style="color: #333;">FindModelName</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="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">extern</span>   <span class="n" style="color: #333;">_AVLListX</span> <span class="n" style="color: #333;">batchLanguageFunctionNamesIndexed</span><span class="p">;</span></span>

</pre>

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</li>

<li id="1f90bcae5572a43ed503911ecef65a7c99ec3d55">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#1f90bcae5572a43ed503911ecef65a7c99ec3d55"><strong>src/core/include/variable.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" 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="92" 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">@@ -92,7 +92,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span>        <span class="n" style="color: #333;">SetFormula</span> <span class="p">(</span><span class="n" style="color: #333;">_Formula</span><span class="o" style="font-weight: 600;">&</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// set the variable to a new formula</span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">void</span>   <span class="n" style="color: #333;">ClearValue</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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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">varValue</span><span class="p">)</span> <span class="p">{</span> <span class="k" style="font-weight: 600;"><span class="idiff left right">d</span>elete</span> <span class="p">(</span><span class="n" style="color: #333;">varValue</span><span class="p">);</span> <span class="n" style="color: #333;">varValue</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="LC95" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">varValue</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;"><span class="idiff left">D</span>elete<span class="idiff right">Object</span></span> <span class="p">(</span><span class="n" style="color: #333;">varValue</span><span class="p">);</span> <span class="n" style="color: #333;">varValue</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="LC96" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span>     <span class="n" style="color: #333;">_Formula</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">get_constraint</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>

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<li id="2a8dd324ded753b0b3c559ac3950a2881ccd7a93">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#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">@@ -2382,20 +2382,20 @@ bool        _LikelihoodFunction::HasBlockChanged(long index) const {</td>

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<pre style="margin: 0;"> <span id="LC2382" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC2383" 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="LC2384" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC2385" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span>      <span class="n" style="color: #333;">_LikelihoodFunction</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RecurseConstantOnPartition</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">blockIndex</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">depend<span class="idiff left right">a</span>nce</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">highestIndex</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cache</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC2385" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span>      <span class="n" style="color: #333;">_LikelihoodFunction</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RecurseConstantOnPartition</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">blockIndex</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">depend<span class="idiff left right">e</span>nce</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">highestIndex</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cache</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="2386" 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="LC2386" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// SLKP 20210102: TODO this needs to be reviewed and confirmed as working.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2387" 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="2387" 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">

2387

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<pre style="margin: 0;"> <span id="LC2387" class="line" lang="cpp">    <span class="n" style="color: #333;">_CategoryVariable</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">thisC</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_CategoryVariable</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">LocateVar</span><span class="p">(</span><span class="n" style="color: #333;">indexCat</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2388" 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">

2388

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<td class="new_line diff-line-num" data-linenumber="2388" 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">

2388

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<pre style="margin: 0;"> <span id="LC2388" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="2389" 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">

2389

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<td class="new_line diff-line-num" data-linenumber="2389" 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="LC2389" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">highestIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="2390" 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">

2390

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<td class="new_line diff-line-num old" data-linenumber="2390" 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="LC2390" 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;">CheckNthBit</span><span class="p">(</span><span class="n" style="color: #333;">depend<span class="idiff left right">a</span>nce</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="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_hidden_markov</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2391" 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">

2391

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<td class="new_line diff-line-num old" data-linenumber="2390" 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="LC2391" class="line" lang="cpp">            <span class="n" style="color: #333;">RecurseCategory</span> <span class="p">(</span><span class="n" style="color: #333;">blockIndex</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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">depend<span class="idiff left right">a</span>nce</span><span class="p">,</span><span class="n" style="color: #333;">highestIndex</span><span class="p">,</span><span class="n" style="color: #333;">weight</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2392" 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="2390" 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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<pre style="margin: 0;">+<span id="LC2390" 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;">CheckNthBit</span><span class="p">(</span><span class="n" style="color: #333;">depend<span class="idiff left right">e</span>nce</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="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_hidden_markov</span><span class="p">())</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2392" 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="2391" 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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<pre style="margin: 0;">+<span id="LC2391" class="line" lang="cpp">            <span class="n" style="color: #333;">RecurseCategory</span> <span class="p">(</span><span class="n" style="color: #333;">blockIndex</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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">depend<span class="idiff left right">e</span>nce</span><span class="p">,</span><span class="n" style="color: #333;">highestIndex</span><span class="p">,</span><span class="n" style="color: #333;">weight</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2392" 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">

2392

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<td class="new_line diff-line-num" data-linenumber="2392" 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="LC2392" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2393" 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">

2393

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<td class="new_line diff-line-num" data-linenumber="2393" 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">

2393

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<pre style="margin: 0;"> <span id="LC2393" class="line" lang="cpp">            <span class="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Refresh</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2394" 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">

2394

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<td class="new_line diff-line-num" data-linenumber="2394" 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="LC2394" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">nI</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetNumberOfIntervals</span> <span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2395" 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">

2395

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<td class="new_line diff-line-num" data-linenumber="2395" 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">

2395

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<pre style="margin: 0;"> <span id="LC2395" class="line" lang="cpp">            <span class="n" style="color: #333;">offsetCounter</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">nI</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2396" 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="2396" 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="LC2396" 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;">long</span> <span class="n" style="color: #333;">k</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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nI</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2397" 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">

2397

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<td class="new_line diff-line-num" data-linenumber="2397" 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">

2397

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<pre style="margin: 0;"> <span id="LC2397" class="line" lang="cpp">                <span class="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetIntervalValue</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2398" 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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<td class="new_line diff-line-num old" data-linenumber="2398" 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="LC2398" class="line" lang="cpp">                <span class="n" style="color: #333;">RecurseConstantOnPartition</span><span class="p">(</span><span class="n" style="color: #333;">blockIndex</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;">1</span><span class="p">,</span><span class="n" style="color: #333;">depend<span class="idiff left right">a</span>nce</span><span class="p">,</span> <span class="n" style="color: #333;">highestIndex</span><span class="p">,</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetIntervalWeight</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">),</span><span class="n" style="color: #333;">cache</span><span class="p">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="2399" 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="2398" 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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<pre style="margin: 0;">+<span id="LC2398" class="line" lang="cpp">                <span class="n" style="color: #333;">RecurseConstantOnPartition</span><span class="p">(</span><span class="n" style="color: #333;">blockIndex</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;">1</span><span class="p">,</span><span class="n" style="color: #333;">depend<span class="idiff left right">e</span>nce</span><span class="p">,</span> <span class="n" style="color: #333;">highestIndex</span><span class="p">,</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetIntervalWeight</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">),</span><span class="n" style="color: #333;">cache</span><span class="p">);</span></span>

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<td class="old_line diff-line-num" data-linenumber="2399" 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="LC2399" class="line" lang="cpp">                <span class="n" style="color: #333;">categID</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">offsetCounter</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">nI</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="2400" 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="2400" 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="LC2400" class="line" lang="cpp">            <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="2401" 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="2401" 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="LC2401" class="line" lang="cpp">            <span class="n" style="color: #333;">offsetCounter</span><span class="o" style="font-weight: 600;">/=</span><span class="n" style="color: #333;">nI</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2450" 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="2450" 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">@@ -2450,7 +2450,7 @@ void      _LikelihoodFunction::RecurseConstantOnPartition (long blockIndex, long</td>

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<pre style="margin: 0;"> <span id="LC2450" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num" data-linenumber="2451" 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="LC2451" 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="LC2452" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num old" data-linenumber="2453" 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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<td class="new_line diff-line-num old" data-linenumber="2453" 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="LC2453" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span>      <span class="n" style="color: #333;">_LikelihoodFunction</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RecurseCategory</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">blockIndex</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">depend<span class="idiff left right">a</span>nce</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">highestIndex</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">weight</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2453" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span>      <span class="n" style="color: #333;">_LikelihoodFunction</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">RecurseCategory</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">blockIndex</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">depend<span class="idiff left right">e</span>nce</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">highestIndex</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">weight</span></span>

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<pre style="margin: 0;"> <span id="LC2454" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_LFENGINE_REWRITE_</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2455" 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="2455" 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="LC2455" class="line" lang="cpp">        <span class="p">,</span><span class="n" style="color: #333;">_SimpleList</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">siteMultipliers</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">runMode</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">runStorage</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="2456" 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="2456" 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="LC2456" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">branchIndex</span><span class="p">,</span>              <span class="n" style="color: #333;">_SimpleList</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">branchValues</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2459" 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="2459" 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">@@ -2459,8 +2459,8 @@ void      _LikelihoodFunction::RecurseCategory(long blockIndex, long index, long</td>

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<td class="old_line diff-line-num" data-linenumber="2459" 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="LC2459" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC2460" class="line" lang="cpp">    <span class="n" style="color: #333;">_CategoryVariable</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">thisC</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_CategoryVariable</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">LocateVar</span><span class="p">(</span><span class="n" style="color: #333;">indexCat</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]);</span></span>

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<td class="old_line diff-line-num" data-linenumber="2461" 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="LC2461" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">highestIndex</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="2462" 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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<td class="new_line diff-line-num old" data-linenumber="2462" 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="LC2462" 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;">CheckNthBit</span><span class="p">(</span><span class="n" style="color: #333;">depend<span class="idiff left right">a</span>nce</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="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_hidden_markov</span><span class="p">())</span></span>

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<td class="old_line diff-line-num old" data-linenumber="2463" 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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<td class="new_line diff-line-num old" data-linenumber="2462" 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="LC2463" class="line" lang="cpp">            <span class="n" style="color: #333;">RecurseCategory</span> <span class="p">(</span><span class="n" style="color: #333;">blockIndex</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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">depend<span class="idiff left right">a</span>nce</span><span class="p">,</span><span class="n" style="color: #333;">highestIndex</span><span class="p">,</span><span class="n" style="color: #333;">weight</span></span>

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<td class="old_line diff-line-num new" data-linenumber="2464" 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="2462" 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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<pre style="margin: 0;">+<span id="LC2462" 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;">CheckNthBit</span><span class="p">(</span><span class="n" style="color: #333;">depend<span class="idiff left right">e</span>nce</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="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_hidden_markov</span><span class="p">())</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2464" 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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<pre style="margin: 0;">+<span id="LC2463" class="line" lang="cpp">            <span class="n" style="color: #333;">RecurseCategory</span> <span class="p">(</span><span class="n" style="color: #333;">blockIndex</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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">depend<span class="idiff left right">e</span>nce</span><span class="p">,</span><span class="n" style="color: #333;">highestIndex</span><span class="p">,</span><span class="n" style="color: #333;">weight</span></span>

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<pre style="margin: 0;"> <span id="LC2464" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_LFENGINE_REWRITE_</span></span>

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<td class="old_line diff-line-num" data-linenumber="2465" 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="2465" 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="LC2465" class="line" lang="cpp">                             <span class="p">,</span><span class="n" style="color: #333;">siteMultipliers</span><span class="p">,</span><span class="n" style="color: #333;">runMode</span><span class="p">,</span><span class="n" style="color: #333;">runStorage</span></span>

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<td class="old_line diff-line-num" data-linenumber="2466" 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="LC2466" 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="2471" 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="2471" 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">@@ -2471,7 +2471,7 @@ void      _LikelihoodFunction::RecurseCategory(long blockIndex, long index, long</td>

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<td class="old_line diff-line-num" data-linenumber="2471" 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="LC2471" class="line" lang="cpp">            <span class="n" style="color: #333;">offsetCounter</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">nI</span><span class="p">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="2472" 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="LC2472" 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;">long</span> <span class="n" style="color: #333;">k</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;">k</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">nI</span><span class="p">;</span> <span class="n" style="color: #333;">k</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="LC2473" class="line" lang="cpp">                <span class="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetIntervalValue</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="2474" 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="LC2474" class="line" lang="cpp">                <span class="n" style="color: #333;">RecurseCategory</span><span class="p">(</span><span class="n" style="color: #333;">blockIndex</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;">1</span><span class="p">,</span><span class="n" style="color: #333;">depend<span class="idiff left right">a</span>nce</span><span class="p">,</span> <span class="n" style="color: #333;">highestIndex</span><span class="p">,</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetIntervalWeight</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2475" 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="2474" 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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<pre style="margin: 0;">+<span id="LC2474" class="line" lang="cpp">                <span class="n" style="color: #333;">RecurseCategory</span><span class="p">(</span><span class="n" style="color: #333;">blockIndex</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;">1</span><span class="p">,</span><span class="n" style="color: #333;">depend<span class="idiff left right">e</span>nce</span><span class="p">,</span> <span class="n" style="color: #333;">highestIndex</span><span class="p">,</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">thisC</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetIntervalWeight</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC2475" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _SLKP_LFENGINE_REWRITE_</span></span>

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<pre style="margin: 0;"> <span id="LC2476" class="line" lang="cpp">                                <span class="p">,</span><span class="n" style="color: #333;">siteMultipliers</span><span class="p">,</span><span class="n" style="color: #333;">runMode</span><span class="p">,</span><span class="n" style="color: #333;">runStorage</span><span class="p">,</span><span class="n" style="color: #333;">branchIndex</span><span class="p">,</span><span class="n" style="color: #333;">branchValues</span></span>

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<pre style="margin: 0;"> <span id="LC2477" 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="2698" 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">@@ -2698,7 +2698,7 @@ void    _LikelihoodFunction::CheckDependentBounds (void) {</td>

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<pre style="margin: 0;"> <span id="LC2698" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC2699" class="line" lang="cpp">        <span class="n" style="color: #333;">_Matrix</span>     <span class="n" style="color: #333;">dependancies</span> <span class="p">(</span><span class="n" style="color: #333;">MAX</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span><span class="n" style="color: #333;">indexDep</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">),</span><span class="n" style="color: #333;">indexInd</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</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="LC2700" class="line" lang="cpp">        </span>

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<pre style="margin: 0;">-<span id="LC2701" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// element (i,j) represents the depend<span class="idiff left right">a</span>nce of i-th dep var on the j-th ind var</span></span>

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<pre style="margin: 0;">+<span id="LC2701" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// element (i,j) represents the depend<span class="idiff left right">e</span>nce of i-th dep var on the j-th ind var</span></span>

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<pre style="margin: 0;"> <span id="LC2702" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// 0 - no dep,</span></span>

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<pre style="margin: 0;"> <span id="LC2703" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// 1 -> monotone increase,</span></span>

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<pre style="margin: 0;"> <span id="LC2704" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// -1 -> monotone decrease</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5350" 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="5350" 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">@@ -5350,7 +5350,7 @@ long    _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle</td>

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<pre style="margin: 0;"> <span id="LC5350" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">leftStep</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC5351" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbosity_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC5352" 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;">512</span><span class="p">];</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="5353" 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="LC5353" 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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">buf</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) HANDLING LEFT BOUNDARY CASES] : LB = %g, current try = %.16g, current evaluated midpoint value = %.16g (%s)"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">leftStep</span><span class="p">,</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"first"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"NOT first"</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC5353" 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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">buf</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) HANDLING LEFT BOUNDARY CASES] : <span class="idiff left">initial = %g, </span>LB = %g, current try = %.16g, current evaluated midpoint value = %.16g (%s)"</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">initialStep</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">lowerBound</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">leftStep</span><span class="p">,</span> <span class="n" style="color: #333;">middleValue</span><span class="p">,</span> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"first"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"NOT first"</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5354" 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>

</pre>

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5355

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<pre style="margin: 0;"> <span id="LC5355" class="line" lang="cpp">            <span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="5356" 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">

5356

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<td class="new_line diff-line-num" data-linenumber="5356" 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="LC5356" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5396" 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="5396" 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">@@ -5396,6 +5396,9 @@ long    _LikelihoodFunction::Bracket (long index, hyFloat& left, hyFloat& middle</td>

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5396

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<pre style="margin: 0;"> <span id="LC5396" class="line" lang="cpp">                    <span class="n" style="color: #333;">middle</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lowerBound</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">2.</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">leftStep</span><span class="p">;</span></span>

</pre>

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5397

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5397

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<pre style="margin: 0;"> <span id="LC5397" class="line" lang="cpp">                    <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>

</pre>

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5398

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<pre style="margin: 0;"> <span id="LC5398" class="line" lang="cpp">                <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC5399" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="5399" 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="5400" 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">

5400

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<pre style="margin: 0;">+<span id="LC5400" class="line" lang="cpp">                <span class="n" style="color: #333;">middleValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SetParametersAndCompute</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">currentValues</span><span class="p">,</span> <span class="n" style="color: #333;">gradient</span><span class="p">);</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="5401" 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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<pre style="margin: 0;">+<span id="LC5401" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre>

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5399

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<td class="new_line diff-line-num" data-linenumber="5402" 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">

5402

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<pre style="margin: 0;"> <span id="LC5402" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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5400

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<td class="new_line diff-line-num" data-linenumber="5403" 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">

5403

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<pre style="margin: 0;"> <span id="LC5403" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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5401

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<td class="new_line diff-line-num" data-linenumber="5404" 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">

5404

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<pre style="margin: 0;"> <span id="LC5404" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7678" 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="7681" 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">@@ -7678,7 +7681,7 @@ void    _LikelihoodFunction::ScanAllVariables (void) {</td>

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7678

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<td class="new_line diff-line-num" data-linenumber="7681" 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">

7681

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<pre style="margin: 0;"> <span id="LC7681" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7679" 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">

7679

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<td class="new_line diff-line-num" data-linenumber="7682" 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">

7682

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<pre style="margin: 0;"> <span id="LC7682" class="line" lang="cpp">    <span class="n" style="color: #333;">avl</span><span class="p">.</span><span class="n" style="color: #333;">ReorderList</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7680" 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">

7680

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<td class="new_line diff-line-num" data-linenumber="7683" 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">

7683

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<pre style="margin: 0;"> <span id="LC7683" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="7681" 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">

7681

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<td class="new_line diff-line-num old" data-linenumber="7684" 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="LC7681" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">templateKind</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 class="c1" style="color: #998; font-style: italic;">// remove depend<span class="idiff left right">a</span>nce of the function from the HMM model specifier</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7684" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">templateKind</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 class="c1" style="color: #998; font-style: italic;">// remove depend<span class="idiff left right">e</span>nce of the function from the HMM model specifier</span></span>

</pre>

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7682

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<pre style="margin: 0;"> <span id="LC7685" class="line" lang="cpp">        <span class="n" style="color: #333;">allVariables</span><span class="p">.</span><span class="n" style="color: #333;">Delete</span> <span class="p">(</span><span class="n" style="color: #333;">allVariables</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">templateKind</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

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7683

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7686

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<pre style="margin: 0;"> <span id="LC7686" class="line" lang="cpp">        <span class="n" style="color: #333;">rankVariables</span><span class="p">.</span><span class="n" style="color: #333;">Delete</span> <span class="p">((</span><span class="n" style="color: #333;">BaseRef</span><span class="p">)(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">templateKind</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC7687" class="line" lang="cpp">    <span class="p">}</span></span>

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<li id="795bd9642f0c76f4bba4eaba7f491566cf16e788">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#795bd9642f0c76f4bba4eaba7f491566cf16e788"><strong>src/core/operation.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="231" 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="231" 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">@@ -231,8 +231,10 @@ _Operation::_Operation  (bool isVar, _String& stuff, bool isG, _VariableContaine</td>

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<pre style="margin: 0;"> <span id="LC231" 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>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp">        <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">theS</span> <span class="p">(</span><span class="n" style="color: #333;">stuff</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theParent</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// SLKP 20210223 : why is this here</span></span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// if a global variable aleady exists, ignore the context?</span></span>

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<pre style="margin: 0;"> <span id="LC236" 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;">LocateVarByName</span><span class="p">(</span><span class="n" style="color: #333;">theS</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp">            </span>

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<pre style="margin: 0;"> <span id="LC238" 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="mi" style="color: #099;">0L</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">FetchVar</span><span class="p">(</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;">IsGlobal</span><span class="p">())</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">                <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</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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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="133fe28f0d337fcb69fd32fa3f4499c2e4c6ea50">

<a href="https://salsa.debian.org/med-team/hyphy/-/commit/6884fa66cf5d542d45a116543c13c6757e02b6ef#133fe28f0d337fcb69fd32fa3f4499c2e4c6ea50"><strong>src/core/parser.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="380" 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">@@ -380,10 +380,13 @@ void       UpdateChangingFlas (_SimpleList const & involvedVariables) {</td>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">DeleteVariable</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">dv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">deleteself</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">do_checks</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="381" 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">

381

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">dv</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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382

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382

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num new" data-linenumber="383" 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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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> </span>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp">        <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</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;">variableNames</span><span class="p">.</span><span class="n" style="color: #333;">Retrieve</span> <span class="p">(</span><span class="n" style="color: #333;">dv</span><span class="p">);</span></span>

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384

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385

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp">        <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">my_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">&</span><span class="sc" style="color: #d14;">'.'</span><span class="p">;</span></span>

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386

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp">        </span>

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387

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">long</span>    <span class="n" style="color: #333;">vidx</span>    <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">variableNames</span><span class="p">.</span><span class="n" style="color: #333;">GetXtra</span> <span class="p">(</span><span class="n" style="color: #333;">dv</span><span class="p">);</span></span>

</pre>

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386

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<td class="new_line diff-line-num" data-linenumber="388" 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">

388

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="389" 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">

389

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"></span>

</pre>

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387

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<td class="new_line diff-line-num" data-linenumber="390" 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="LC390" class="line" lang="cpp">        <span class="n" style="color: #333;">UpdateChangingFlas</span> <span class="p">(</span><span class="n" style="color: #333;">vidx</span><span class="p">);</span></span>

</pre>

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388

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<td class="new_line diff-line-num" data-linenumber="391" 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">

391

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="392" 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">

392

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp">        <span class="n" style="color: #333;">_SimpleList</span> <span class="n" style="color: #333;">recCache</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="547" 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="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -547,7 +550,7 @@ void DeleteTreeVariable (long tree_variable_index, _SimpleList & parms, _String</td>

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547

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550

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp">        </span>

</pre>

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548

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551

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp">        <span class="n" style="color: #333;">indices_to_delete</span><span class="p">.</span><span class="n" style="color: #333;">Each</span> <span class="p">([]</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">var_idx</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="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">{</span></span>

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549

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<td class="new_line diff-line-num" data-linenumber="552" 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">

552

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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cpp">            <span class="n" style="color: #333;">_Variable</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">delvar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LocateVar</span> <span class="p">(</span><span class="n" style="color: #333;">var_idx</span><span class="p">);</span></span>

</pre>

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550

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<pre style="margin: 0;">-<span id="LC550" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//printf ("Deleting variable %s\n" , delvar->GetName()->get_str());</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//printf ("<span class="idiff left right">DeleteTree::</span>Deleting variable %s\n" , delvar->GetName()->get_str());</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC554" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">delvar</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ObjectClass</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">TREE</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="cpp">                <span class="n" style="color: #333;">variableNames</span><span class="p">.</span><span class="n" style="color: #333;">Delete</span> <span class="p">(</span><span class="n" style="color: #333;">delvar</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetName</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="LC556" class="line" lang="cpp">                <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">((</span><span class="n" style="color: #333;">_SimpleList</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">variablePtrs</span><span class="p">))[</span><span class="n" style="color: #333;">delvar</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_index</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="671" 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">@@ -671,12 +674,12 @@ bool CheckReceptacleAndStore (_String name, _String fID, bool checkValid, HBLObj</td>

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<pre style="margin: 0;"> <span id="LC674" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC675" 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="LC676" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span>  <span class="nf" style="color: #900; font-weight: 600;">InsertVar</span> <span class="p">(</span><span class="n" style="color: #333;">_Variable</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">theV</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC674" class="line" lang="cpp">        </span>

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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC679" 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;">variableNames</span><span class="p">.</span><span class="n" style="color: #333;">Insert</span> <span class="p">(</span><span class="n" style="color: #333;">theV</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theName</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC676" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC677" 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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDefiningATree</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kTreeNodeBeingCreated</span><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="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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isDefiningATree</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">kTreeNodeBeingCreated</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>

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<pre style="margin: 0;"> <span id="LC682" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// automatically fix duplicate autogenerated tree node name</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="LC683" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">trySuffix</span>  <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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681

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<td class="new_line diff-line-num" data-linenumber="684" 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">

684

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<pre style="margin: 0;"> <span id="LC684" class="line" lang="cpp">        <span class="n" style="color: #333;">_String</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tryName</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_String</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="682" 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">

682

</td>

<td class="new_line diff-line-num" data-linenumber="685" 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">

685

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC685" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>

</pre>

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