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<h3>
Nilesh Patra pushed to branch master
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/cb557a21988717038e912e13ab03563e6e3df1b6">cb557a21</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-18T20:06:36+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/e5b51d8b41be01b7403fe58fde204cf04555868d">e5b51d8b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-18T20:06:37+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.23+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/6b5647e236540cbf6b70950285ffdc33f2d6c868">6b5647e2</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-18T20:06:48+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.5.23+dfsg'
Update to upstream version '2.5.23+dfsg'
with Debian dir 663e8a5e5fa591dd68e426eff00d81ba38caca26</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/93ac5b946e31deb92501e95fb4d9ee737d6b4f44">93ac5b94</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-18T20:07:16+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#e5a6f1ed046081016d3663d7c080e9a742d096d0">
.github/workflows/coverage.yml
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#4ed0809c2483f5150cdfd2c3bf07d212387406d0">
res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf
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<li class="file-stats">
<a href="#80cb7c212661a2afbd05c16dce9f84f45709578e">
res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
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<li class="file-stats">
<a href="#cf5243a3058ebeab74574f8cd2c771cd63a43208">
res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf
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<li class="file-stats">
<a href="#13df3044c13d443b9b6ad8712b47d3bc84725272">
res/TemplateBatchFiles/SelectionAnalyses/SLAC.bf
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<li class="file-stats">
<a href="#48abec8e0d198814ad3898dd7c82ef8b52eef776">
res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
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<li class="file-stats">
<a href="#b8a362ed8e8b5d27762dcb255aa270b7e616d311">
src/core/batchlanhelpers.cpp
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<li class="file-stats">
<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">
src/core/global_things.cpp
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<li class="file-stats">
<a href="#2a8dd324ded753b0b3c559ac3950a2881ccd7a93">
src/core/likefunc.cpp
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<li class="file-stats">
<a href="#d3c93b0241ae67c1806a451588ccdec77e0ca3f3">
src/core/trie.cpp
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<li class="file-stats">
<a href="#aeaccdf9a873c05871ba3cd1bca1ae0e9f8254e4">
src/mains/unix.cpp
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<h4>Changes:</h4>
<li id="e5a6f1ed046081016d3663d7c080e9a742d096d0">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#e5a6f1ed046081016d3663d7c080e9a742d096d0"><strong>.github/workflows/coverage.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,7 @@ jobs:</td>
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<td class="diff-line-num old_line" 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">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Get HyPhy code</span></span>
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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install and activate miniconda</span></span>
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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(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="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">goanpeca/setup-miniconda@v1</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(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="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">conda-incubator/setup-miniconda@v2</span></span></span>
</pre>
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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(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="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">activate-environment</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">hyphy-test-env'</span></span>
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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(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="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;">environment-file</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">.coveralls.env.yml'</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.23+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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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="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Wed, 18 Nov 2020 20:07:16 +0000</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">hyphy (2.5.22+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#4ed0809c2483f5150cdfd2c3bf07d212387406d0"><strong>res/TemplateBatchFiles/SelectionAnalyses/BUSTED.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,6 +166,8 @@ busted.json[busted.json.background] = busted.has_background;</td>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="brainfuck"></span>
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167
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<pre style="margin: 0;"> <span id="LC167" 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;">startTimer (busted</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Preliminary model fitting"</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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168
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="brainfuck"></span>
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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;">namespace_tag = "busted";</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="brainfuck"></span>
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169
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">namespace busted {</span></span>
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170
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> doGTR ("busted");</span></span>
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171
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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>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#80cb7c212661a2afbd05c16dce9f84f45709578e"><strong>res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -159,6 +159,7 @@ prime.pairwise_counts = genetic_code.ComputePairwiseDifferencesAndExpectedSites(</td>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" 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;">startTimer (prime</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Model fitting"</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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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="brainfuck"></span>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (Type (debug</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">checkpoint) != "String") {</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> namespace_tag = "prime";</span></span>
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162
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> namespace prime {</span></span>
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163
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> doGTR ("prime");</span></span>
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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>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#cf5243a3058ebeab74574f8cd2c771cd63a43208"><strong>res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -263,6 +263,8 @@ if (relax.do_srv) {</td>
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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;">startTimer (relax</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Preliminary model fitting"</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="LC265" class="line" lang="brainfuck"></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;">namespace_tag = "relax";</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;">namespace relax {</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;"> doGTR ("relax");</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;">}</span></span>
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<li id="13df3044c13d443b9b6ad8712b47d3bc84725272">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#13df3044c13d443b9b6ad8712b47d3bc84725272"><strong>res/TemplateBatchFiles/SelectionAnalyses/SLAC.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -145,6 +145,8 @@ utility.ForEachPair (slac.selected_branches, "_partition_", "_selection_",</td>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">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;">startTimer (slac</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Model fitting"</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="LC147" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">namespace_tag = "slac";</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">namespace slac {</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> doGTR ("slac");</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#48abec8e0d198814ad3898dd7c82ef8b52eef776"><strong>res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -268,6 +268,8 @@ fel.table_output_options = {terms.table_options.header : TRUE, terms.table_optio</td>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="brainfuck"></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;">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;">startTimer (fel</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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Model fitting"</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="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;">namespace_tag = "fel";</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="brainfuck"></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;">namespace fel {</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;"> doGTR ("fel");</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;">}</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">@@ -394,12 +396,26 @@ fel.site_patterns = alignments.Extract_site_patterns ((fel.filter_specification[</td>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// alpha = alpha_scaler * branch_length</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// beta = beta_scaler_test * branch_length or beta_nuisance_test * branch_length</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">-<span id="LC397" 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 (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">case_respecting_node_names</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_node_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></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;"> '_node_class_ = (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</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="LC399" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler = fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_class_</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="LC400" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">apply_proportional_site_constraint ("fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_tree"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _node_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> (( fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">final_partitioned_mg_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length</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;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</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="LC401" 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="LC399" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lengths_by_class = {};</span></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (_node_; in; fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">case_respecting_node_names) {</span></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;"> _node_class_ = (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</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="LC403" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler = fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_class_</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="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lengths_by_class</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_class_</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;">= fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">apply_proportional_site_constraint ("fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_tree"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _node_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _beta_scaler</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> (( fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">final_partitioned_mg_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length</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;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_node_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="brainfuck"></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ignorable = {};</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t; in; fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable) {</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ( fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lengths_by_class</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == 0) {</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" 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;">\n"</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;">FormatLongStringToWidth(</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nb" style="color: #0086b3;">></span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">WARNING</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> The cumulative branch length in the _" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "_ class is 0</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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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Rates along these branches are not identifiable; testing will not be formally conducted (all p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">values set to 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;"> 72)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="brainfuck"><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;">\n"); </span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ignorable </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = 1;</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ignorable </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = 0;</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" 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="LC418" 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="LC419" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">// create the likelihood function for this site</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">@@ -422,7 +438,7 @@ fel.queue = mpi.CreateQueue ({"LikelihoodFunctions": {{"fel.site_likelihood"}},</td>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Models" : {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mg_rev"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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439
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<pre style="margin: 0;"> <span id="LC439" 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 class="c1" style="color: #998; font-style: italic;">"libv3/tasks/ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "libv3/convenience/math</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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<pre style="margin: 0;"> <span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Functions" : {{"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">apply_proportional_site_constraint"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</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;"> "Variables" : {{"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_keys"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">permutations"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"> </span>"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler"</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;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">permutation"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">final_partitioned_mg_results"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_tested_classes"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">has_background"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler"</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;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pairwise"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_class_counter"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_count"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">permutations"}}</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "Variables" : {{"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_keys"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">permutations"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">"fel</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">ignorable"</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;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler"</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;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">permutation"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">final_partitioned_mg_results"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_tested_classes"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">has_background"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler"</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;">fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pairwise"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_class_counter"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_count"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">permutations"}}</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;"> });</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="brainfuck"></span>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -642,6 +658,8 @@ function fel.apply_proportional_site_constraint (tree_name, node_name, alpha_par</td>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`alpha_parameter` := (`alpha_factor`) * fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length__;</span></span>
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659
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> `node_name`</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">`beta_parameter` := (`beta_factor`) * fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length__;</span></span>
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<pre style="margin: 0;"> <span id="LC660" 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="LC661" 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="LC662" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> return fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length;</span></span>
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<pre style="margin: 0;"> <span id="LC663" 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="LC664" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">//</span><span class="nf" style="color: #900; font-weight: 600;">----------------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="brainfuck"></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">@@ -685,17 +703,27 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (vi</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> vv; in; v) {</span></span>
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704
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">pnames</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">vi</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;">vv;</span></span>
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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv"){</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler"</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;">75</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;">25);</span></span>
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<pre style="margin: 0;">+<span id="LC708" 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="LC709" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> start</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">grid </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> values;</span></span>
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<pre style="margin: 0;"> <span id="LC710" 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="LC711" 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="LC691" 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="LC712" 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="LC713" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> GetString (p</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;"> </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="LC714" 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 (p);</span></span>
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<pre style="margin: 0;">+<span id="LC715" 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 (values);</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> assert (0);</span></span>
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<pre style="margin: 0;">+<span id="LC717" 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="LC718" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</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;"> {</span></span>
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693
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "OPTIMIZATION_METHOD" : "nedler</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mead"</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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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "OPTIMIZATION_PRECISION" : 1e</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>
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> "OPTIMIZATION_START_GRID" : start</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">grid </span></span>
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723
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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697
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724
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<pre style="margin: 0;"> <span id="LC724" 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="LC698" 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="LC725" 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="LC726" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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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;"> /**</span></span>
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700
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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;"> infer and report ancestral substitutions</span></span>
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701
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729
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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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -712,8 +740,6 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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712
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740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ');</span></span>
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713
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>
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714
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742
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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716
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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743
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> snapshot = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">TakeLFStateSnapshot (lf);</span></span>
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718
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> alternative = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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719
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745
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> alternative </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;">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;"> = results</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -738,20 +764,17 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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738
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ref_parameter = (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"VALUEINDEXORDER"</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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739
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="brainfuck"></span>
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740
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> ^ref_parameter = sum /denominator;</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>
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741
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="brainfuck"></span>
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742
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (testable == 1) {</span></span>
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743
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770
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<pre style="margin: 0;"> <span id="LC770" 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;">SetConstraint ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</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;">tree_attributes</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">background"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">ref_parameter</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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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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745
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<pre style="margin: 0;">-<span id="LC745" 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 (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_gname_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> '</span></span>
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747
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<pre style="margin: 0;">-<span id="LC747" 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 ("REF " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> `&ref_parameter`);</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (_gname_; in; ^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable") {</span></span>
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748
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> _pname_ = (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_gname_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>
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749
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_pname_ != `&ref_parameter`) {</span></span>
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750
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<pre style="margin: 0;">-<span id="LC750" 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 (_pname_ </span><span class="nf" style="color: #900; font-weight: 600;">+</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;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> `&ref_parameter`);</span></span>
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751
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<pre style="margin: 0;">-<span id="LC751" 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;">SetConstraint (_pname_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">`&ref_parameter`</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="LC774" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (_pname_ != ref_parameter && (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ignorable")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_pname_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> == 0) {</span></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetConstraint (_pname_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">ref_parameter</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="LC776" 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="LC753" 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="LC754" 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="LC777" 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="LC778" 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="LC779" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</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;"> {"OPTIMIZATION_METHOD" : "nedler</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mead"});</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">@@ -764,12 +787,17 @@ lfunction fel.handle_a_site (lf, filter_data, partition_index, pattern_info, mod</td>
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> for (v2 = v </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 1; v2 </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> testable; v2</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="LC788" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> v1n = (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable")</span><span class="p">[</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;">;</span></span>
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> v2n = (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branches</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">testable")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v2</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="LC767" class="line" lang="brainfuck"></span>
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">RestoreLFStateFromSnapshot (lf_id</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> snapshot);</span></span>
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<pre style="margin: 0;">-<span id="LC769" 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;">SetConstraint ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">(^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v2n</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>
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</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;"> {"OPTIMIZATION_METHOD" : "nedler</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mead"});</span></span>
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pairwise</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n </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;"> v2n</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (pairwise</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n </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;"> v2n</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;">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;"> = results</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="LC791" 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="LC792" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ignorable")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> || (^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ignorable")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v2n</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="LC793" 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 (v1n </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;"> v2n </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " is ignorable");</span></span>
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (pairwise</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n </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;"> v2n</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) = alternative;</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else { </span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" 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;">SetConstraint ((^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">(^"fel</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">scaler_parameter_names")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v2n</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>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> Optimize (results</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;"> {"OPTIMIZATION_METHOD" : "nedler</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mead"});</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> pairwise</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n </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;"> v2n</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping);</span></span>
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> (pairwise</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">v1n </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;"> v2n</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;">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;"> = results</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="LC800" 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="LC801" 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="LC802" 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="LC803" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> } else {</span></span>
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<li id="b8a362ed8e8b5d27762dcb255aa270b7e616d311">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#b8a362ed8e8b5d27762dcb255aa270b7e616d311"><strong>src/core/batchlanhelpers.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">@@ -68,14 +68,18 @@ _String const _HYGenerateANameSpace () {</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//____________________________________________________________________________________</span></span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">_HYClearANameSpace</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">nm</span><span class="p">)</span> <span class="p">{</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*BufferToConsole("Deleting key: ");</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> BufferToConsole(nm.get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> NLToConsole();</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> ObjectToConsole(&_HY_HBL_Namespaces);</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> NLToConsole();*/</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">_HY_HBL_Namespaces</span><span class="p">.</span><span class="n" style="color: #333;">Delete</span><span class="p">(</span><span class="n" style="color: #333;">nm</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC79" 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="LC80" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadModelList</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="LC78" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ReadModelList</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="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">templateModelList</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">_String</span> <span class="n" style="color: #333;">modelListFile</span> <span class="p">(</span><span class="n" style="color: #333;">GetStandardDirectory</span> <span class="p">(</span><span class="n" style="color: #333;">HY_HBL_DIRECTORY_TEMPLATE_MODELS</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&</span> <span class="s" style="color: #d14;">"models.lst"</span><span class="p">),</span></span>
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<li id="07aceb8d215a75908cea626d9c80bc2a7c06639c">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#07aceb8d215a75908cea626d9c80bc2a7c06639c"><strong>src/core/global_things.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,7 +121,7 @@ namespace hy_global {</td>
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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>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">kErrorStringMatrixExportError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Export matrix called with a non-polynomial matrix argument"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="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>
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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">2</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">kHyPhyVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.2<span class="idiff left right">3</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> </span>
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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>
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127
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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>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#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">@@ -256,8 +256,14 @@ void BenchmarkThreads (_LikelihoodFunction* lf) {</td>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetThreadCount</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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257
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">TimeDifference</span> <span class="n" style="color: #333;">timer</span><span class="p">;</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetIthIndependent</span> <span class="p">(</span><span class="n" style="color: #333;">alterIndex</span><span class="p">,</span><span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">alterIndex</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Compute</span> <span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hy_mpi_node_rank</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetIthIndependent</span> <span class="p">(</span><span class="n" style="color: #333;">alterIndex</span><span class="p">,</span><span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">alterIndex</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Compute</span> <span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"></span>
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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">@@ -276,6 +282,7 @@ hyFloat tdiff = timer.TimeSinceStart();</td>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetThreadCount</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="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">TimeDifference</span> <span class="n" style="color: #333;">timer</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetIthIndependent</span> <span class="p">(</span><span class="n" style="color: #333;">alterIndex</span><span class="p">,</span><span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetIthIndependent</span><span class="p">(</span><span class="n" style="color: #333;">alterIndex</span><span class="p">));</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> </span>
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279
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">lf</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Compute</span> <span class="p">();</span></span>
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280
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">tdiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">timer</span><span class="p">.</span><span class="n" style="color: #333;">TimeSinceStart</span><span class="p">();</span></span>
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281
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tdiff</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">minDiff</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="4063" style="width: 35px; color: rgba(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">@@ -4063,15 +4070,8 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4063
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4070
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<pre style="margin: 0;"> <span id="LC4070" class="line" lang="cpp"> <span class="n" style="color: #333;">SetupLFCaches</span> <span class="p">();</span></span>
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4064
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4071
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<pre style="margin: 0;"> <span id="LC4071" class="line" lang="cpp"> <span class="n" style="color: #333;">SetupCategoryCaches</span> <span class="p">();</span></span>
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4065
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4072
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<pre style="margin: 0;"> <span id="LC4072" class="line" lang="cpp"> <span class="n" style="color: #333;">computationalResults</span><span class="p">.</span><span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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4066
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<pre style="margin: 0;">-<span id="LC4066" class="line" lang="cpp"> <span class="n" style="color: #333;">_variables_changed_during_last_compute</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_SimpleList</span> <span class="p">();</span></span>
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4067
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<pre style="margin: 0;">-<span id="LC4067" class="line" lang="cpp"> <span class="n" style="color: #333;">variables_changed_during_last_compute</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_AVLList</span> <span class="p">(</span><span class="n" style="color: #333;">_variables_changed_during_last_compute</span><span class="p">);</span></span>
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4068
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4073
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<pre style="margin: 0;"> <span id="LC4073" class="line" lang="cpp"> </span>
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4069
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<pre style="margin: 0;">-<span id="LC4069" 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;">indexInd</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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4070
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<pre style="margin: 0;">-<span id="LC4070" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">GetIthIndependentVar</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">varFlags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">HY_VARIABLE_CHANGED</span><span class="p">)</span> <span class="p">{</span></span>
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4071
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<pre style="margin: 0;">-<span id="LC4071" class="line" lang="cpp"> <span class="n" style="color: #333;">variables_changed_during_last_compute</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">InsertNumber</span> <span class="p">(</span><span class="n" style="color: #333;">GetIthIndependentVar</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_index</span><span class="p">());</span></span>
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4072
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<pre style="margin: 0;">-<span id="LC4072" class="line" lang="cpp"> <span class="p">}</span></span>
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4073
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<pre style="margin: 0;">-<span id="LC4073" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC4074" class="line" lang="cpp"></span>
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4074
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<pre style="margin: 0;">+<span id="LC4074" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC4075" class="line" lang="cpp"></span>
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4076
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4076
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<pre style="margin: 0;"> <span id="LC4076" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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4077
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<pre style="margin: 0;"> <span id="LC4077" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hy_mpi_node_rank</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4101,13 +4101,13 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4101
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<pre style="margin: 0;"> <span id="LC4101" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4102
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<pre style="margin: 0;"> <span id="LC4102" class="line" lang="cpp"></span>
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4103
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<pre style="margin: 0;"> <span id="LC4103" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4104" class="line" lang="cpp"> <span class="n" style="color: #333;">_variables_changed_during_last_compute</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_SimpleList</span> <span class="p">();</span></span>
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4105
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<pre style="margin: 0;">+<span id="LC4105" class="line" lang="cpp"> <span class="n" style="color: #333;">variables_changed_during_last_compute</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">_AVLList</span> <span class="p">(</span><span class="n" style="color: #333;">_variables_changed_during_last_compute</span><span class="p">);</span></span>
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4106
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<pre style="margin: 0;">+<span id="LC4106" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC4107" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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4108
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<pre style="margin: 0;"> <span id="LC4108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hy_mpi_node_rank</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC4109" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC4107" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC4110" class="line" lang="cpp"> <span class="n" style="color: #333;">BenchmarkThreads</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC4109" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC4110" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC4111" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __HYPHYMPI__</span></span>
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<pre style="margin: 0;"> <span id="LC4112" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC4113" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -4133,7 +4133,7 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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<pre style="margin: 0;"> <span id="LC4133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">keepStartingPoint</span><span class="p">)</span> <span class="p">{</span></span>
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4134
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<pre style="margin: 0;"> <span id="LC4134" class="line" lang="cpp"> <span class="n" style="color: #333;">indexInd</span><span class="p">.</span><span class="n" style="color: #333;">Each</span> <span class="p">([</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">untag</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;">v</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="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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4135
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<pre style="margin: 0;"> <span id="LC4135" 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;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GetIthIndependentVar</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="LC4136" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">HasBeenInitialized</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC4136" 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 class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">iv</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">IsGlobal</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">HasBeenInitialized</span><span class="p">())</span> <span class="p">{</span></span>
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4137
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4137
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<pre style="margin: 0;"> <span id="LC4137" 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;">iv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">IsModified</span><span class="p">())</span> <span class="p">{</span></span>
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4138
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<pre style="margin: 0;"> <span id="LC4138" class="line" lang="cpp"> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">MarkModified</span><span class="p">();</span></span>
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4139
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4139
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<pre style="margin: 0;"> <span id="LC4139" class="line" lang="cpp"> <span class="n" style="color: #333;">untag</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4178,6 +4178,13 @@ _Matrix* _LikelihoodFunction::Optimize (_AssociativeList const * options)</td>
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4178
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<pre style="margin: 0;"> <span id="LC4178" class="line" lang="cpp"> <span class="p">}</span></span>
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4179
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<pre style="margin: 0;"> <span id="LC4179" class="line" lang="cpp"> <span class="p">}</span></span>
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4180
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<pre style="margin: 0;"> <span id="LC4180" class="line" lang="cpp"> <span class="p">}</span></span>
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4181
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<pre style="margin: 0;">+<span id="LC4181" class="line" lang="cpp"> </span>
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4182
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<pre style="margin: 0;">+<span id="LC4182" 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;">indexInd</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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4183
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<pre style="margin: 0;">+<span id="LC4183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">GetIthIndependentVar</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">varFlags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">HY_VARIABLE_CHANGED</span><span class="p">)</span> <span class="p">{</span></span>
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4184
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<pre style="margin: 0;">+<span id="LC4184" class="line" lang="cpp"> <span class="n" style="color: #333;">variables_changed_during_last_compute</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">InsertNumber</span> <span class="p">(</span><span class="n" style="color: #333;">GetIthIndependentVar</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_index</span><span class="p">());</span></span>
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4185
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<pre style="margin: 0;">+<span id="LC4185" class="line" lang="cpp"> <span class="p">}</span></span>
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4186
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<pre style="margin: 0;">+<span id="LC4186" class="line" lang="cpp"> <span class="p">}</span></span>
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4187
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<pre style="margin: 0;">+<span id="LC4187" class="line" lang="cpp"></span>
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4188
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<pre style="margin: 0;"> <span id="LC4188" class="line" lang="cpp"></span>
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4189
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<pre style="margin: 0;"> <span id="LC4189" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if !defined __UNIX__ || defined __HEADLESS__</span></span>
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4183
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4190
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<pre style="margin: 0;"> <span id="LC4190" class="line" lang="cpp"> <span class="n" style="color: #333;">SetStatusBarValue</span> <span class="p">(</span><span class="mi" style="color: #099;">5</span><span class="p">,</span><span class="n" style="color: #333;">maxSoFar</span><span class="p">,(</span><span class="n" style="color: #333;">likeFuncEvalCallCount</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">evalsIn</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">timer</span><span class="p">.</span><span class="n" style="color: #333;">TimeSinceStart</span><span class="p">());</span></span>
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<li id="d3c93b0241ae67c1806a451588ccdec77e0ca3f3">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#d3c93b0241ae67c1806a451588ccdec77e0ca3f3"><strong>src/core/trie.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">@@ -344,10 +344,11 @@ bool _Trie::Delete (const _String& key){</td>
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344
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">emptySlots</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">history</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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345
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">payload</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">history</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">parents</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">history</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]]</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="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">parentList</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="n" style="color: #333;">list_data</span><span class="p">)[</span><span class="n" style="color: #333;"><span class="idiff left">history</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">list_data</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>];</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">_SimpleList</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">parentList</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="n" style="color: #333;">list_data</span><span class="p">)[</span><span class="n" style="color: #333;"><span class="idiff left">k</span></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">history</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">list_data</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">];</span></span>
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">parentNode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parentList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">FindStepping</span> <span class="p">(</span><span class="n" style="color: #333;">history</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">],</span><span class="mi" style="color: #099;">2</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">parentList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Delete</span> <span class="p">(</span><span class="n" style="color: #333;">parentNode</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">parentList</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Delete</span> <span class="p">(</span><span class="n" style="color: #333;">parentNode</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">DeleteObject</span> <span class="p">(</span><span class="n" style="color: #333;">current_list</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC353" 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="p">)</span><span class="n" style="color: #333;">list_data</span><span class="p">)[</span><span class="n" style="color: #333;">history</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nil</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">inserted_values</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -450,7 +451,9 @@ BaseRef _Trie::toStr(unsigned long) {</td>
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451
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC453" 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;">this_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RetrieveStringFromPath</span><span class="p">(</span><span class="n" style="color: #333;">traversal_history</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alph</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">serialized</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'"'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">this_string</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">GetValue</span> <span class="p">(</span><span class="n" style="color: #333;">traversal_history</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">traversal_history</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]));</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">serialized</span><span class="p">)</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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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">serialized</span><span class="p">).</span><span class="n" style="color: #333;">AppendNewInstance</span><span class="p">(</span><span class="n" style="color: #333;">this_string</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">serialized</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">:"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="n" style="color: #333;">GetValue</span> <span class="p">(</span><span class="n" style="color: #333;">traversal_history</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">traversal_history</span><span class="p">.</span><span class="n" style="color: #333;">lLength</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">]));</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">doComma</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">serialized</span><span class="p">)</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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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<li id="aeaccdf9a873c05871ba3cd1bca1ae0e9f8254e4">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/2f1b4ebae84f25fe800d3e0f134358c42d70884e...93ac5b946e31deb92501e95fb4d9ee737d6b4f44#aeaccdf9a873c05871ba3cd1bca1ae0e9f8254e4"><strong>src/mains/unix.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">@@ -694,51 +694,6 @@ void SetStatusLineUser (_String const s) {</td>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef __UNITTEST__</span></span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*long N = 1000L;</span></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> long repeats = 20L;</span></span>
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> long density = 0.25 * RAND_MAX;</span></span>
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> auto start = std::chrono::high_resolution_clock::now();</span></span>
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> srand(time(0));</span></span>
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> _Matrix::switchThreshold = atoi (argv[1]);</span></span>
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printf ("%ld\n", _Matrix::switchThreshold);</span></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long i = 0; i < N; i++) {</span></span>
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> _Matrix test (61,61,false,true);</span></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> test.ForEachCellNumeric([density] (hyFloat& e, long i, long r, long c) -> void {</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (r != c && rand() < density) {</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> e = genrand_real1 ();</span></span>
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714
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> } else {</span></span>
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715
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> e = 0.0;</span></span>
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716
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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717
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> });</span></span>
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718
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long r = 0; r < 61; r++) {</span></span>
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719
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<pre style="margin: 0;">-<span id="LC719" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> double s = 0.;</span></span>
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720
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long c = 0; c < 61; c++) {</span></span>
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721
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> s += test (r, c);</span></span>
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722
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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723
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> test.theData[r*61+r] = -s;</span></span>
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724
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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725
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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726
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> test.AmISparse();</span></span>
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727
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //ObjectToConsole(&test);</span></span>
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728
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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729
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //printf ("%d\n", test.is_dense());</span></span>
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730
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (long j = 0; j < repeats; j++) {</span></span>
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731
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> DeleteObject (test.Exponentiate());</span></span>
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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //return 0;</span></span>
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733
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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735
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="cpp"></span>
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736
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> auto end = std::chrono::high_resolution_clock::now();</span></span>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> std::chrono::duration<double> elapsed = end - start;</span></span>
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738
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> printf ("%15.12g s\n", elapsed.count());</span></span>
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739
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<pre style="margin: 0;">-<span id="LC739" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> </span></span>
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740
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<pre style="margin: 0;">-<span id="LC740" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> return 0;*/</span></span>
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741
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="cpp"> </span>
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742
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697
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp"> </span>
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743
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef _COMPARATIVE_LF_DEBUG_DUMP</span></span>
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744
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699
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">comparative_lf_debug_matrix_content_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">doFileOpen</span> <span class="p">(</span><span class="n" style="color: #333;">_COMPARATIVE_LF_DEBUG_DUMP</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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