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GitLab

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<h3>

Andreas Tille 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/ed2ea04c8671c093cf2b8b5382fa8572b903ae1d">ed2ea04c</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-05-02T12:18:05+02:00</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/2147996cdad34ba5032b2231731c0bd18d606fb7">2147996c</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-05-02T12:18:06+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.38+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/6df45388512ca8a163cbe3bde9591b1745019707">6df45388</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-05-02T12:18:17+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.5.38+dfsg'

Update to upstream version '2.5.38+dfsg'

with Debian dir aed35afe4db5645439678beb46005d25beb6d3a2</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/4f0aba6e86789e08a9608db344716433dac9383e">4f0aba6e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2022-05-02T12:25:09+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>20 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#e4fd9bcc64f7c0236c7e16a07df70a48ebf4827d">

res/TemplateBatchFiles/LEISR.bf

</a>

</li>

<li class="file-stats">

<a href="#80cb7c212661a2afbd05c16dce9f84f45709578e">

res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf

</a>

</li>

<li class="file-stats">

<a href="#cf5243a3058ebeab74574f8cd2c771cd63a43208">

res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf

</a>

</li>

<li class="file-stats">

<a href="#5162429bd3f362a69890c6b040d4be37e11a6308">

res/TemplateBatchFiles/files.lst

</a>

</li>

<li class="file-stats">

<a href="#5dfec713e3892a936e8b5a63db56c03bee3ec252">

res/TemplateBatchFiles/libv3/all-terms.bf

</a>

</li>

<li class="file-stats">

<a href="#94156df91590185798157c724050369c6294262f">

res/TemplateBatchFiles/libv3/models/codon/BS_REL.bf

</a>

</li>

<li class="file-stats">

<a href="#95a7c74b0e59bc9dc8d85b6ac4b02d308b4e09fb">

res/TemplateBatchFiles/libv3/models/codon/MG_REV.bf

</a>

</li>

<li class="file-stats">

<a href="#9f6d2efd39d3afa147f430ca6d771b8d64f20a55">

res/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf

</a>

</li>

<li class="file-stats">

<a href="#e8578acaed39aa42e302cfc6b43e09678d292e72">

res/TemplateBatchFiles/libv3/models/codon/MSS.bf

</a>

</li>

<li class="file-stats">

<a href="#0ad5f4d1790906a0091532d9ca355a6162bf3c31">

res/TemplateBatchFiles/libv3/models/model_functions.bf

</a>

</li>

<li class="file-stats">

<a href="#801d4bca405dfccac3b1e451b211ca98bd00d599">

res/TemplateBatchFiles/libv3/models/parameters.bf

</a>

</li>

<li class="file-stats">

<a href="#5c5226a707906d461dd112286b111fe4809fac66">

res/TemplateBatchFiles/libv3/tasks/ancestral.bf

</a>

</li>

<li class="file-stats">

<a href="#59d202cc6599be3167fc3bd731039997dcaf9c72">

src/core/fstring.cpp

</a>

</li>

<li class="file-stats">

<a href="#07aceb8d215a75908cea626d9c80bc2a7c06639c">

src/core/global_things.cpp

</a>

</li>

<li class="file-stats">

<a href="#972df0539c47811332eda7005af635463c77eef8">

src/core/include/function_templates.h

</a>

</li>

<li class="file-stats">

<a href="#0aac57334e127d66d9818be138193215c7262bbe">

src/core/include/matrix.h

</a>

</li>

<li class="file-stats">

<a href="#81843dd3cf849d08e0f197d837dd373534c7c756">

src/core/matrix.cpp

</a>

</li>

<li class="file-stats">

<a href="#9f127084157a2a4e11faf03320db0541dbae15dc">

src/core/tree_evaluator.cpp

</a>

</li>

<li class="file-stats">

<a href="#aeaccdf9a873c05871ba3cd1bca1ae0e9f8254e4">

src/mains/unix.cpp

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.38+dfsg-1) unstable; urgency=medium</span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Mon, 02 May 2022 12:18:35 +0200</span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre></td>

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

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

1

</td>

<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">hyphy (2.5.36+dfsg-1) unstable; urgency=medium</span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * New upstream version</span>

</pre></td>

</tr>

</table>

<br>

</li>

<li id="e4fd9bcc64f7c0236c7e16a07df70a48ebf4827d">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#e4fd9bcc64f7c0236c7e16a07df70a48ebf4827d"><strong>res/TemplateBatchFiles/LEISR.bf</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

</td>

<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">RequireVersion("2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left deletion">3</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff right deletion">.</span></span><span class="c1" style="color: #998; font-style: italic;">5");</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">RequireVersion("2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition">5</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">2</span>5");</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">LoadFunctionLibrary("libv3/UtilityFunctions</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bf");</span></span>

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ utility.ToggleEnvVariable ("NORMALIZE_SEQUENCE_NAMES", 1);</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis_description = {</span></span>

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<td class="new_line diff-line-num" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">info: "LEISR (Likelihood Estimation of Individual Site Rates) infer relative amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid or nucleotide rates from a fixed nucleotide or amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid alignment and tree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> with possibility for partitions</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Relative site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">specific substitution rates are</span></span>

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    inferred by first optimizing alignment</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">wide branch lengths</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> and then inferring a site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">specific uniform tree scaler</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>

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<td class="new_line diff-line-num old" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC34" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">version: "0</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 deletion">4</span>"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">version: "0</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 addition">5</span>"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference: "Spielman</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> S</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">J</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> and Kosakovsky Pond</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> S</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">L</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> (2018)</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Relative evolutionary rate inference in HyPhy with PeerJ 6:e4339</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> DOI 10</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">7717/peerj</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">4339 ; Pupko</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;"> Bell</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> R</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> E</span><span class="nf" style="color: #900; font-weight: 600;">.,</span><span class="c1" style="color: #998; font-style: italic;"> Mayrose</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> I</span><span class="nf" style="color: #900; font-weight: 600;">.,</span><span class="c1" style="color: #998; font-style: italic;"> Glaser</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> F</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> & Ben</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">Tal</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;"> Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Bioinformatics 18</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> S71–S77 (2002)</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>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">authors: "Sergei L Kosakovsky Pond and Stephanie J Spielman"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">contact: "{spond</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">stephanie</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">spielman}@temple</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">edu"</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,7 +42,11 @@ io.DisplayAnalysisBanner(leisr.analysis_description);</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC44" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/***************************************** LOAD DATASET **********************************************************/</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC45" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">SetDialogPrompt ("Specify a multiple sequence alignment file");</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("alignment"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "A multiple sequence alignment file in one of the formats supported by HyPhy");</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("tree"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">      "A phylogenetic tree (optionally annotated with {})"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> null</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Please select a tree file for the data:");</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">SetDialogPrompt ("A multiple sequence alignment file");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC50" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alignment_info  = alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReadNucleotideDataSet ("leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">dataset"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> None);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC52" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">name_mapping = leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alignment_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">name_mapping")</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">@@ -57,7 +61,6 @@ leisr.partition_count = Abs (leisr.partitions_and_trees);</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification = alignments</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DefineFiltersForPartitions (leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partitions_and_trees</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">dataset" </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alignment_info);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC63" class="line" lang="brainfuck"></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC60" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC64" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("relative_rates"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Data"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Input alignment description");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("relative_rates"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Data"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Loaded **" </span><span class="nf" style="color: #900; font-weight: 600;">+</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC66" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alignment_info </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sequences</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;"> "** sequences</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>

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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">@@ -71,11 +74,15 @@ io.ReportProgressMessageMD ("relative_rates", "Data", "Loaded **" +</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC74" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">protein_type    = "Protein";</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nucleotide_type = "Nucleotide";</span></span>

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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("type"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">     "Data type (`leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">protein_type` or `leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nucleotide_type`)"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nucleotide_type);</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis_type  = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SelectAnOption ({{leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">protein_type </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Infer relative rates from a protein (amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid) alignment"}</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nucleotide_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Infer relative rates from a nucleotide alignment"}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC81" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                    "Select your analysis type:");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC82" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("model"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">     "Substitution model");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num old" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC78" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis_type ==  leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">protein_type) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC85" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis_type ==  leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">protein_type) {<span class="idiff left right addition">    </span></span></span>

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<td class="new_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_model  = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SelectAnOption (models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">protein</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">empirical_models</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Select a protein model:");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generators = models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">protein</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">empirical</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">plusF_generators;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,6 +92,9 @@ else {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generators = models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DNA</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generators;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC93" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC94" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC95" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("rate</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">variation"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">     "Optimize branch lengths with rate variation?"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "No");</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC96" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC97" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC98" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">use_rate_variation = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SelectAnOption( {{"Gamma"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Use a four</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">category discrete gamma distribution when optimizing branch lengths</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>

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<td class="new_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC99" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                    {"GDD"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Use a four</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">category general discrete distribution when optimizing branch lengths</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>

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<td class="new_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC100" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                    {"No"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Do not consider rate variation when optimizing branch lengths</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,8 +102,7 @@ leisr.use_rate_variation = io.SelectAnOption( {{"Gamma", "Use a four-category di</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC102" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                    "Optimize branch lengths with rate variation?");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC103" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC104" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Baseline</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription(type){</span></span>

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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC95" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    def = Call( leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generators</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_model</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> type);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC96" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return def;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC105" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return Call( leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generators</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_model</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> type);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC106" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC107" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC108" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Baseline</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">withGamma(type){</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="365" style="width: 35px; color: rgba(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">@@ -365,8 +374,11 @@ selection.io.json_store_key_value_pair (leisr.json_content, None, utility.getGlo</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC374" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                         leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC375" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC376" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        </span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC368" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        </span></span>

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<td class="new_line diff-line-num old" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC369" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_content</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alignment_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">file</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LEISR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json");</span></span>

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<td class="old_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC377" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("output"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Write the analysis report file to"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alignment_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">file</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LEISR</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json");</span></span>

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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC378" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_content </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;">json</span><span class="p">]</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;">PromptUserForFilePath ("Save the resulting JSON file to");</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC379" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC380" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    </span></span>

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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC381" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolJSON (leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_content</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_content </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;">json</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC382" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC383" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC384" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="400" style="width: 35px; color: rgba(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">@@ -388,12 +400,12 @@ lfunction leisr.handle_a_site (lf, filter_data, partition_index, pattern_info, m</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC400" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="old_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC401" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetEnvVariable ("USE_LAST_RESULTS"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> TRUE);</span></span>

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<td class="new_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC402" 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;">SetValue (^"leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_scaler_name"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC391" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    /*</span></span>

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<td class="old_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC403" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">    </span>    /*</span></span>

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<td class="new_line diff-line-num" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="new_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC393" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     SLKP 20171210</span></span>

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<td class="old_line diff-line-num old" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC394" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     RESET the global rate value to a default avoid weird optimization issues because of bad starting conditions</span></span>

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<td class="old_line diff-line-num old" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC395" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     (e</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">g</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> if the previous site was saturated)</span></span>

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<td class="old_line diff-line-num old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC396" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    */</span></span>

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<td class="old_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     <span class="idiff left right addition">    </span>SLKP 20171210</span></span>

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<td class="old_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC406" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     <span class="idiff left right addition">    </span>RESET the global rate value to a default avoid weird optimization issues because of bad starting conditions</span></span>

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<td class="old_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC407" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     <span class="idiff left right addition">    </span>(e</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">g</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> if the previous site was saturated)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC408" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">    </span>    */</span></span>

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<td class="new_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC409" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC411" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (pattern_info </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">is_constant")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="404" style="width: 35px; color: rgba(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">@@ -404,13 +416,37 @@ lfunction leisr.handle_a_site (lf, filter_data, partition_index, pattern_info, m</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC416" class="line" lang="brainfuck"><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;"> =  estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeLF (lf);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC417" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC418" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    } else {</span></span>

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<td class="new_line diff-line-num old" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC407" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC408" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">          ^(utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_scaler_name")) = 1;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC409" 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>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC419" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         scaler = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_scaler_name");</span></span>

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<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC420" 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>

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<td class="new_line diff-line-num new" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC421" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            "0" : {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                scaler : 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">01</span></span>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC423" 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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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            "1" : {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                scaler : 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1</span></span>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC426" 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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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            "2" : {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                scaler : 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5</span></span>

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<td class="new_line diff-line-num new" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

429

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC429" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

430

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            "3" : {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

431

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                scaler : 1</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

432

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC432" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

433

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            "4" : {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

434

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                scaler : 2</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

435

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC435" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

436

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            "5" : {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

437

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                scaler : 10</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

438

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC438" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

439

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        };</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

440

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

441

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC441" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

442

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC442" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

443

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC443" 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

444

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        });</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

445

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

446

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC446" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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410

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<td class="new_line diff-line-num" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

447

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC447" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

411

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<td class="new_line diff-line-num" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

448

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

412

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<td class="new_line diff-line-num old" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

413

</td>

<td class="new_line diff-line-num old" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC413" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    profile = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetProfileCI (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_scaler_name")</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;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">95);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

449

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC449" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    profile = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetProfileCI (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("leisr</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_model_scaler_name")</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;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">95);               </span></span>

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<td class="old_line diff-line-num" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

414

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<td class="new_line diff-line-num" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

450

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC450" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    profile</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="old_line diff-line-num" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

415

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<td class="new_line diff-line-num" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

451

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="old_line diff-line-num" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

416

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<td class="new_line diff-line-num" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

452

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return profile;</span></span>

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<br>

</li>

<li id="80cb7c212661a2afbd05c16dce9f84f45709578e">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#80cb7c212661a2afbd05c16dce9f84f45709578e"><strong>res/TemplateBatchFiles/SelectionAnalyses/PRIME.bf</strong></a>

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<td class="old_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

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<td class="new_line diff-line-num old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">RequireVersion("2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">7");</span></span>

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<td class="old_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">RequireVersion("2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">3</span>7");</span></span>

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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="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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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    Load library files</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,8 +22,6 @@ LoadFunctionLibrary("modules/selection_lib.ibf");</td>

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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="new_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC25" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

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<td class="new_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC26" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" 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">

27

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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">debug</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">checkpoint = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetEnvVariable ("DEBUG_CHECKPOINT");</span></span>

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26

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/*</span><span class="nf" style="color: #900; font-weight: 600;">------------------------------------------------------------------------------</span><span class="c1" style="color: #998; font-style: italic;"> </span></span>

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<td class="old_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    Display analysis information</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,7 +38,7 @@ prime.analysis_description = {</td>

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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    inferred </span><span class="nf" style="color: #900; font-weight: 600;">--</span><span class="c1" style="color: #998; font-style: italic;"> the non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous rate on branches NOT selected for testing</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Multiple partitions within a NEXUS file are also supported</span></span>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC39" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for recombination </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> aware analysis</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>

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<td class="old_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC40" 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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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC43" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">version: "0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left deletion">0</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion">1</span>"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

41

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC41" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">version: "0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition">1</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">0</span>"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<td class="new_line diff-line-num" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference: "TBD"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="new_line diff-line-num" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">authors: "Sergei L</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Kosakovsky Pond"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC44" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">contact: "spond@temple</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">edu"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -74,7 +72,7 @@ prime.pvalue = 0.1;</td>

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<td class="old_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC72" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json = {</span></span>

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

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<td class="new_line diff-line-num" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis: prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis_description</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC74" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    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;">fits: {}</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC77" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    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="nf" style="color: #900; font-weight: 600;"><span class="idiff left right deletion">,</span></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC75" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">timers: {}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">};</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC77" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">display_orders =   {  </span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,19 +108,21 @@ the next set of variables.</td>

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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC108" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</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;">composition</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">string = "";</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC109" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC110" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC113" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_screen_output  = {{"Codon"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Partition"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alpha"</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;"> "Property Description"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Importance"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"Most common codon substitutions at this site"}};</span></span>

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<td class="old_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC111" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_screen_output  = {{"Codon"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Partition"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left addition">"#subs"</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition"> "#AA"</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition"> </span>"alpha"</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;"> "Property Description"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Importance"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"Most common codon substitutions at this site"}};</span></span>

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<td class="old_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_output_options = {  terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">header : TRUE</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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<td class="new_line diff-line-num" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC113" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">minimum_column_width: 12</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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<td class="new_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC114" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">align : "center"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC115" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">column_widths: {</span></span>

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<td class="old_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC116" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "0" : 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC117" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "1" : 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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120

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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC120" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "2" : <span class="idiff left right deletion">12</span></span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC121" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "3" : <span class="idiff left right deletion">12</span></span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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122

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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC122" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "4" : <span class="idiff left right deletion">40</span></span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC118" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "2" : <span class="idiff left right addition">8</span></span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC119" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "3" : <span class="idiff left right addition">8</span></span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC120" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "4" : <span class="idiff left right addition">12</span></span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC121" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "5" : 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC124" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "6" : 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC125" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "7" : 70}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC122" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "6" : 40</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC123" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "7" : 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC124" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "8" : 12</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC125" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    "9" : 70}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC126" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                             };</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" style="width: 35px; color: rgba(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">@@ -142,6 +142,12 @@ prime.property_set = io.SelectAnOption (</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC142" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC143" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            "The set of properties to use in the model");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC144" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC145" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">property_set == "Custom") {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC146" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    KeywordArgument ("property</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">file"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "JSON file which defines amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid properties");</span></span>

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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC147" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">property_set = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ParseJSON(io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUserForFilePathRead ("JSON file which defines amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid properties"));</span></span>

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC148" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    console</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log ("</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">Loaded a set of `Abs(prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">property_set)` properties");</span></span>

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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC150" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

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<td class="new_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">KeywordArgument ("impute</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">states"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Use site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">level model fits to impute likely character states for each sequence"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "No");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC152" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">impute_states = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SelectAnOption (</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="300" style="width: 35px; color: rgba(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">@@ -294,6 +300,10 @@ prime.site.property_model =  model.generic.DefineModel("models.codon.MG_REV_PROP</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC300" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC301" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_names</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC302" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        None);</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC304" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC305" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">residue_properties</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = prime</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;">property_model </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">residue_properties</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;         </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC306" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">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;">translation_table</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = prime</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;">property_model </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">translation_table</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC307" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC309" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">properties               = prime</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;">property_model </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">residue_properties</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -309,14 +319,18 @@ prime.lambda_range = {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC320" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC321" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="new_line diff-line-num old" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC312" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers = { <span class="idiff left right deletion">6</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 3*prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">properties</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;"> 2};</span></span>

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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers = { <span class="idiff left right addition">10</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 3*prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">properties</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;"> 2};</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC323" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="old_line diff-line-num old" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC314" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</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;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "alpha;"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</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;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "Synonymous substitution rate at a site";</span></span>

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<td class="old_line diff-line-num old" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC315" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</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;"> = "&beta;"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "Log of property independent non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous rate a site";</span></span>

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<td class="new_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC316" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2</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;"> = "Total branch length"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2</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;"> = "The total length of branches contributing to inference at this site</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> and used to scale dN</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">dS";</span></span>

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<td class="new_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC317" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</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;"> = "PRIME LogL"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</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;"> = "Site Log</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">likelihood under the PRIME model";</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

318

</td>

<td class="new_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC318" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</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;"> = "FEL LogL"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</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;"> = "Site Log</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">likelihood under the FEL model";</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

319

</td>

<td class="new_line diff-line-num old" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</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;"> = "p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</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;"> = "Omnibus p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value (any property is important)";</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

324

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC324" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</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;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "&alpha;"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</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;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "Synonymous substitution rate at a site";</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

325

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC325" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</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;"> = "&beta;"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "Property independent non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous rate a site";</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

326

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC326" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2</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;"> = "FEL &alpha;"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2</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;"> = "Synonymous substitution rate at a site (FEL model)";</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

327

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC327" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</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;"> = "FEL &beta;"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</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;"> = "Log of property independent non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous rate a site";</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

328

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC328" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</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;"> = "Total branch length"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</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;"> = "The total length of branches contributing to inference at this site</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> and used to scale dN</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">dS";</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

329

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC329" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</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;"> = "# subs"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</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;"> = "The number of amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid substitutions that occurred at this site";</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

330

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">6</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;"> = "# aa"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">6</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;"> = "The number of unique amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acids occurring at that site";</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC331" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">7</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;"> = "PRIME LogL"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">7</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;"> = "Site Log</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">likelihood under the PRIME model";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC332" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">8</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;"> = "FEL LogL"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">8</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;"> = "Site Log</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">likelihood under the FEL model";</span></span>

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<td class="old_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">9</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;"> = "p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value"; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">9</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;"> = "Omnibus p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value (any property is important)";</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC334" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                         </span></span>

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<td class="new_line diff-line-num" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambdas = {};                                                                      </span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="339" style="width: 35px; color: rgba(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">@@ -325,7 +339,7 @@ io.ReportProgressMessageMD ("PRIME", "property-description", "Using the followin</td>

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<td class="new_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC339" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC340" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i = 1;</span></span>

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<td class="old_line diff-line-num" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC341" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name = {};</span></span>

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<td class="old_line diff-line-num old" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC328" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value_indices = {"Overall" : <span class="idiff left right deletion">5</span>};</span></span>

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<td class="old_line diff-line-num new" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC342" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value_indices = {"Overall" : <span class="idiff left right addition">9</span>};</span></span>

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<td class="old_line diff-line-num" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC343" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</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;">count = {"Overall" : 0};</span></span>

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<td class="new_line diff-line-num" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC344" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC345" class="line" lang="brainfuck"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="333" style="width: 35px; color: rgba(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="347" style="width: 35px; color: rgba(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">@@ -333,9 +347,9 @@ for (key, value; in; prime.properties ) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC347" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("PRIME"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "property</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">description"</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;"> key);</span></span>

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<td class="new_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC348" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="old_line diff-line-num" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

335

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<td class="new_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC349" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p = prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">property_variable_prefix </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (prime</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;">property_model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">residue_name_map</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;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

336

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<td class="new_line diff-line-num old" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left deletion">3</span></span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "&lambda;" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion">3</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "Importance for " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> key;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC337" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left deletion">4</span></span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "p" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion">4</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value for non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">zero effect of " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> key;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC338" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left deletion">5</span></span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "LogL" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion">5</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "Log likelihood when there is no effect of " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> key;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC350" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition">7</span></span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "&lambda;" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">7</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "Importance for " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> key;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC351" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition">8</span></span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "p" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">8</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "p</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">value for non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">zero effect of " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> key;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC352" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition">9</span></span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "LogL" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">9</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3</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;"> = "Log likelihood when there is no effect of " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> key;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC353" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="new_line diff-line-num" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC354" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddGlobal (prime</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;">property_model</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> key);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC355" 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;">DeclareGlobal ( prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {});</span></span>

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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">@@ -346,12 +360,13 @@ for (key, value; in; prime.properties ) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC360" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambdas </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parameter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_lambda</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC361" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">parameter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_lambda</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = key;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC362" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">property_to_index </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1;</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC349" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value_indices</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = <span class="idiff left right deletion">4</span></span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC363" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value_indices</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = <span class="idiff left right addition">8</span></span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i*3;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC364" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</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;">count</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 0;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC365" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">i </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC366" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC367" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC368" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC369" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC370" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddGlobal (prime</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;">property_model</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_non_syn_rate </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameter_site_beta);</span></span>

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<td class="new_line diff-line-num" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC371" 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;">DeclareGlobal ( prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_non_syn_rate</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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<td class="new_line diff-line-num" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC372" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">//parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetRange ( prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">baseline_non_syn_rate</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambda_range);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="384" style="width: 35px; color: rgba(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">@@ -384,6 +399,8 @@ function prime.rate_to_screen (name, value) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC399" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC400" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</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;">significant_site = {{"" </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;">((prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_specification</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">prime</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;">partition</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">coverage</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;">prime</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;">site</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>

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<td class="new_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC401" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    prime</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;">partition </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>

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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC402" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    Format(prime</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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  // #subs</span></span>

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<td class="old_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC403" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    Format(prime</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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">6</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  // #AA</span></span>

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<td class="new_line diff-line-num" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    Format(prime</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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  // alpha</span></span>

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<td class="new_line diff-line-num" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    Format(prime</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;">row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">3)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  // beta</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC406" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">property_report_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  // property name</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="395" style="width: 35px; color: rgba(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="412" style="width: 35px; color: rgba(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">@@ -395,6 +412,7 @@ prime.report.significant_site = {{"" + (1+((prime.filter_specification[prime.rep</td>

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<td class="new_line diff-line-num" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC412" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC413" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results        = {};</span></span>

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<td class="old_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC414" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">imputed_leaf_states = {};</span></span>

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<td class="old_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sub_mapping   = {};</span></span>

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<td class="old_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC416" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC417" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_index = 0; prime</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="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_count; prime</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="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>

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<td class="old_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC418" class="line" lang="brainfuck"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="479" style="width: 35px; color: rgba(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="497" style="width: 35px; color: rgba(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">@@ -479,9 +497,8 @@ for (prime.partition_index = 0; prime.partition_index < prime.partition_count; p</td>

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<td class="old_line diff-line-num" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC497" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    /* run the main loop over all unique site pattern combinations */</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC498" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="old_line diff-line-num" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC499" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pattern_count = 1;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC482" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEachPair (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_patterns</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_pattern_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_pattern_info_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC483" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        '</span></span>

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<td class="old_line diff-line-num old" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC484" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressBar(""</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Working on site pattern " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pattern_count) </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;"> Abs (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_patterns));</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC500" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (_pattern_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _pattern_info_; in; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_patterns) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC501" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">          io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressBar(""</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Working on site pattern " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pattern_count) </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;"> Abs (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_patterns));</span></span>

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<td class="new_line diff-line-num" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC502" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           if (_pattern_info_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">is_constant")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>

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<td class="new_line diff-line-num" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC503" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">store_results (</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;">None</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">{"0" : "prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_likelihood"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC504" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                             "1" : "prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_likelihood_property"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="503" style="width: 35px; color: rgba(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="520" style="width: 35px; color: rgba(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">@@ -503,19 +520,16 @@ for (prime.partition_index = 0; prime.partition_index < prime.partition_count; p</td>

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<td class="new_line diff-line-num" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC520" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                                    "prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">store_results");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC521" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

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<td class="new_line diff-line-num" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC522" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pattern_count  </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC506" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        '</span></span>

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<td class="old_line diff-line-num old" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC507" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    );</span></span>

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<td class="old_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC523" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }  </span></span>

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<td class="new_line diff-line-num" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC524" class="line" lang="brainfuck"></span>

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509

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<td class="new_line diff-line-num" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC525" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    mpi</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">QueueComplete (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">queue);</span></span>

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<td class="old_line diff-line-num" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC526" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_matrix = {Abs (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">prime</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="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Rows (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers)};</span></span>

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<td class="old_line diff-line-num old" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC511" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num old" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC512" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEachPair (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">prime</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="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_key_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_value_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC513" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    '</span></span>

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<td class="new_line diff-line-num new" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

527

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC527" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="old_line diff-line-num new" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

528

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC528" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (_key_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _value_; in; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">prime</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>

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<td class="new_line diff-line-num" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

529

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC529" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index = 0; prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> Rows (prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">table_headers); prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>

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515

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<td class="new_line diff-line-num" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC530" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_matrix </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">_key_</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _value_</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

531

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC531" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="old_line diff-line-num old" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

517

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<td class="new_line diff-line-num old" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC517" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    '</span></span>

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<td class="old_line diff-line-num old" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

518

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<td class="new_line diff-line-num old" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC518" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    );</span></span>

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<td class="old_line diff-line-num new" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

532

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC532" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

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519

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<td class="new_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC533" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC534" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">prime</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;"> = prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">partition_matrix;</span></span>

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<td class="old_line diff-line-num" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC535" class="line" lang="brainfuck"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="530" style="width: 35px; color: rgba(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="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -530,6 +544,9 @@ if (prime.impute_states) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    (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;">MLE</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">prime_imputed_states</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">imputed_leaf_states;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC545" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC546" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC547" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">(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;">MLE</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitutions</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sub_mapping;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC548" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC549" class="line" lang="brainfuck"></span>

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

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC550" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">for (key</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> value; in;  prime</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;">count) {</span></span>

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<td class="new_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC551" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("PRIME"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "results"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "** Found _" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> value </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "_ sites where " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> key </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " property was important at p </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;"> prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">pvalue </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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC552" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="586" style="width: 35px; color: rgba(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="603" style="width: 35px; color: rgba(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">@@ -586,7 +603,7 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC603" 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 (pattern_info);</span></span>

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<td class="old_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC604" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    GetString   (lfInfo</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf_fel</span><span class="nf" style="color: #900; font-weight: 600;">,-</span><span class="c1" style="color: #998; font-style: italic;">1);   </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC605" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num old" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC589" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    //utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetEnvVariable ("VERBOSITY_LEVEL"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1<span class="idiff left right deletion">0</span>);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC606" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    //utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetEnvVariable ("VERBOSITY_LEVEL"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC607" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC608" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    //TODO Datafilters hardcode</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Trees hardcode</span><span class="nf" style="color: #900; font-weight: 600;">.</span></span>

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<td class="old_line diff-line-num" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC609" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    ExecuteCommands (filter_data);</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="607" style="width: 35px; color: rgba(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="624" style="width: 35px; color: rgba(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">@@ -607,7 +624,7 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>

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<td class="new_line diff-line-num" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC624" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta" :</span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 0;</span></span>

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625

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC625" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC626" 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_fel</span></span>

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<td class="new_line diff-line-num old" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC610" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"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;"> OPTIMIZATION_PRECISION: 1e</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">4}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC627" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {"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 class="idiff left addition">"</span>OPTIMIZATION_PRECISION<span class="idiff right addition">"</span>: 1e</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">4}</span></span>

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611

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC628" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    );</span></span>

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<td class="new_line diff-line-num" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC629" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    fel = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEs (lf_fel</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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613

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<td class="new_line diff-line-num" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

630

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC630" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    fel</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>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="628" style="width: 35px; color: rgba(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="645" style="width: 35px; color: rgba(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">@@ -628,37 +645,119 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>

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<td class="new_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC645" 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 ("prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Eval(^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta")</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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<td class="new_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC646" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">   </span></span>

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<td class="new_line diff-line-num" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC647" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

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<td class="old_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC648" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

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<td class="new_line diff-line-num" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC649" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     start_grid = {};</span></span>

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<td class="old_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC650" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     propN = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambdas");</span></span>

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633

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<td class="new_line diff-line-num" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

651

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC651" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

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<td class="old_line diff-line-num old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

634

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<td class="new_line diff-line-num old" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC634" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     for (sp = 0; sp </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 100; sp </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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635

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<td class="new_line diff-line-num old" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC635" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point = {};</span></span>

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<td class="new_line diff-line-num old" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC636" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha"</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>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

637

</td>

<td class="new_line diff-line-num old" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC637" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta"</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;">5</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;">5);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

638

</td>

<td class="new_line diff-line-num old" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC638" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta_nuisance"</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;">5</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;">5);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

652

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC652" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     point = {};</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

653

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC653" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

654

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC654" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

655

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC655" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     save_beta = ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

656

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC656" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta_nuisance"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta_nuisance";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

657

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC657" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

658

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC658" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     for (l; in; ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambdas") {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

659

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC659" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">l</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 0;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

660

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC660" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

661

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC661" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     start_grid </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> point;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

662

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC662" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     propNames = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Values (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambdas");</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

663

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC663" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     ranges = {};</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

664

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC664" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     r_unit = {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

665

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC665" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        ^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lower_bound" : </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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

666

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC666" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        ^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">upper_bound" : 1</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

667

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC667" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     };</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

668

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC668" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

669

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC669" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     for (k</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">l; in; ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambdas") {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

670

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC670" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        ranges</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">l</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = r_unit;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

671

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC671" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     }</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

672

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC672" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">          </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

673

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC673" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">          </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

674

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC674" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     for (sp = 0; sp </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> 20; sp </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

</td>

<td class="new_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

675

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC675" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (l; in; ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambdas") {</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

640

</td>

<td class="new_line diff-line-num old" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC640" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">          point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">l</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = <span class="idiff left deletion">Random (</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion">-</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff deletion">0</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff deletion">5</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff deletion">0</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion">5)</span>;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

676

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC676" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">          point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">l</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = <span class="idiff left addition">0</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">0</span>;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

</td>

<td class="new_line diff-line-num" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

677

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC677" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

678

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC678" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">propNames </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;"> propN) $ 1</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = Random (</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>

</pre></td>

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642

</td>

<td class="new_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

679

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC679" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        start_grid </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> point;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

643

</td>

<td class="new_line diff-line-num" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

680

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC680" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     }</span></span>

</pre></td>

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644

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681

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC681" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

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<td class="old_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

682

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC682" class="line" lang="brainfuck"></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

683

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC683" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     for (sp; in; estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">LHC (ranges</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 40)) {</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

684

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC684" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point = {};</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

685

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC685" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

686

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC686" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = Random (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha" * 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha" * 2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">0);</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

687

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC687" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = Random (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta" * 0</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta" * 2</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">0);</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

688

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC688" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="new_line diff-line-num new" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

689

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC689" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (l</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">v; in; sp) {</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

690

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC690" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">          point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">l</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = v </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

691

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC691" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

692

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC692" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        start_grid </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> point;</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

693

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC693" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

694

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC694" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_alpha";</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

695

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC695" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        point </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_beta";</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

696

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC696" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

697

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC697" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        start_grid </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> point;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

698

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC698" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

699

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC699" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

645

</td>

<td class="new_line diff-line-num" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

700

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC700" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

646

</td>

<td class="new_line diff-line-num" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

701

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC701" 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 (start_grid);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

647

</td>

<td class="new_line diff-line-num" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

702

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC702" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

</td>

<td class="new_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

703

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC703" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

649

</td>

<td class="new_line diff-line-num old" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC649" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     //Export (lfe</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf_prop);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

650

</td>

<td class="new_line diff-line-num old" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC650" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     //fprintf ("/Users/sergei/Desktop/prime</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;"> ^"MPI_NODE_ID" </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;">bf"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">CLEAR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">lfe);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

651

</td>

<td class="new_line diff-line-num old" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC651" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

704

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC704" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // Export (lfe</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> ^lf_prop);</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

705

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC705" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // fprintf ("/Users/sergei/Desktop/PRIME/site</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;"> (pattern_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"sites"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="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 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;">bf"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">CLEAR_FILE</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">lfe);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

652

</td>

<td class="new_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

706

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC706" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

707

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC707" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

653

</td>

<td class="new_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC708" 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_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

654

</td>

<td class="new_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC709" 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>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

655

</td>

<td class="new_line diff-line-num" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC710" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            //"OPTIMIZATION_METHOD" : "gradient</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">descent"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

656

</td>

<td class="new_line diff-line-num old" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC656" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            "OPTIMIZATION_START_GRID" : start_grid</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

711

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC711" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            "OPTIMIZATION_START_GRID" : start_grid</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

712

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC712" 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;">4</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

657

</td>

<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC713" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        });</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

658

</td>

<td class="new_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC714" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

715

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC715" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

716

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC716" 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 ("\n" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ^"LF_INITIAL_GRID_MAXIMUM_VALUE" </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;">  ^"LF_INITIAL_GRID_MAXIMUM" </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;"> 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 class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

717

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC717" 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_prop);</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

718

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC718" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

719

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC719" 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 ("\n" </span><span class="nf" style="color: #900; font-weight: 600;">+</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 class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

659

</td>

<td class="new_line diff-line-num" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC720" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

660

</td>

<td class="new_line diff-line-num old" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC660" 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 ("\n" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ^"LF_INITIAL_GRID_MAXIMUM" </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;"> 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 class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "\n");</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

721

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC721" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    altL = 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>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

722

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC722" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

723

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC723" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // fit all of the nulls</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

724

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC724" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

725

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC725" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    constrained_models = {};</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

726

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC726" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

727

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC727" 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;">ExtractMLEsOptions (lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {});</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

728

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC728" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

729

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC729" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    while (TRUE) {</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

730

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC730" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        done = TRUE;</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

731

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC731" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (k</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">l; in; ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambdas") {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

732

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC732" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            ^l = 0;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

733

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC733" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            // FORCE UPDATE DEPENDENT VARIABLES</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

734

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC734" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            LFCompute (^lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_START_COMPUTE);</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

735

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC735" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            LFCompute (^lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">results);</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

736

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC736" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            LFCompute (^lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_DONE_COMPUTE);</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

737

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC737" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            ^l := 0;  </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

738

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC738" 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_prop);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

739

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC739" 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 (k </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;"> (</span><span class="nf" style="color: #900; font-weight: 600;">-</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 class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> altL));</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

740

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC740" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (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 class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> altL </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 1e</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">2) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

741

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC741" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                done = FALSE;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

742

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC742" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                break;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

743

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC743" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

744

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC744" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            constrained_models</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEsOptions (lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</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;">globals_only" : TRUE});</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

745

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC745" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            (constrained_models</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

746

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC746" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            ^l = 0;        </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

747

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC747" 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;">ApplyExistingEstimates (lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> alternative</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;">globals_only");</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

748

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC748" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

661

</td>

<td class="new_line diff-line-num" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC749" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

750

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC750" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (done) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

751

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC751" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            break;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

752

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC752" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        } else {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

753

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC753" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">              ^l = 0;      </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

754

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC754" 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_prop);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

755

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC755" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">              altL = 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>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

756

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC756" 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 ("REOPTIMIZED : " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> altL);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

757

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC757" 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;">ExtractMLEsOptions (lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {});</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

758

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC758" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">             </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

759

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC759" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC760" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

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662

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<td class="new_line diff-line-num" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC761" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    character_map = None;    </span></span>

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663

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<td class="new_line diff-line-num" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC762" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">impute_states") {</span></span>

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664

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<td class="new_line diff-line-num" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC763" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        DataSet anc = ReconstructAncestors ( ^lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> {{0}}</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> MARGINAL</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> DOLEAVES);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="679" style="width: 35px; color: rgba(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="778" style="width: 35px; color: rgba(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">@@ -679,32 +778,12 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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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<td class="new_line diff-line-num" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC779" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    ancestral_info = ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">build (lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">FALSE);</span></span>

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<td class="new_line diff-line-num" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC780" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    branch_substitution_information = (ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeSubstitutionBySite (ancestral_info</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">None))</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitutions"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC781" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    branch_mapping = ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeCompressedSubstitutionsBySite (ancestral_info</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">0);</span></span>

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<td class="new_line diff-line-num" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC782" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    DeleteObject (ancestral_info);</span></span>

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683

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<td class="new_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC783" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="old_line diff-line-num old" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

684

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<td class="new_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC684" 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;">ExtractMLEsOptions (lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</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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<td class="old_line diff-line-num old" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

685

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<td class="new_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC685" 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="old_line diff-line-num old" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

686

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<td class="new_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC686" 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 (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="old_line diff-line-num old" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

687

</td>

<td class="new_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC687" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num old" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

688

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<td class="new_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC688" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     </span></span>

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<td class="old_line diff-line-num old" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

689

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<td class="new_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC689" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    // fit all of the nulls</span></span>

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<td class="old_line diff-line-num old" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

690

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<td class="new_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC690" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

691

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<td class="new_line diff-line-num old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC691" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    constrained_models = {};</span></span>

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<td class="old_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

784

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC784" 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 (branch_substitution_information);</span></span>

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<td class="old_line diff-line-num" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

692

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<td class="new_line diff-line-num" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC785" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="old_line diff-line-num old" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

693

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC693" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     for (k</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">l; in; ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lambdas") {</span></span>

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<td class="old_line diff-line-num old" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

694

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC694" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        ^l = 0;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

695

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC695" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        // FORCE UPDATE DEPENDENT VARIABLES</span></span>

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<td class="old_line diff-line-num old" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

696

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC696" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        LFCompute (^lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_START_COMPUTE);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

697

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC697" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        LFCompute (^lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">results);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

698

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC698" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        LFCompute (^lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">LF_DONE_COMPUTE);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

699

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC699" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        ^l := 0;  </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

700

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC700" 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_prop);</span></span>

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<td class="old_line diff-line-num old" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

701

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC701" 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 (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>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

702

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC702" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        constrained_models</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMLEsOptions (lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</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;">globals_only" : TRUE});</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

703

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC703" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        (constrained_models</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">k</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span 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>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

704

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC704" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        ^l = 0;        </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

705

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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC705" 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;">ApplyExistingEstimates (lf_prop</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> alternative</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;">globals_only");</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

706

</td>

<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC706" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     }</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

707

</td>

<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC707" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

786

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC786" 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;"> = altL;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

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<td class="new_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

787

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC787" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<td class="new_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

788

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC788" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

710

</td>

<td class="new_line diff-line-num" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC789" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return {</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="712" style="width: 35px; color: rgba(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="791" style="width: 35px; color: rgba(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">@@ -712,6 +791,7 @@ lfunction prime.handle_a_site (lf_fel, lf_prop, filter_data, partition_index, pa</td>

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<td class="old_line diff-line-num" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

712

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<td class="new_line diff-line-num" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

791

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC791" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative") : alternative</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<td class="new_line diff-line-num" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

792

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC792" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Null"): Null</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

</td>

<td class="new_line diff-line-num" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

793

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC793" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">residue_properties") : constrained_models</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC794" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitutions") : branch_mapping</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<td class="new_line diff-line-num" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

795

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC795" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_selection_attributes") : branch_substitution_information</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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<td class="new_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

796

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC796" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">prime_imputed_states") : character_map</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

717

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<td class="new_line diff-line-num" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC797" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    };</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="761" style="width: 35px; color: rgba(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="841" style="width: 35px; color: rgba(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">@@ -761,27 +841,45 @@ function prime.report.echo (prime.report.site, prime.report.partition, prime.rep</td>

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761

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<td class="new_line diff-line-num" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

841

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC841" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">store_results (node</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> result</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> arguments) {</span></span>

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762

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<td class="new_line diff-line-num" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

842

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC842" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

763

</td>

<td class="new_line diff-line-num" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

843

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC843" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    sub_profile = result</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;">branch_selection_attributes")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

764

</td>

<td class="new_line diff-line-num old" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC764" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

765

</td>

<td class="new_line diff-line-num old" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC765" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

766

</td>

<td class="new_line diff-line-num old" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC766" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

767

</td>

<td class="new_line diff-line-num old" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC767" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (None != sub_profile) {</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

768

</td>

<td class="new_line diff-line-num old" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC768" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

769

</td>

<td class="new_line diff-line-num old" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC769" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       total_sub_count = 0;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

844

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC844" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    sub_map = result</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;">substitutions")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

845

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC845" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    pattern_info    = arguments </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

770

</td>

<td class="new_line diff-line-num" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

846

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC846" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

771

</td>

<td class="new_line diff-line-num" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

847

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC847" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

772

</td>

<td class="new_line diff-line-num old" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC772" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

848

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC848" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (None != sub_profile) {   </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

849

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC849" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        total_sub_count = 0;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

773

</td>

<td class="new_line diff-line-num" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

850

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC850" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        sub_by_count = {"Overall" : {}};</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

774

</td>

<td class="new_line diff-line-num" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

851

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC851" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

775

</td>

<td class="new_line diff-line-num" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

852

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC852" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (p</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">v; in; ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">properties") {</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

776

</td>

<td class="new_line diff-line-num" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

853

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC853" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            sub_by_count</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">p</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = {};     </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

777

</td>

<td class="new_line diff-line-num" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

854

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC854" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

855

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC855" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

856

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC856" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        sub_counts = 0;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

857

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC857" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        aa_counts = {};</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

858

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC858" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

859

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC859" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        partition_index = arguments </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

778

</td>

<td class="new_line diff-line-num" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

860

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC860" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

861

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC861" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

</td>

<td class="new_line diff-line-num" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

862

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC862" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (i</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> v; in; sub_profile) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

780

</td>

<td class="new_line diff-line-num" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

863

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC863" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            for (j</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> b; in; v) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

781

</td>

<td class="new_line diff-line-num" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

864

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC864" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                c = Abs (b);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

782

</td>

<td class="new_line diff-line-num" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

865

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC865" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                total_sub_count </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= c;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

</td>

<td class="new_line diff-line-num" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

866

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC866" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                ai = (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_table")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

</td>

<td class="new_line diff-line-num" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

867

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC867" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                aj = (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_table")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">j</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

868

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC868" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

869

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC869" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

870

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC870" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

871

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC871" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (Abs (ai) && Abs (aj)) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

872

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC872" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    if (ai != aj) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

873

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC873" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        for (idx</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> br; in; b) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

874

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC874" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            if (((^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">selected_branches")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">br</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;">test") {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

875

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC875" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                sub_counts </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

876

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC876" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

877

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC877" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

878

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC878" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

879

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC879" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    aa_counts </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">ai</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 1;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

880

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC880" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    aa_counts </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">aj</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 1;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

881

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC881" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

882

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC882" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

</td>

<td class="new_line diff-line-num" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

883

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC883" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (Abs (ai) == 0) {ai = "?";}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

786

</td>

<td class="new_line diff-line-num" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

884

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC884" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (Abs (aj) == 0) {aj = "?";}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

787

</td>

<td class="new_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC885" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="804" style="width: 35px; color: rgba(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="902" style="width: 35px; color: rgba(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">@@ -804,7 +902,7 @@ lfunction prime.store_results (node, result, arguments) {</td>

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<td class="old_line diff-line-num" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

804

</td>

<td class="new_line diff-line-num" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

902

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC902" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

805

</td>

<td class="new_line diff-line-num" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

903

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC903" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

806

</td>

<td class="new_line diff-line-num" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

904

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC904" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

807

</td>

<td class="new_line diff-line-num old" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC807" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

905

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC905" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

808

</td>

<td class="new_line diff-line-num" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

906

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC906" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        sub_profile = {};</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

809

</td>

<td class="new_line diff-line-num" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

907

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC907" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (p</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">count; in; sub_by_count) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

810

</td>

<td class="new_line diff-line-num" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

908

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC908" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="825" style="width: 35px; color: rgba(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="923" style="width: 35px; color: rgba(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">@@ -825,17 +923,15 @@ lfunction prime.store_results (node, result, arguments) {</td>

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<td class="old_line diff-line-num" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

825

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<td class="new_line diff-line-num" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

923

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC923" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

826

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<td class="new_line diff-line-num" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

924

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC924" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

827

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<td class="new_line diff-line-num" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

925

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC925" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

828

</td>

<td class="new_line diff-line-num old" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC828" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    partition_index = arguments </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

829

</td>

<td class="new_line diff-line-num old" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC829" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    pattern_info    = arguments </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

830

</td>

<td class="new_line diff-line-num" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

926

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC926" class="line" lang="brainfuck"></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

831

</td>

<td class="new_line diff-line-num old" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC831" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    nrows = <span class="idiff left right deletion">6</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 3*^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">properties</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">N";</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

927

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC927" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    nrows = <span class="idiff left right addition">10</span> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 3*^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">properties</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">N";</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

832

</td>

<td class="new_line diff-line-num" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

928

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC928" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    result_row          = { nrows</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1 };</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

833

</td>

<td class="new_line diff-line-num" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

929

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC929" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

834

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<td class="new_line diff-line-num" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

930

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC930" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (i; in; ^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p_value_indices") {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

</td>

<td class="new_line diff-line-num" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

931

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC931" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row  </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 1</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

<td class="new_line diff-line-num" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

932

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC932" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

837

</td>

<td class="new_line diff-line-num" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

933

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC933" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

838

</td>

<td class="new_line diff-line-num old" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC838" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

934

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC934" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> <span class="idiff left right addition"> </span></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

839

</td>

<td class="new_line diff-line-num" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

935

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC935" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (None != result) { // not a constant site</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

840

</td>

<td class="new_line diff-line-num" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

936

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC936" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        omninbus_ll = (result</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;">alternative")</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;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

841

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<td class="new_line diff-line-num" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

937

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC937" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        lrt = {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;">LRT") : 2*(omninbus_ll</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">(result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"fel"</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;">)};</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="843" style="width: 35px; color: rgba(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="939" style="width: 35px; color: rgba(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">@@ -843,8 +939,12 @@ lfunction prime.store_results (node, result, arguments) {</td>

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<td class="old_line diff-line-num" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

843

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<td class="new_line diff-line-num" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

939

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC939" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

844

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<td class="new_line diff-line-num" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

940

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC940" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </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;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</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;">alternative")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameter_site_alpha"));</span></span>

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<td class="old_line diff-line-num" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

845

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<td class="new_line diff-line-num" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

941

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC941" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </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;"> = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (result</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;">alternative")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameter_site_beta"));</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

846

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<td class="new_line diff-line-num old" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC846" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (result</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;">alternative")</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;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

847

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<td class="new_line diff-line-num old" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC847" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"fel"</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;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

942

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC942" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2</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;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"fel"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameter_site_alpha"));</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

943

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC943" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">3</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;">GetGlobalMLE (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"fel"</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameter_site_beta"));</span></span>

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<td class="old_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

944

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC944" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = sub_counts;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

945

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC945" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">6</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;">Array1D (aa_counts);</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

946

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC946" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">7</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (result</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;">alternative")</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;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

947

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC947" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">8</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (result</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"fel"</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;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

848

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<td class="new_line diff-line-num" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC948" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        p_values       = {"Overall" : lrt </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;">p_value")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">};</span></span>

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<td class="old_line diff-line-num" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

949

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC949" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        //result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">5</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = lrt </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;">p_value")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

950

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC950" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="857" style="width: 35px; color: rgba(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="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -857,38 +957,44 @@ lfunction prime.store_results (node, result, arguments) {</td>

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<td class="new_line diff-line-num" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC957" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    sum </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= (alternative_lengths</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 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;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MLE")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

958

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC958" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

859

</td>

<td class="new_line diff-line-num" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

959

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC959" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

860

</td>

<td class="new_line diff-line-num old" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC860" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">2</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = sum;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="960" style="width: 35px; color: rgba(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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC960" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">4</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = sum;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

961

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC961" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

962

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC962" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

862

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<td class="new_line diff-line-num" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC963" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (key</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> prop; in; result</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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">residue_properties")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>

</pre></td>

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<td class="new_line diff-line-num old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC863" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            property_index = ((^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">property_to_index")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">)*3</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion">6</span>;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

964

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC964" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            property_index = ((^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">property_to_index")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">)*3</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">10</span>;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

864

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<td class="new_line diff-line-num" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

965

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC965" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            ll             = prop</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;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

865

</td>

<td class="new_line diff-line-num" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

966

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC966" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            pv             = 1</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">CChi2 (2*(omninbus_ll</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">ll)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">1);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

866

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<td class="new_line diff-line-num" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

967

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC967" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            rate           = (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

867

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<td class="new_line diff-line-num" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

968

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC968" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            rate           = ((((result</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;">alternative")</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;">global")</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;">rate</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">MLE")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

969

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC969" 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 (omninbus_ll);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

868

</td>

<td class="new_line diff-line-num" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

970

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC970" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">property_index</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;"> = rate;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

869

</td>

<td class="new_line diff-line-num" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

971

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC971" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            p_values </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = pv;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

870

</td>

<td class="new_line diff-line-num" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

972

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC972" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">property_index</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">2</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;"> = ll;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

871

</td>

<td class="new_line diff-line-num" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

973

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC973" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

872

</td>

<td class="new_line diff-line-num" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

974

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC974" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

975

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC975" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

873

</td>

<td class="new_line diff-line-num" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

976

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC976" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        p_values = math</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">HolmBonferroniCorrection(p_values);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

874

</td>

<td class="new_line diff-line-num old" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC874" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion">5</span></span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Overall"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

977

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC977" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        result_row</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition">(^"prime</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">p_value_indices")</span></span><span class="p"><span class="idiff addition">[</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">"Overall"</span></span><span class="p"><span class="idiff right addition">]</span>]</span><span class="c1" style="color: #998; font-style: italic;"> = p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"Overall"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

875

</td>

<td class="new_line diff-line-num" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

978

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC978" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (key</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> prop; in; result</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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">residue_properties")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

876

</td>

<td class="new_line diff-line-num old" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC876" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            property_index = ((^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p<span class="idiff left deletion">roperty_to_index</span>")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">)<span class="idiff deletion">*3</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion">+</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion">6</span>;</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

877

</td>

<td class="new_line diff-line-num old" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC877" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">property_index</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left deletion">+</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion">1</span></span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

979

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC979" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            property_index = ((^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p<span class="idiff left right addition">_value_indices</span>")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

980

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC980" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            result_row </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">property_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = p_values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local_to_property_name")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">key</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

878

</td>

<td class="new_line diff-line-num" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

981

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC981" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

879

</td>

<td class="new_line diff-line-num" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

982

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC982" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

880

</td>

<td class="new_line diff-line-num" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

983

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC983" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }   </span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

984

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC984" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

985

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC985" 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 (result_row);</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

881

</td>

<td class="new_line diff-line-num" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC986" class="line" lang="brainfuck"></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

882

</td>

<td class="new_line diff-line-num" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

987

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC987" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">EnsureKey (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> partition_index);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

883

</td>

<td class="new_line diff-line-num" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

988

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC988" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">EnsureKey (^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">imputed_leaf_states"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> partition_index);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

884

</td>

<td class="new_line diff-line-num old" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC884" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

989

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC989" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    <span class="idiff left addition">utility</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">EnsureKey (^"prime</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">sub_mapping"</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition"> partition_index);</span></span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

</td>

<td class="new_line diff-line-num" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

990

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC990" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

886

</td>

<td class="new_line diff-line-num" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

991

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC991" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    sites_mapping_to_pattern = pattern_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sites")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

</td>

<td class="new_line diff-line-num" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

992

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC992" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    sites_mapping_to_pattern</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">count = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (sites_mapping_to_pattern);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

888

</td>

<td class="new_line diff-line-num old" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC888" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

993

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC993" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

889

</td>

<td class="new_line diff-line-num" data-linenumber="994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

994

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC994" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> sites_mapping_to_pattern</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">count; i</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

890

</td>

<td class="new_line diff-line-num" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

995

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC995" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        site_index = sites_mapping_to_pattern</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

891

</td>

<td class="new_line diff-line-num" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

996

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC996" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        ((^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">site_results")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">site_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = result_row;</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

997

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC997" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        ((^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sub_mapping")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">site_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = sub_map;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

892

</td>

<td class="new_line diff-line-num" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

998

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC998" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        ((^"prime</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">imputed_leaf_states")</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">partition_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">site_index</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = result</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;">prime_imputed_states"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

893

</td>

<td class="new_line diff-line-num" data-linenumber="999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

999

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC999" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        prime</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;">echo (site_index</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="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> result_row);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

894

</td>

<td class="new_line diff-line-num" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1000

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1000" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre></td>

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</table>

<br>

</li>

<li id="cf5243a3058ebeab74574f8cd2c771cd63a43208">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#cf5243a3058ebeab74574f8cd2c771cd63a43208"><strong>res/TemplateBatchFiles/SelectionAnalyses/RELAX.bf</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +45,7 @@ relax.analysis_description = {</td>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="new_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC45" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                Version 4</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1 adds further support for multiple hit models"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC46" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                               terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">version : "3</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">1"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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47

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                               terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference : "RELAX: Detecting Relaxed Selection in a Phylogenetic Framework (2015)</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> Mol Biol Evol 32 (3): 820</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">832"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC48" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                               terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">authors : "Sergei L Kosakovsky Pond</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Ben Murrell</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Steven Weaver and Temple iGEM / UCSD viral evolution g<span class="idiff left right deletion">roup</span>"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                               terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">authors : "Sergei L Kosakovsky Pond</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Ben Murrell</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> Steven Weaver and Temple iGEM / UCSD viral evolution g"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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49

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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                               terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">contact : "spond@temple</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">edu"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC50" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                               terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">requirements : "in</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">frame codon alignment and a phylogenetic tree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> with at least two groups of branches defined using the {} notation (one group can be defined as all unlabeled branches)"</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                              };</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" style="width: 35px; color: rgba(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="63" style="width: 35px; color: rgba(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">@@ -63,6 +63,7 @@ relax.synonymous_rate_classes     = 3;</td>

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC63" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SRV                         = "Synonymous site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">to</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">site rates";</span></span>

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<td class="new_line diff-line-num" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC64" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv_posteriors  = "Synonymous site</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">posteriors";</span></span>

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<td class="new_line diff-line-num" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">srv_viterbi = "Viterbi synonymous rate path";</span></span>

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<td class="old_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">kGroupMode                   = "Group mode";</span></span>

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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC67" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">initial_ranges              = {};</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">@@ -172,7 +173,8 @@ relax.multi_hit = io.SelectAnOption ({</td>

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<td class="new_line diff-line-num old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC175" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">numbers_of_tested_groups == 2) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC176" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC177" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis_run_mode != relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">kGroupMode) {</span></span>

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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_sets = {relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test_branches_name : "test"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC179" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                           relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference_branches_name : "reference"}; </span></span>

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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC180" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">} else {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(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="195" style="width: 35px; color: rgba(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">@@ -193,14 +195,15 @@ function relax.echo_group (group, description) {</td>

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<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC195" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEachPair (relax</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="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_partition_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_selection_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC196" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">          "_selection_ = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Filter (_selection_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '_selector_'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '_selector_ == group');</span></span>

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<td class="new_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC197" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">group_choices</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">group</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = 'Set ' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> group </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ' with ' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (_selection_) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ' branches';</span></span>

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<td class="old_line diff-line-num old" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC196" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD('RELAX'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  'selector'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '* Selected ' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Abs(_selection_) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ' branches as the _`group`_ set: \\\`' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Join ('</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Keys(_selection_)) </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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC198" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD('RELAX'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  'selector'</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 addition">\n</span>* Selected ' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Abs(_selection_) </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ' branches as the _`group`_ set: \\\`' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Join ('</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> '</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Keys(_selection_)) </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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199

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC199" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC200" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">};</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC201" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC202" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC203" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC204" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_sets </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">echo_group"</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;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC205" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC203" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left deletion">numbers_of_tested_groups </span></span><span class="nb" style="color: #0086b3;"><span class="idiff deletion">></span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion"> 2</span>) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC206" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition">analysis_run_mode == relax</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">kGroupMode</span>) {</span></span>

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<td class="new_line diff-line-num" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC207" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    KeywordArgument ("reference</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">group"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  "Branches to use as the reference group"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> null);</span></span>

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<td class="new_line diff-line-num" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC208" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference_set_name = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SelectAnOption (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">group_choices</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Choose the set of branches to use as the _reference_ group");</span></span>

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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC209" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_sets </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference_set_name</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 0) {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="618" style="width: 35px; color: rgba(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">@@ -615,7 +618,7 @@ if (relax.model_set == "All") { // run all the models</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC618" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC619" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/* now fit the two main models for RELAX */</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC620" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num old" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC618" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion">numbers_of_tested_groups == 2</span>) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

621

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC621" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition">analysis_run_mode == relax</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">kGroupMode</span>) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

619

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<td class="new_line diff-line-num" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC622" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alt"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Fitting the alternative model to test K != 1");</span></span>

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<td class="old_line diff-line-num" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

620

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<td class="new_line diff-line-num" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC623" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">} else {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

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<td class="new_line diff-line-num" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

624

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC624" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD ("RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alt"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Fitting the alternative model with individual K parameters for " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">numbers_of_tested_groups </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " branch groups");</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="627" style="width: 35px; color: rgba(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="630" style="width: 35px; color: rgba(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">@@ -627,7 +630,7 @@ selection.io.startTimer (relax.json [terms.json.timers], "RELAX alternative mode</td>

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<td class="old_line diff-line-num" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

627

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<td class="new_line diff-line-num" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

630

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC630" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_object_map = {};</span></span>

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<td class="old_line diff-line-num" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

628

</td>

<td class="new_line diff-line-num" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC631" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_to_relax_parameter = {};</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

629

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<td class="new_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC632" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

630

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<td class="new_line diff-line-num old" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC630" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right deletion">numbers_of_tested_groups == 2</span>) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

633

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC633" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left addition">analysis_run_mode != relax</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">kGroupMode</span>) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<td class="new_line diff-line-num" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

634

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC634" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_object_map                  </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = None;</span></span>

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<td class="old_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

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<td class="new_line diff-line-num" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

635

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC635" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference_model_namespace                 = "relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">reference";</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

633

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<td class="new_line diff-line-num" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

636

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC636" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_object_map                  </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">test"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = None;</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="941" style="width: 35px; color: rgba(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="944" style="width: 35px; color: rgba(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">@@ -941,7 +944,10 @@ function relax.FitMainTestPair () {</td>

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941

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944

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC944" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit =  estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">FitLF (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">filter_names</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">trees</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> { "0" : relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_map}</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">general_descriptive</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;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_object_map</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span 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;">run_options</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">retain_lf_object: TRUE});</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

942

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<td class="new_line diff-line-num" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

945

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC945" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ReportProgressMessageMD("RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alt"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "* " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_fit (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 9</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_data_info</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">data</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sample_size</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">));</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

943

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<td class="new_line diff-line-num" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

946

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC946" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

944

</td>

<td class="new_line diff-line-num old" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC944" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

947

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC947" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    KeywordArgument ("save</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;"> "Save RELAX alternative model fit to this file (default is not to save)"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "/dev/null");</span></span>

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<td class="old_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

948

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC948" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">save_fit_path = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUserForFilePath ("Save RELAX model fit to this file </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">'/dev/null' to skip</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">");</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

949

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC949" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolLFToPath(relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">likelihood_function</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">save_fit_path);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

950

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC950" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

945

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<td class="new_line diff-line-num" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

951

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC951" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  if (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">numbers_of_tested_groups == 2) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

946

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<td class="new_line diff-line-num" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

952

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC952" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC953" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">          relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fitted</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">K = estimators</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetGlobalMLE (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">k);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1017" style="width: 35px; color: rgba(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">@@ -1011,6 +1017,7 @@ function relax.FitMainTestPair () {</td>

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<td class="new_line diff-line-num" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1017" 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;">report_dnds (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">inferred_distribution_ref);</span></span>

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<td class="new_line diff-line-num" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1018

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1018" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1013

</td>

<td class="new_line diff-line-num" data-linenumber="1019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1019

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1019" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                         relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit = relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">take2;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1020

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1020" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolLFToPath(relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">take2</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">likelihood_function</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">save_fit_path);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1014

</td>

<td class="new_line diff-line-num" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1021

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1021" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                 }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1015

</td>

<td class="new_line diff-line-num" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1022

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1022" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1016

</td>

<td class="new_line diff-line-num" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1023

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1023" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            DeleteObject (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">take2);</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1038" style="width: 35px; color: rgba(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="1045" style="width: 35px; color: rgba(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">@@ -1038,9 +1045,7 @@ function relax.FitMainTestPair () {</td>

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<td class="old_line diff-line-num" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1038

</td>

<td class="new_line diff-line-num" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1045

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1045" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">report_multi_hit  (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">distribution_for_json</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "RELAX"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "alt</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">mh");</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1039

</td>

<td class="new_line diff-line-num" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1046

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1046" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_report_srv (relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> FALSE);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1040

</td>

<td class="new_line diff-line-num" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1047

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1047" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1041

</td>

<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1041" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    KeywordArgument ("save</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;"> "Save RELAX alternative model fit to this file (default is not to save)"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "/dev/null");</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1042

</td>

<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1042" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SpoolLFToPath(relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">likelihood_function</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">PromptUserForFilePath ("Save RELAX model fit to this file </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">'/dev/null' to skip</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">"));</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1043

</td>

<td class="new_line diff-line-num old" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1043" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1048

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1048" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1044

</td>

<td class="new_line diff-line-num" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1049

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1049" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> selection</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">json_store_lf (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="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1045

</td>

<td class="new_line diff-line-num" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1050

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1050" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                         relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_name</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1046

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<td class="new_line diff-line-num" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1051

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1051" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                                         relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alternative_model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">fit</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log_likelihood</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1523" style="width: 35px; color: rgba(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="1528" style="width: 35px; color: rgba(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">@@ -1523,7 +1528,7 @@ lfunction relax.BS_REL._DefineQ (bs_rel, namespace) {</td>

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<td class="old_line diff-line-num" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1523

</td>

<td class="new_line diff-line-num" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1528

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1528" 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>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1524

</td>

<td class="new_line diff-line-num" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1529

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1529" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">select_branches(partition_info) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1525

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<td class="new_line diff-line-num" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1530

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1530" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1526

</td>

<td class="new_line diff-line-num old" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1526" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    kGroupMode = <span class="idiff left deletion">"</span>Group<span class="idiff right deletion"> m</span>ode";</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1531

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1531" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    kGroupMode = <span class="idiff left addition">^"relax</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">k</span>Group<span class="idiff right addition">M</span>ode";</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1527

</td>

<td class="new_line diff-line-num" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1532

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1532" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1528

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<td class="new_line diff-line-num" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1533

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1533" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">CheckAssertion("utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D (`&partition_info`) == 1"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "RELAX only works on a single partition dataset");</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1529

</td>

<td class="new_line diff-line-num" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1534

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1534" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    available_models = {};</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1535" style="width: 35px; color: rgba(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="1540" style="width: 35px; color: rgba(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">@@ -1535,7 +1540,8 @@ lfunction relax.select_branches(partition_info) {</td>

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<td class="old_line diff-line-num" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1535

</td>

<td class="new_line diff-line-num" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1540

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1540" 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 (tree_for_analysis</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">trees</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_map")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_value_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "`&available_models`</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_value_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1");</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1536

</td>

<td class="new_line diff-line-num" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1541

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1541" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    list_models   = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">sortStrings(utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Keys(available_models)); // get keys</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1537

</td>

<td class="new_line diff-line-num" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1542

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1542" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    option_count  = Abs (available_models);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1538

</td>

<td class="new_line diff-line-num old" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1538" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1543

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1543" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1544

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1539

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<td class="new_line diff-line-num" data-linenumber="1545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1545

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1545" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">CheckAssertion    ("`&option_count` </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">= 2"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "RELAX requires at least one designated set of branches in the tree</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">");</span></span>

</pre></td>

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1540

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<td class="new_line diff-line-num" data-linenumber="1546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1546

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1546" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1541

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<td class="new_line diff-line-num" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1547

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1547" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    nontrivial_groups = option_count;</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1546" style="width: 35px; color: rgba(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="1552" style="width: 35px; color: rgba(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">@@ -1546,20 +1552,25 @@ lfunction relax.select_branches(partition_info) {</td>

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1546

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<td class="new_line diff-line-num" data-linenumber="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1552

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1552" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="old_line diff-line-num" data-linenumber="1547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1547

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<td class="new_line diff-line-num" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1553" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    run_mode = None;   </span></span>

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<td class="old_line diff-line-num" data-linenumber="1548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1548

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<td class="new_line diff-line-num" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1554

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1554" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="old_line diff-line-num old" data-linenumber="1549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1549

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<td class="new_line diff-line-num old" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1549" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (nontrivial_groups </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">= 3) { // could run as a group set</span></span>

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<td class="old_line diff-line-num new" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1555

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1555" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1556" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1557" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> if (nontrivial_groups </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">= 2) { // could run as a group set</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1550

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<td class="new_line diff-line-num" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1558

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1558" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         run_mode = io</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SelectAnOption ({</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1551

</td>

<td class="new_line diff-line-num" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1559

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1559" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                 {kGroupMode</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Run the test for equality of selective regimes among  " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> nontrivial_groups </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " groups of branches"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1552

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<td class="new_line diff-line-num" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1560

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1560" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                 {"Classic mode"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Select one test and one reference group of branches</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> with the rest of the branches treated as unclassified"}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1553

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<td class="new_line diff-line-num" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1561

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1561" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         }</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Group test mode");</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1554

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<td class="new_line diff-line-num" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1562" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         if (run_mode == kGroupMode) {</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1555

</td>

<td class="new_line diff-line-num" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1563

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1563" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                  utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetEnvVariable ("relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">numbers_of_tested_groups"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> nontrivial_groups);</span></span>

</pre></td>

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<td class="new_line diff-line-num old" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1556" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                  utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ForEachPair (tree_for_analysis</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">trees</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_map")</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_key_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "_value_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1557

</td>

<td class="new_line diff-line-num old" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1557" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                 if ('' == _value_ ) {</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1558

</td>

<td class="new_line diff-line-num old" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1558" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                         `&tree_configuration`</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_key_</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('relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">unclassified_branches_name');</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1559

</td>

<td class="new_line diff-line-num old" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1559" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                 } else {</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1560

</td>

<td class="new_line diff-line-num old" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1560" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                         `&tree_configuration`</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_key_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _value_;</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1561

</td>

<td class="new_line diff-line-num old" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1561" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                 }</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1562

</td>

<td class="new_line diff-line-num old" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1562" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                         ");                         </span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1564

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1564" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                  </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1565

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1565" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                  for (_key_</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> _value_; in; tree_for_analysis</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">trees</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model_map")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1566

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1566" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                     if ('' == _value_ ) {</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1567

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1567" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                             tree_configuration</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_key_</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('relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">unclassified_branches_name');</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1568

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1568" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                         } else {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1569

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1569" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                 tree_configuration</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_key_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = _value_;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1570

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1570" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                         }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1571

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1571" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                  }</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1572

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1572" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                  </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="1563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1573

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1573" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                  utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetEnvVariable ("relax</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">analysis_run_mode"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> kGroupMode);</span></span>

</pre></td>

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1563

</td>

<td class="new_line diff-line-num" data-linenumber="1574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1574

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1574" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         }</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1564

</td>

<td class="new_line diff-line-num" data-linenumber="1575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1575

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1575" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> }</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="1565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1565

</td>

<td class="new_line diff-line-num" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1576

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1576" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

</pre></td>

</tr>

</table>

<br>

</li>

<li id="5162429bd3f362a69890c6b040d4be37e11a6308">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#5162429bd3f362a69890c6b040d4be37e11a6308"><strong>res/TemplateBatchFiles/files.lst</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,7 +92,6 @@</td>

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<td class="old_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

</td>

<td class="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">"BST","Use the improved branch-site REL method of Yang and Nielsen (2005) to look for episodic selection in sequences.","YangNielsenBranchSite2005.bf";</span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

</td>

<td class="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">"BT","Test whether a branch (or branches) in the tree evolves under different dN and dS than the rest of the tree.","TestBranchDNDS.bf";</span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

</td>

<td class="new_line diff-line-num" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">"NY","Test for positive selection using the approach of Nielsen and Yabg, by sampling global dN/dS from an array of distributions, and using Bayesian posterior to identify the sites with dN/dS>1.","NielsenYang.bf";</span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

95

</td>

<td class="new_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">"PSM","Test for positive selection using the approach of Nielsen and Yang, by sampling global dN/dS from an array of distributions, and using Bayesian posterior to identify the sites with dN/dS>1. Multiple subsets of one data set with shared dN/dS.","MFPositiveSelection.bf";</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

96

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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

95

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

97

</td>

<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

96

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">"","Test for recombination.","!Recombination";</span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">"GARD","[GARD] Screen an alignment using GARD (requires an MPI environment).","GARD.bf";</span>

</pre></td>

</tr>

</table>

<br>

</li>

<li id="5dfec713e3892a936e8b5a63db56c03bee3ec252">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#5dfec713e3892a936e8b5a63db56c03bee3ec252"><strong>res/TemplateBatchFiles/libv3/all-terms.bf</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="397" style="width: 35px; color: rgba(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="397" style="width: 35px; color: rgba(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">@@ -397,6 +397,8 @@ namespace terms{</td>

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397

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<td class="new_line diff-line-num" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

397

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC397" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        data                    = "data";</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

398

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<td class="new_line diff-line-num" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

398

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC398" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        residue_properties      = "residue_properties";</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

399

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<td class="new_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(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>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC399" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        argument_collector      = "prompt_and_define";</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC400" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC401" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        nonsyn_multipliers      = "non</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">synonymous multipliers";</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="400" style="width: 35px; color: rgba(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>

<td class="new_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

402

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC402" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="403" style="width: 35px; color: rgba(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>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC403" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(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>

<td class="new_line diff-line-num" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

404

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC404" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

</table>

<br>

</li>

<li id="94156df91590185798157c724050369c6294262f">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#94156df91590185798157c724050369c6294262f"><strong>res/TemplateBatchFiles/libv3/models/codon/BS_REL.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">@@ -14,6 +14,8 @@ LoadFunctionLibrary("../../convenience/math.bf");</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">*/</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_term = "alpha";</span></span>

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC20" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription</span></span>

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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC21" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {String} type</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +47,7 @@ lfunction models.codon.BS_REL.ModelDescription(type, code, components) {</td>

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">constrain_branch_length"): "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">constrain_branch_length"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC48" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">frequency_estimator"): "frequencies</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">empirical</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">corrected</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">CF3x4"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">q_ij"): ""</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> // set for individual components in models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_DefineQ</span></span>

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<td class="old_line diff-line-num old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC48" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">time"): "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left deletion">DNA</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion">generic</span></span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Time"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">time"): "models</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 addition">BS_REL</span></span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Time"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">defineQ"): "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_DefineQ"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC52" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue("terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">post_definition"): "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">post_definition"</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC53" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    };</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,7 +115,7 @@ lfunction models.codon.BS_REL_Per_Branch_Mixing._DefineQ(bs_rel, namespace) {</td>

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<td class="new_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC115" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       ExecuteCommands ("</span></span>

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<td class="new_line diff-line-num" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC116" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>

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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC117" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            return models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC116" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                <span class="idiff left right deletion">'alpha</span>'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC118" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                <span class="idiff left addition">^'models</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">codon</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">BS_REL</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">rate_term</span>'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC119" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                'beta_`component`'</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;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC120" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                'omega`component`'</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;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component));</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC121" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }"</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" style="width: 35px; color: rgba(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">@@ -140,6 +142,8 @@ lfunction models.codon.BS_REL_Per_Branch_Mixing._DefineQ(bs_rel, namespace) {</td>

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<td class="new_line diff-line-num" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC144" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ExtractMixtureDistribution (bs_rel) {</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC145" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC147" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    count = bs_rel </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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">components")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC149" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (Type (count) == "Matrix") {</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">@@ -149,14 +153,23 @@ lfunction models.codon.BS_REL.ExtractMixtureDistribution (bs_rel) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    rates = {count</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1};</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC154" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    weights = {count</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 1};</span></span>

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<td class="new_line diff-line-num old" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (i = 1; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= count; i</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) {</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC153" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        rates </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ((bs_rel</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;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">global")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> i)</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC154" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> count ) {</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC155" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            weights </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ((bs_rel</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;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">global")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (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;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_aux_weight")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> i )</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

156

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC156" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (bs_rel</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">type"</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;">local") {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC157" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">         for (i = 1; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= count; i</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC158" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            rates </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ((bs_rel</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;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">local")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> i)</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC159" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> count ) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC160" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                weights </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ((bs_rel</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;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">local")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (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;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_aux_weight")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> i )</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC161" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC162" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC163" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        return {"rates" : rates</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "weights" : weights</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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate" : ((bs_rel</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;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">local")</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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">};</span></span>

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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC164" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    } else {</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (i = 1; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= count; i</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">=1) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            rates </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ((bs_rel</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;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">global")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> i)</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC167" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> count ) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC168" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                weights </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = ((bs_rel</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;">parameters")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">global")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AddCategory (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;">mixture</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mixture_aux_weight")</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> i )</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC169" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC170" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="new_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC171" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC172" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC159" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC173" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return {"rates" : rates</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "weights" : weights };</span></span>

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<td class="new_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC174" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC175" class="line" lang="brainfuck"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="239" style="width: 35px; color: rgba(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="252" style="width: 35px; color: rgba(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">@@ -239,7 +252,7 @@ lfunction models.codon.BS_REL._DefineQ(bs_rel, namespace) {</td>

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<td class="new_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC252" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       ExecuteCommands ("</span></span>

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<td class="new_line diff-line-num" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC253" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC254" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">               return models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC242" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                <span class="idiff left right deletion">'alpha</span>'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC255" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                <span class="idiff left addition">^'models</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">codon</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">BS_REL</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">rate_term</span>'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC256" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                'beta_`component`'</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;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC257" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                'omega`component`'</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;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component));</span></span>

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<td class="new_line diff-line-num" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC258" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }"</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="397" style="width: 35px; color: rgba(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="410" style="width: 35px; color: rgba(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">@@ -397,7 +410,7 @@ function models.codon.BS_REL.post_definition(model) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC411" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">get_branch_length(model</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> tree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> node) {</span></span>

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<td class="new_line diff-line-num old" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC400" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC413" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

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<td class="new_line diff-line-num" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC414" 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;">SetLocalModelParameters (model</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> tree</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> node);</span></span>

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<td class="old_line diff-line-num" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC415" 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;">SetCategoryVariables   (model);</span></span>

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<td class="old_line diff-line-num" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    bl = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetEnvVariable ("BRANCH_LENGTH_STENCIL");</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">@@ -431,7 +444,7 @@ lfunction models.codon.BS_REL._DefineQ.MH (bs_rel, namespace) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC444" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    rg = "function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>

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<td class="new_line diff-line-num" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC446" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                   return models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_TRIP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num old" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    <span class="idiff left right deletion">'alpha</span>'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC447" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    <span class="idiff left addition">^'models</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">codon</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">BS_REL</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">rate_term</span>'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC448" class="line" lang="brainfuck"><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;"> component</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;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component__)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC449" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    'omega' </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> component</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;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component__)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC450" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    'delta'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multiple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="495" style="width: 35px; color: rgba(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">@@ -482,7 +495,7 @@ lfunction models.codon.BS_REL_SRV._DefineQ.MH (bs_rel, namespace) {</td>

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<td class="new_line diff-line-num" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC495" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="new_line diff-line-num" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC496" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    rg = "function rate_generator (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model) {</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC497" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                   return models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_TRIP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">_GenerateRate_generic (fromChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> toChar</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model_type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">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;">translation_table')</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

485

</td>

<td class="new_line diff-line-num old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC485" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    <span class="idiff left right deletion">'alpha</span>'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

498

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC498" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    <span class="idiff left addition">^'models</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">codon</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">BS_REL</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">rate_term</span>'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">getGlobalValue('terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

486

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<td class="new_line diff-line-num" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC499" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    'beta_`component`'</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;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">nonsynonymous_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

487

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<td class="new_line diff-line-num" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

500

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC500" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    'omega`component`'</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;">AddCategory (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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">omega_ratio')</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> component)</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

488

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<td class="new_line diff-line-num" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

501

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC501" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    'delta'</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> 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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">multiple_hit_rate')</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="561" style="width: 35px; color: rgba(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="574" style="width: 35px; color: rgba(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">@@ -561,3 +574,10 @@ lfunction models.codon.BS_REL_SRV._DefineQ.MH (bs_rel, namespace) {</td>

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<td class="old_line diff-line-num" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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<td class="new_line diff-line-num" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

574

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC574" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

</td>

<td class="new_line diff-line-num" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

575

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC575" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return bs_rel;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

563

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<td class="new_line diff-line-num" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

576

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC576" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

577

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC577" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

578

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC578" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">function models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Time (options) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

579

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC579" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (options == terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">global) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

580

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC580" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        return  models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">DNA</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Time (options);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

581

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC581" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre></td>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC582" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">BS_REL</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_term;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC583" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span></pre></td>

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<br>

</li>

<li id="95a7c74b0e59bc9dc8d85b6ac4b02d308b4e09fb">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#95a7c74b0e59bc9dc8d85b6ac4b02d308b4e09fb"><strong>res/TemplateBatchFiles/libv3/models/codon/MG_REV.bf</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -148,7 +148,6 @@ function models.codon.MG_REV.set_branch_length(model, value, parameter) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC148" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if ( null != models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta &&  null != models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha) {</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC149" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC150" class="line" lang="brainfuck"></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC151" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC151" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC152" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC153" class="line" lang="brainfuck"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -209,8 +208,7 @@ function models.codon.MG_REV.set_branch_length(model, value, parameter) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC208" 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;">RemoveConstraint(models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta);</span></span>

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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC209" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    Eval ("`models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p` =" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> Eval(models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta));</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC210" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                } else { // beta IS constrained</span></span>

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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC212" 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 (models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetConstraint (models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"");</span></span>

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<td class="new_line diff-line-num old" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC213" 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 (models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">"");</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC211" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC212" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC213" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    /** the branch length expression is going to be in terms of ** template ** parameters</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> but constraints will be in</span></span>

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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC214" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        terms of instantiated parameters</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> so the expression to solve for needs to be temporarily bound to the global variable **/</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" style="width: 35px; color: rgba(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="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -218,7 +216,11 @@ function models.codon.MG_REV.set_branch_length(model, value, parameter) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC216" 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 ( models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>

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<td class="new_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC217" 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 ( models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">  models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC218" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC219" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC220" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC221" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    ExecuteCommands("FindRoot (models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lp</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">(" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_string</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ")</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> 3*value </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha </span><span 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;">0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;">10000)");</span></span>

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<td class="new_line diff-line-num new" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC222" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    </span></span>

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<td class="new_line diff-line-num new" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC223" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                        </span></span>

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<td class="new_line diff-line-num" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC224" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    Eval("`models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p` =" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">lp);</span></span>

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<td class="new_line diff-line-num" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC225" 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;">RemoveConstraint ( models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">beta);</span></span>

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<td class="new_line diff-line-num" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC226" 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;">RemoveConstraint ( models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">alpha</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p);</span></span>

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</li>

<li id="9f6d2efd39d3afa147f430ca6d771b8d64f20a55">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#9f6d2efd39d3afa147f430ca6d771b8d64f20a55"><strong>res/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="379" style="width: 35px; color: rgba(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="379" style="width: 35px; color: rgba(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">@@ -379,7 +379,6 @@ lfunction models.codon.MG_REV_PROP.ModelDescription(type, code, properties) {</td>

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<td class="new_line diff-line-num" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC379" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    mg_base</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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">residue_name_map")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ValidateIDs (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Keys (mg_base</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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">residue_properties")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">));</span></span>

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<td class="new_line diff-line-num" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC380" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    mg_base</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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">post_definition")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_PROP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">post_definition";</span></span>

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<td class="new_line diff-line-num" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC381" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    mg_base</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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = "models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_PROP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length";</span></span>

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<td class="new_line diff-line-num old" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC382" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC382" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return mg_base;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC383" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC384" class="line" lang="brainfuck"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="387" style="width: 35px; color: rgba(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">@@ -388,6 +387,7 @@ lfunction models.codon.MG_REV_PROP.ModelDescription(type, code, properties) {</td>

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<td class="new_line diff-line-num" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC387" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {String or AssociativeList} properties</span></span>

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<td class="old_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC388" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @return {AssociativeList}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC389" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * Convert a set of amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid properties into the expected format</span></span>

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<td class="old_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC390" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * This will also recenter the properties (mean 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> variance of 1)</span></span>

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<td class="new_line diff-line-num" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC391" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC392" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC393" class="line" lang="brainfuck"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="428" style="width: 35px; color: rgba(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="428" style="width: 35px; color: rgba(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">@@ -428,7 +428,25 @@ lfunction models.codon.MG_REV_PROP._munge_properties (properties) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC429" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

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<td class="old_line diff-line-num old" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC431" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="new_line diff-line-num new" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="old_line diff-line-num new" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (key</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> value; in; properties) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        sum  = 0;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        sum2 = 0;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (aa</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> prop; in; value) {</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            sum </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= prop;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            sum2 </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= prop*prop;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        sum = sum / 20;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        norm = Sqrt (sum2 / 20 </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> sum*sum);</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (aa</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> prop; in; value) {</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC446" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            value </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">aa</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (prop</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">sum) / norm;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC447" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }       </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC449" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="new_line diff-line-num" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC450" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    assert (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Array1D(properties) </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 0</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "At least one valid property set must be defined");</span></span>

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<td class="new_line diff-line-num" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC451" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return properties;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC452" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="480" style="width: 35px; color: rgba(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">@@ -480,7 +498,6 @@ lfunction models.codon.MG_REV_PROP._GenerateRate_generic (fromChar, toChar, name</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC498" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            nuc_rate = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AppendMultiplicativeTerm (nuc_rate</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> nuc_p);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC499" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC500" class="line" lang="brainfuck"></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC483" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC501" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        rate_entry = nuc_rate;</span></span>

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<td class="old_line diff-line-num" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC502" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC503" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (_tt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">fromChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> != _tt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="531" style="width: 35px; color: rgba(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">@@ -514,6 +531,7 @@ lfunction models.codon.MG_REV_PROP._GenerateRate_generic (fromChar, toChar, name</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC531" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                rate_entry </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= "*Exp(</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;"> Join("</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;">aa_rate) </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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC532" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</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;">alpha_term</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = alpha;</span></span>

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<td class="new_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC533" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                rate_entry = "Min(10000</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;"> rate_entry  </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;"> beta </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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC534" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC535" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">             }</span></span>

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<td class="old_line diff-line-num" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC536" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        } else {</span></span>

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<td class="new_line diff-line-num" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC537" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (model_type == 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;">local")) {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="562" style="width: 35px; color: rgba(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">@@ -544,7 +562,7 @@ lfunction  models.codon.MG_REV_PROP.post_definition (model) {</td>

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<td class="new_line diff-line-num" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC562" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="new_line diff-line-num" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC563" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC564" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_PROP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">set_branch_length(model</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> value</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> parameter) {</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC547" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC565" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="new_line diff-line-num" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC566" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Has (model</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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV_PROP</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">mean_prop"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Number")) {</span></span>

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<td class="new_line diff-line-num" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC567" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">      properties = model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetLocalParameters_RegExp(model</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;">propertyImportance (""));</span></span>

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<td class="new_line diff-line-num" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC568" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">      for (tag</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> id; in; properties) {</span></span>

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<br>

</li>

<li id="e8578acaed39aa42e302cfc6b43e09678d292e72">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#e8578acaed39aa42e302cfc6b43e09678d292e72"><strong>res/TemplateBatchFiles/libv3/models/codon/MSS.bf</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,7 @@ lfunction model.codon.MSS.prompt_and_define (type, code) {</td>

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<td class="new_line diff-line-num" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        {"SynREV"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Each set of codons mapping to the same amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid class have a separate substitution rate (Valine == neutral)"}</span></span>

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<td class="new_line diff-line-num" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        {"SynREV2"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Each pair of synonymous codons mapping to the same amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid class and separated by a transition have a separate substitution rate (no rate scaling))"}</span></span>

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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        {"SynREV2g"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Each pair of synonymous codons mapping to the same amino</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">acid class and separated by a transition have a separate substitution rate (Valine == neutral)</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;"> All between</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">class synonymous substitutions share a rate</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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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC32" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        {"SynREVCodon"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Each <span class="idiff left deletion">set of codons mapping to the same amino</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff deletion">-</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right deletion">acid class have a separate</span> substitution rate (fully estimated)"}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        {"SynREVCodon"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Each <span class="idiff left right addition">codon pair that is exchangeable gets its own</span> substitution rate (fully estimated)"}</span></span>

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<td class="old_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        {"Random"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Random partition (specify how many classes; largest class = neutral)"}</span></span>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        {"File"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "Load a TSV partition from file (prompted for neutral class)"}</span></span>

</pre></td>

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

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

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -68,11 +68,13 @@ lfunction model.codon.MSS.prompt_and_define (type, code) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC70" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (partitioning_option == "SynREV" || partitioning_option == "SynREVCodon" ) {</span></span>

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<td class="new_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC71" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        bins    = {};</span></span>

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<td class="new_line diff-line-num old" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC72" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        mapping = {};</span></span>

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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC71" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        bins          = {};</span></span>

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<td class="old_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        mapping       = {};</span></span>

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<td class="old_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC73" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        mapping_codon = {};</span></span>

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<td class="new_line diff-line-num" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC74" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        tt = gc </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;">translation_table"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (codon; in; gc </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;">sense_codons"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) {</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC76" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            mapping</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = tt</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            mapping_codon </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = codon;</span></span>

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<td class="new_line diff-line-num" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            bins</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">mapping</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC79" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (partitioning_option == "SynREV") {</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,7 +83,7 @@ lfunction model.codon.MSS.prompt_and_define (type, code) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC83" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            );</span></span>

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<td class="new_line diff-line-num" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC84" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="new_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        return  models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription(type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="new_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC84" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_classes" : mapping</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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">neutral" : ""}</span></span>

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<td class="old_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC86" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           {^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_classes" : mapping<span class="idiff left addition">_codon</span></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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">neutral" : ""</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition"> ^"terms</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">model</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff addition">MSS</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">.</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition">normalize" : FALSE</span>}</span></span>

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<td class="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        );</span></span>

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC88" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">   }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC89" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">   </span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="176" style="width: 35px; color: rgba(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="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -176,6 +178,7 @@ lfunction model.codon.MSS.prompt_and_define (type, code) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC179" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">  </span></span>

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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC180" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription(type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> codon_classes) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC181" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC182" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    m = Call ("models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MG_REV</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ModelDescription"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> type</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> code);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC183" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="new_line diff-line-num" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC184" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (^"fitter</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">frequency_type" == "F3x4") {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(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="271" style="width: 35px; color: rgba(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">@@ -268,6 +271,14 @@ lfunction models.codon.MSS._GenerateRate (fromChar, toChar, namespace, model_typ</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC271" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC272" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            class_from = (model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_classes"</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;">fromChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC273" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            class_to   = (model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_classes"</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;">toChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC274" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC275" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC276" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if ((Abs (class_from) && Abs (class_to)) == FALSE) {</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC277" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                class_from = (model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">codon_classes"</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;">fromChar</span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">toChar</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC278" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                class_to = class_from;</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC279" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC280" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC281" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            assert (Abs (class_from) && Abs (class_to)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "The neutral class for `fromChar` to `toChar` is not specified in the model definition");</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC282" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC283" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (class_from == class_to) {</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC284" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (class_from == nr) {</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="300" style="width: 35px; color: rgba(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">@@ -300,21 +311,26 @@ lfunction models.codon.MSS._GenerateRate (fromChar, toChar, namespace, model_typ</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC311" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        codon_rate = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ApplyNameSpace(between_rate</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC312" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    }</span></span>

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<td class="new_line diff-line-num" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC313" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">between"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = codon_rate;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC303" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            <span class="idiff left right deletion">    </span></span></span>

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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC314" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC315" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                } else {</span></span>

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<td class="old_line diff-line-num old" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC305" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    if (model_type == 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;">local")) {</span></span>

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<td class="old_line diff-line-num old" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC306" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        codon_rate = alpha </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;"> class_from </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;"> class_to;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC316" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    if (class_from </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> class_to == nr) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC317" 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 ("NEUTRAL");</span></span>

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<td class="old_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC318" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        codon_rate  = 1;</span></span>

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<td class="old_line diff-line-num" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC319" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    } else {</span></span>

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<td class="old_line diff-line-num old" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC308" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        codon_rate = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ApplyNameSpace(alpha </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;"> class_from </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;"> class_to</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC320" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        if (model_type == 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;">local")) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC321" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            codon_rate = alpha </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;"> class_from </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;"> class_to;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC322" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        } else {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC323" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            codon_rate = parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ApplyNameSpace(alpha </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;"> class_from </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;"> class_to</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> namespace);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC324" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC325" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</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;">alpha_term </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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">syn_rate_between" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> class_from </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " and "  </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> class_to</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = codon_rate;</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC326" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    }</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC310" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    (_GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">model_type</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;">alpha_term </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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">MSS</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">syn_rate_between" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> class_from </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> " and "  </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> class_to</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = codon_rate;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC327" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC328" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                rate_entry </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;"> codon_rate;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC329" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC330" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC331" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC332" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        _GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p</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;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">rate_entry")</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = rate_entry;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC317" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC333" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    <span class="idiff left right addition"> </span>}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC334" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC335" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return _GenerateRate</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC336" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<br>

</li>

<li id="0ad5f4d1790906a0091532d9ca355a6162bf3c31">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#0ad5f4d1790906a0091532d9ca355a6162bf3c31"><strong>res/TemplateBatchFiles/libv3/models/model_functions.bf</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="402" style="width: 35px; color: rgba(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="402" style="width: 35px; color: rgba(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">@@ -402,11 +402,15 @@ function models.generic.SetBranchLength (model, value, parameter) {</td>

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<td class="new_line diff-line-num" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC404" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">     if (Abs((model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC405" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC406" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (Type (model </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_string</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) == "String") {</span></span>

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<td class="old_line diff-line-num" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

406

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<td class="new_line diff-line-num" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC407" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">expression = model </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_string</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC408" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC409" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (Abs((model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">) </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 1) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC410" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

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<td class="new_line diff-line-num" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC411" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl = Call (model </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">time</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</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">type</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC412" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span></span>

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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC413" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                 </span></span>

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<td class="new_line diff-line-num" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC414" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl;</span></span>

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<td class="new_line diff-line-num" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC415" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                if (parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">IsIndependent (models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p) == FALSE) {</span></span>

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<td class="new_line diff-line-num" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC416" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                     models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl = utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">First (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">UniqueValues ((model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local</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;"> "_name_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="418" style="width: 35px; color: rgba(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="422" style="width: 35px; color: rgba(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">@@ -418,14 +422,27 @@ function models.generic.SetBranchLength (model, value, parameter) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC422" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                     }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC423" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                     models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl;</span></span>

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420

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

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421

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<td class="new_line diff-line-num old" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC421" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> </span></span>

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<td class="new_line diff-line-num" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC427" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitution = {};</span></span>

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423

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<td class="new_line diff-line-num old" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC423" 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 (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">UniqueValues ((model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local</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;"> "_name_"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

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424

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<td class="new_line diff-line-num old" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC424" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            'if (_name_ != models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl) {</span></span>

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425

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<td class="new_line diff-line-num old" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC425" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitution </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = Eval (parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> _name_);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC426" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                             }');</span></span>

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<td class="new_line diff-line-num old" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC427" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC428" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC429" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span></span>

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<td class="new_line diff-line-num new" data-linenumber="430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC430" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                for (_name_; in; utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">UniqueValues ((model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC431" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC432" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    if (_name_ != models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl) {</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC433" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        if (parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">IsIndependent (parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> _name_)) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC434" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitution </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = Eval (parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> _name_);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC435" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        } else {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC436" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                            models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitution </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> _name_;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC437" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        }</span></span>

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<td class="old_line diff-line-num new" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC438" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    } else {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC439" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                        models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitution </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">_name_</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> _name_;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC440" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                    }</span></span>

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<td class="new_line diff-line-num new" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC441" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                }</span></span>

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<td class="new_line diff-line-num new" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC442" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                </span></span>

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<td class="new_line diff-line-num new" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl;              </span></span>

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<td class="new_line diff-line-num" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC444" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">expression = Simplify (models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">expression</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">substitution);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC445" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">               </span></span>

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<td class="new_line diff-line-num" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC446" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            } else {</span></span>

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<td class="new_line diff-line-num" data-linenumber="447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC447" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl = (Columns ((model</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">local</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;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="new_line diff-line-num" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC448" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">p = parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="440" style="width: 35px; color: rgba(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="457" style="width: 35px; color: rgba(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">@@ -440,7 +457,7 @@ function models.generic.SetBranchLength (model, value, parameter) {</td>

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<td class="old_line diff-line-num" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC457" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                      messages</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log ("models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength: " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ":=(" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> value</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_scaler</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ")*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t);</span></span>

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<td class="old_line diff-line-num" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC458" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num" data-linenumber="442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC459" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                  } else {</span></span>

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<td class="old_line diff-line-num old" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC443" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                   <span class="idiff left right deletion"> </span> Eval (parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ":=(" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> value</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_scaler</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ")*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> value</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC460" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                          <span class="idiff left right addition">    </span>Eval (parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ":=(" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> value</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_scaler</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ")*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> value</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC461" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                          messages</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">log ("models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength: " </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> parameter </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> "</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">bl </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ":=(" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> value</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">model</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">branch_length_scaler</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> ")*" </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> models</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">generic</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetBranchLength</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">t);</span></span>

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445

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC462" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                                  }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC463" class="line" lang="brainfuck"></span>

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<br>

</li>

<li id="801d4bca405dfccac3b1e451b211ca98bd00d599">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#801d4bca405dfccac3b1e451b211ca98bd00d599"><strong>res/TemplateBatchFiles/libv3/models/parameters.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">@@ -634,26 +634,50 @@ function parameters.helper.copy_definitions(target, source) {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC634" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC636" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>

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<td class="new_line diff-line-num old" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC637" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name pparameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetStickBreakingDistribution</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC637" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name pparameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetStickBreakingDistribution<span class="idiff left right addition">Prefix</span></span></span>

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<td class="new_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC638" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {AssociativeList} parameters</span></span>

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<td class="new_line diff-line-num" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC639" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {Matrix} values</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC640" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * #param {String|} prefix to use for variable names</span></span>

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<td class="new_line diff-line-num" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC641" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @returns nothing</span></span>

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<td class="new_line diff-line-num" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC642" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>

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<td class="new_line diff-line-num old" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC643" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetStickBreakingDistribution (parameters</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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<td class="new_line diff-line-num new" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC644" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetStickBreakingDistribution<span class="idiff left addition">Prefix</span> (parameters</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> values</span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff addition">,</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right addition"> prefix</span>) {</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC645" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    rate_count = Rows (values);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC646" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    left_over  = 1;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC646" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC647" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> rate_count; i </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>

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<td class="new_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC648" 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;">SetValue ((parameters</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"rates"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC649" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> rate_count </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1) {</span></span>

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<td class="new_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC650" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            break_here = values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> / left_over;</span></span>

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<td class="new_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC651" 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;">SetValue ((parameters</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"weights"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> break_here);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC652" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            left_over = left_over * (1</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">break_here);</span></span>

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<td class="new_line diff-line-num old" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC653" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">       }</span></span>

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<td class="new_line diff-line-num new" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC647" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    </span></span>

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<td class="new_line diff-line-num new" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC648" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    if (utility</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">Has (parameters</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;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate"</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "String")) {</span></span>

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<td class="new_line diff-line-num new" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC649" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        alpha = parameters </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">^"terms</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">synonymous_rate"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC650" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> rate_count; i </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC651" 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 (prefix </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (parameters</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"rates"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">AppendMultiplicativeTerm (prefix </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;"> values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> "");</span></span>

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<td class="new_line diff-line-num new" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC652" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> rate_count </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

653

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC653" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                break_here = values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> / left_over;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

654

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC654" 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;">SetValue (prefix </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (parameters</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"weights"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> break_here);</span></span>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

655

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC655" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                left_over = left_over * (1</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">break_here);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

656

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC656" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

657

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC657" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }    </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

658

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC658" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    } else {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

659

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC659" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        for (i = 0; i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> rate_count; i </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

660

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC660" 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;">SetValue (prefix </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (parameters</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"rates"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">0</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">);</span></span>

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<td class="new_line diff-line-num new" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

661

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC661" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if (i </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;"> rate_count </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> 1) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

662

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC662" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                break_here = values</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> / left_over;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

663

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC663" 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;">SetValue (prefix </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;"> (parameters</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"weights"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">)</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">i</span><span class="p">]</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> break_here);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

664

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC664" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                left_over = left_over * (1</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">break_here);</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

665

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC665" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           }</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC666" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

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654

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<td class="new_line diff-line-num" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

667

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC667" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

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668

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC668" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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656

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669

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC669" class="line" lang="brainfuck"></span>

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<td class="new_line diff-line-num new" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

670

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC670" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>

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<td class="new_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

671

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC671" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name pparameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetStickBreakingDistribution</span></span>

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<td class="new_line diff-line-num new" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

672

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC672" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {AssociativeList} parameters</span></span>

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<td class="old_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

673

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC673" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {Matrix} values</span></span>

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<td class="new_line diff-line-num new" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

674

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC674" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @returns nothing</span></span>

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<td class="new_line diff-line-num new" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

675

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC675" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>

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676

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC676" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

677

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC677" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction parameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">SetStickBreakingDistribution (parameters</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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<td class="new_line diff-line-num new" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

678

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC678" 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;">SetStickBreakingDistributionPrefix (parameters</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> values</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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<td class="new_line diff-line-num new" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

679

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC679" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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680

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC680" class="line" lang="brainfuck"></span>

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657

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<td class="new_line diff-line-num" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC681" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/**</span></span>

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<td class="new_line diff-line-num" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC682" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name pparameters</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">GetStickBreakingDistribution</span></span>

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<td class="new_line diff-line-num" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC683" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {AssociativeList} parameters</span></span>

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<br>

</li>

<li id="5c5226a707906d461dd112286b111fe4809fac66">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#5c5226a707906d461dd112286b111fe4809fac66"><strong>res/TemplateBatchFiles/libv3/tasks/ancestral.bf</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="539" style="width: 35px; color: rgba(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="539" style="width: 35px; color: rgba(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">@@ -539,7 +539,6 @@ lfunction ancestral.ComputeSubstitutionBySite (ancestral_data, site, branch_filt</td>

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539

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<td class="new_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC539" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        own_state    = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MATRIX"</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;">self</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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540

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<td class="new_line diff-line-num" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC540" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        parent_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MATRIX"</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;">parent</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC541" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC542" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC542" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if  ((own_state != parent_state) && (own_state != </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1) && (parent_state != </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1)) {</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC543" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            own_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MAPPING"</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;">own_state</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC544" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            parent_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MAPPING"</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;">parent_state</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">@@ -557,6 +556,57 @@ lfunction ancestral.ComputeSubstitutionBySite (ancestral_data, site, branch_filt</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC556" class="line" lang="brainfuck"></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC557" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC558" class="line" lang="brainfuck"></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC559" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/*******************************************</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC560" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> **</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC561" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeCompressedSubstitutionsBySite</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC562" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * computes the minimal representation of character states needed to recover the substitution </span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC563" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * history</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC564" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC565" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {Dictionary} ancestral_data </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> the dictionary returned by ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">build</span></span>

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<td class="new_line diff-line-num new" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC566" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @param {Number} site </span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;"> the 0</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">based index of a site</span></span>

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<td class="new_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC569" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @returns</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

570

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC570" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        {</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

571

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC571" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           "root"   : "state"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

572

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC572" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           "branch1" : "state"</span><span class="nf" style="color: #900; font-weight: 600;">,</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

573

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC573" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">           "branch2" : "state"</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

574

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC574" 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>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

575

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC575" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

576

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC576" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

577

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC577" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        character state at the root and at every branch that is different from </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

578

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC578" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        its parent</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

579

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC579" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

580

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC580" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> */</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

581

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC581" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

582

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC582" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/*******************************************/</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

583

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC583" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

584

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC584" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

585

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC585" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">lfunction ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeCompressedSubstitutionsBySite (ancestral_data</span><span class="nf" style="color: #900; font-weight: 600;">,</span><span class="c1" style="color: #998; font-style: italic;"> site) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

586

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC586" class="line" lang="brainfuck"></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

587

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC587" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    result   = {};</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

588

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC588" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    branches = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"DIMENSIONS"</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;">"BRANCHES"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

589

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC589" class="line" lang="brainfuck"></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

590

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC590" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    for (b = 1; b </span><span class="nb" style="color: #0086b3;"><</span><span class="c1" style="color: #998; font-style: italic;">= branches; b </span><span class="nf" style="color: #900; font-weight: 600;">+</span><span class="c1" style="color: #998; font-style: italic;">= 1) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

591

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC591" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        self   = b;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

592

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC592" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        parent = ((ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"TREE_AVL"</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;">b</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;">"Parent"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

593

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC593" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        own_state    = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MATRIX"</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;">self</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

594

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC594" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        if (parent </span><span class="nb" style="color: #0086b3;">></span><span class="c1" style="color: #998; font-style: italic;"> 0) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

595

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC595" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            parent_state = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MATRIX"</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;">parent</span><span class="nf" style="color: #900; font-weight: 600;">-</span><span class="c1" style="color: #998; font-style: italic;">1</span><span class="p">][</span><span class="c1" style="color: #998; font-style: italic;">site</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

596

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC596" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        </span></span>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

597

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC597" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            if  ((own_state != parent_state)) {</span></span>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

598

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC598" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">                result </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">(((ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"TREE_AVL"</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;">b</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;">"Name"</span><span class="p">]]</span><span class="c1" style="color: #998; font-style: italic;"> = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MAPPING"</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;">own_state</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

599

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC599" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

600

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC600" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        } else {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

601

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC601" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">            result </span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"root"</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;"> = (ancestral_data</span><span class="p">[</span><span class="c1" style="color: #998; font-style: italic;">"MAPPING"</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;">own_state</span><span class="p">]</span><span class="c1" style="color: #998; font-style: italic;">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

602

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC602" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">        }</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

603

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC603" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    }</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

604

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC604" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

605

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC605" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

606

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC606" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">    return  result;</span></span>

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<td class="new_line diff-line-num new" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC607" class="line" lang="brainfuck"></span>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

608

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC608" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

609

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC609" class="line" lang="brainfuck"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

560

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<td class="new_line diff-line-num" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

610

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC610" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;">/*******************************************</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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<td class="new_line diff-line-num" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC611" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> **</span></span>

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<td class="old_line diff-line-num" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

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<td class="new_line diff-line-num" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC612" class="line" lang="brainfuck"><span class="c1" style="color: #998; font-style: italic;"> * @name ancestral</span><span class="nf" style="color: #900; font-weight: 600;">.</span><span class="c1" style="color: #998; font-style: italic;">ComputeSiteComposition</span></span>

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<br>

</li>

<li id="59d202cc6599be3167fc3bd731039997dcaf9c72">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#59d202cc6599be3167fc3bd731039997dcaf9c72"><strong>src/core/fstring.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="575" style="width: 35px; color: rgba(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">@@ -575,14 +575,29 @@ HBLObjectRef _FString::SubstituteAndSimplify(HBLObjectRef arguments, HBLObjectRe</td>

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575

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<td class="new_line diff-line-num" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

575

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp">          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">variable_reference</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

576

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<td class="new_line diff-line-num" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

576

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp">            <span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">replacement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argument_substitution_map</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetByKey</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">variable_reference</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">GetName</span><span class="p">());</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

577

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<td class="new_line diff-line-num" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

577

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC577" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">replacement</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

578

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp">              <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">replacement</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ObjectClass</span> <span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">STRING</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

579

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp">                  <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">sub_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LocateVarByName</span> <span class="p">(((</span><span class="n" style="color: #333;">_FString</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">replacement</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Compute</span><span class="p">())</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_str</span><span class="p">());</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

580

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp">                  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sub_idx</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

581

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp">                      <span class="n" style="color: #333;">current_term</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetAVariable</span><span class="p">(</span><span class="n" style="color: #333;">sub_idx</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

582

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp">                      <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

583

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp">                  <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

584

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp">              <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

578

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<td class="new_line diff-line-num" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

585

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC585" class="line" lang="cpp">              <span class="n" style="color: #333;">current_term</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetAVariable</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>

</pre></td>

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579

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<td class="new_line diff-line-num" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC586" class="line" lang="cpp">              <span class="n" style="color: #333;">current_term</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">SetNumber</span> <span class="p">((</span><span class="n" style="color: #333;">HBLObjectRef</span><span class="p">)</span><span class="n" style="color: #333;">replacement</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">makeDynamic</span><span class="p">());</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

580

</td>

<td class="new_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC587" class="line" lang="cpp">            <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

</td>

<td class="new_line diff-line-num" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC588" class="line" lang="cpp">          <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

582

</td>

<td class="new_line diff-line-num" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

589

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC589" class="line" lang="cpp">        <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

590

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp">        <span class="n" style="color: #333;">evaluator</span><span class="p">.</span><span class="n" style="color: #333;">SimplifyConstants</span><span class="p">();</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

591

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp">        <span class="n" style="color: #333;">_Polynomial</span><span class="o" style="font-weight: 600;">*</span>    <span class="n" style="color: #333;">is_poly</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">_Polynomial</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">evaluator</span><span class="p">.</span><span class="n" style="color: #333;">ConstructPolynomial</span><span class="p">();</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

592

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_poly</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

593

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//StringToConsole("Secondary simplify\n");</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

594

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp">            <span class="n" style="color: #333;">_Formula</span> <span class="n" style="color: #333;">pf</span> <span class="p">(</span><span class="n" style="color: #333;">is_poly</span><span class="p">);</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

595

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp">            <span class="n" style="color: #333;">evaluator</span><span class="p">.</span><span class="n" style="color: #333;">Duplicate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pf</span><span class="p">);</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

596

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp">        <span class="p">}</span> </span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

597

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp">      <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

598

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp">          <span class="n" style="color: #333;">evaluator</span><span class="p">.</span><span class="n" style="color: #333;">SimplifyConstants</span><span class="p">();</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

</td>

<td class="new_line diff-line-num" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC599" class="line" lang="cpp">      <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

600

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC600" class="line" lang="cpp">      </span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

585

</td>

<td class="new_line diff-line-num old" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC585" class="line" lang="cpp">      <span class="n" style="color: #333;">evaluator</span><span class="p">.</span><span class="n" style="color: #333;">SimplifyConstants</span><span class="p">();</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

586

</td>

<td class="new_line diff-line-num" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

601

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_returnStringOrUseCache</span><span class="p">(((</span><span class="n" style="color: #333;">_String</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">evaluator</span><span class="p">.</span><span class="n" style="color: #333;">toStr</span><span class="p">(</span><span class="n" style="color: #333;">kFormulaStringConversionNormal</span><span class="p">)),</span> <span class="n" style="color: #333;">cache</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

</td>

<td class="new_line diff-line-num" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

602

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC602" class="line" lang="cpp">    <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

</td>

<td class="new_line diff-line-num" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

603

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC603" class="line" lang="cpp">  <span class="p">}</span></span>

</pre></td>

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<br>

</li>

<li id="07aceb8d215a75908cea626d9c80bc2a7c06639c">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#07aceb8d215a75908cea626d9c80bc2a7c06639c"><strong>src/core/global_things.cpp</strong></a>

<hr>

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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">@@ -122,7 +122,7 @@ namespace hy_global {</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp">                     <span class="n" style="color: #333;">kErrorStringDatasetRefIndexError</span> <span class="p">(</span><span class="s" style="color: #d14;">"Dataset index reference out of range"</span><span class="p">),</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp">                     <span class="n" style="color: #333;">kErrorStringMatrixExportError</span>    <span class="p">(</span><span class="s" style="color: #d14;">"Export matrix called with a non-polynomial matrix argument"</span><span class="p">),</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp">                     <span class="n" style="color: #333;">kErrorStringNullOperand</span>          <span class="p">(</span><span class="s" style="color: #d14;">"Attempting to operate on an undefined value; this is probably the result of an earlier 'soft' error condition"</span><span class="p">),</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC125" class="line" lang="cpp">                     <span class="n" style="color: #333;">kHyPhyVersion</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.3<span class="idiff left right deletion">6</span>"</span><span class="p">),</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp">                     <span class="n" style="color: #333;">kHyPhyVersion</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"2.5.3<span class="idiff left right addition">8</span>"</span><span class="p">),</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp">                    <span class="n" style="color: #333;">kNoneToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"None"</span><span class="p">,</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp">                    <span class="n" style="color: #333;">kNullToken</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"null"</span><span class="p">,</span></span>

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<li id="972df0539c47811332eda7005af635463c77eef8">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#972df0539c47811332eda7005af635463c77eef8"><strong>src/core/include/function_templates.h</strong></a>

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -156,7 +156,7 @@ void ArrayForEach(ARG_TYPE *array, unsigned long dimension,</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">ARG_TYPE</span><span class="p">></span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">InitializeArray</span><span class="p">(</span><span class="n" style="color: #333;">ARG_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">array</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;">dimension</span><span class="p">,</span></span>

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<td class="new_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp">                     <span class="n" style="color: #333;">ARG_TYPE</span> <span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll_count(8)</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp">  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll_count(8)</span></span>

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<td class="old_line diff-line-num" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp">  <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC161" 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;">dimension</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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp">    <span class="n" style="color: #333;">array</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;">value</span><span class="p">;</span></span>

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<li id="0aac57334e127d66d9818be138193215c7262bbe">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#0aac57334e127d66d9818be138193215c7262bbe"><strong>src/core/include/matrix.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="342" style="width: 35px; color: rgba(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="342" style="width: 35px; color: rgba(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">@@ -342,7 +342,8 @@ public:</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC342" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// otherwise returns the largest element</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp">    <span class="n" style="color: #333;">hyFloat</span>  <span class="n" style="color: #333;">AbsValue</span>                        <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

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<td class="old_line diff-line-num old" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC345" class="line" lang="cpp">    </span>

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<td class="old_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp">    <span class="n" style="color: #333;">hyFloat</span>  <span class="n" style="color: #333;">L11Norm</span>                         <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

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<td class="old_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> </span>

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<td class="old_line diff-line-num" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">CALLBACK</span><span class="p">></span>  <span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">ApplyScalarOperation</span> <span class="p">(</span><span class="n" style="color: #333;">CALLBACK</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">functor</span><span class="p">,</span> <span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">cache</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp">    </span>

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<td class="old_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// return the matrix of logs of every matrix element</span></span>

</pre></td>

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<br>

</li>

<li id="81843dd3cf849d08e0f197d837dd373534c7c756">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#81843dd3cf849d08e0f197d837dd373534c7c756"><strong>src/core/matrix.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3302" style="width: 35px; color: rgba(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="3302" style="width: 35px; color: rgba(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">@@ -3302,6 +3302,20 @@ hyFloat _Matrix::AbsValue (void) const{</td>

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<td class="new_line diff-line-num" data-linenumber="3302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3302" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>

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<td class="old_line diff-line-num" data-linenumber="3303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3303" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="old_line diff-line-num" data-linenumber="3304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3304" class="line" lang="cpp"></span>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3305" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3306" class="line" lang="cpp"><span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">L11Norm</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3307" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_numeric</span><span class="p">())</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3308" class="line" lang="cpp">        <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">norm</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3309" class="line" lang="cpp"></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3310" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ForEach</span> <span class="p">([</span><span class="o" style="font-weight: 600;">&</span><span class="p">]</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">{</span><span class="n" style="color: #333;">norm</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">);},</span></span>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3311" class="line" lang="cpp">                 <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">]</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;">index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">hyFloat</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">];});</span></span>

</pre></td>

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<td class="new_line diff-line-num new" data-linenumber="3312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3312" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3313" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">norm</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3314

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3314" class="line" lang="cpp">    <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3315

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3315" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3316

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3316" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3317

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3317" class="line" lang="cpp"><span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3318

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3318" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3319" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//_____________________________________________________________________________________________</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3320" class="line" lang="cpp"><span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">_Matrix</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Abs</span> <span class="p">(</span><span class="n" style="color: #333;">HBLObjectRef</span> <span class="n" style="color: #333;">cache</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3321" class="line" lang="cpp"><span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3410" style="width: 35px; color: rgba(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="3424" style="width: 35px; color: rgba(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">@@ -3410,7 +3424,7 @@ void    _Matrix::AddMatrix  (_Matrix& storage, _Matrix& secondArg, bool subtract</td>

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3410

</td>

<td class="new_line diff-line-num" data-linenumber="3424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3424

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3424" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3425" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="3426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3426

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3426" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="3413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="3427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC3413" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="3414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3427" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3414

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<td class="new_line diff-line-num" data-linenumber="3428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3428

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3428" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC ivdep</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3415

</td>

<td class="new_line diff-line-num" data-linenumber="3429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3429

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3429" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma ivdep</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3416

</td>

<td class="new_line diff-line-num" data-linenumber="3430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3430

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3430" class="line" lang="cpp">               <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upto</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3454,7 +3468,7 @@ void    _Matrix::AddMatrix  (_Matrix& storage, _Matrix& secondArg, bool subtract</td>

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<td class="old_line diff-line-num" data-linenumber="3454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3454

</td>

<td class="new_line diff-line-num" data-linenumber="3468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3468

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3468" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3455

</td>

<td class="new_line diff-line-num" data-linenumber="3469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3469

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3469" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3456

</td>

<td class="new_line diff-line-num" data-linenumber="3470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3470

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3470" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>

</pre></td>

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

<td class="old_line diff-line-num old" data-linenumber="3457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3457

</td>

<td class="new_line diff-line-num old" data-linenumber="3471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC3457" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="3471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3471

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3471" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3458

</td>

<td class="new_line diff-line-num" data-linenumber="3472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3472

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3472" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC ivdep</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3459

</td>

<td class="new_line diff-line-num" data-linenumber="3473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3473

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3473" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma ivdep</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3460

</td>

<td class="new_line diff-line-num" data-linenumber="3474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3474

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3474" class="line" lang="cpp">               <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">upto</span><span class="p">;</span> <span class="n" style="color: #333;">idx</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">8</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3998" style="width: 35px; color: rgba(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="4012" style="width: 35px; color: rgba(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">@@ -3998,7 +4012,7 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix const& secondArg) const</td>

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<td class="old_line diff-line-num" data-linenumber="3998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3998

</td>

<td class="new_line diff-line-num" data-linenumber="4012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4012

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4012" class="line" lang="cpp">                            <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="3999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3999

</td>

<td class="new_line diff-line-num" data-linenumber="4013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4013

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4013" class="line" lang="cpp">                            <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4000

</td>

<td class="new_line diff-line-num" data-linenumber="4014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4014

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4014" class="line" lang="cpp">                            <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="4001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4001

</td>

<td class="new_line diff-line-num old" data-linenumber="4015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC4001" class="line" lang="cpp">                            <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="4002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="4015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4015

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4015" class="line" lang="cpp">                            <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="4002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4002

</td>

<td class="new_line diff-line-num" data-linenumber="4016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4016

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4016" class="line" lang="cpp">                            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">vDim</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4003

</td>

<td class="new_line diff-line-num" data-linenumber="4017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4017

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4017" class="line" lang="cpp">                                <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">;</span></span>

</pre></td>

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4004

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<td class="new_line diff-line-num" data-linenumber="4018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4018

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4018" class="line" lang="cpp">                                <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4380" style="width: 35px; color: rgba(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="4394" style="width: 35px; color: rgba(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">@@ -4380,7 +4394,7 @@ void    _Matrix::Multiply  (_Matrix& storage, _Matrix const& secondArg) const</td>

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4380

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<td class="new_line diff-line-num" data-linenumber="4394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4394

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4394" class="line" lang="cpp">                                  <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="4381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4381

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<td class="new_line diff-line-num" data-linenumber="4395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4395

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4395" class="line" lang="cpp">                                  <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="4382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4382

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<td class="new_line diff-line-num" data-linenumber="4396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4396

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4396" class="line" lang="cpp">                                  <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="4383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4383

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<td class="new_line diff-line-num old" data-linenumber="4397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC4383" class="line" lang="cpp">                                  <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="4384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4397" class="line" lang="cpp">                                  <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="4384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="4398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4398" class="line" lang="cpp">                                  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">dimm4</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="4385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4385

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<td class="new_line diff-line-num" data-linenumber="4399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4399

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4399" class="line" lang="cpp">                                      <span class="n" style="color: #333;">float64x2_t</span> <span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="4386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4386

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<td class="new_line diff-line-num" data-linenumber="4400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4400

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4400" class="line" lang="cpp">                                      <span class="n" style="color: #333;">DO_GROUP_OP1</span> <span class="p">(</span><span class="n" style="color: #333;">D4</span><span class="p">,</span> <span class="n" style="color: #333;">B4</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5638" style="width: 35px; color: rgba(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">@@ -5624,6 +5638,7 @@ _Matrix*    _Matrix::Exponentiate (hyFloat scale_to, bool check_transition, _Mat</td>

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5624

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<td class="new_line diff-line-num" data-linenumber="5638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5638

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5638" class="line" lang="cpp">                <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">stash2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5625

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<td class="new_line diff-line-num" data-linenumber="5639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5639

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5639" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">//  = new hyFloat[hDim*(1+vDim)];</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5626

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<td class="new_line diff-line-num" data-linenumber="5640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5640

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5640" class="line" lang="cpp">        </span>

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<td class="old_line diff-line-num new" data-linenumber="5627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5641

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5641" class="line" lang="cpp"> </span>

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<td class="old_line diff-line-num" data-linenumber="5627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5627

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<td class="new_line diff-line-num" data-linenumber="5642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5642

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5642" 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;">is_polynomial</span><span class="p">())</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5628

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<td class="new_line diff-line-num" data-linenumber="5643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5643" class="line" lang="cpp">            <span class="n" style="color: #333;">stash</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">alloca</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">hDim</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">vDim</span><span class="p">));</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5629

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<td class="new_line diff-line-num" data-linenumber="5644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5644

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5644" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">theIndex</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5663" style="width: 35px; color: rgba(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="5678" style="width: 35px; color: rgba(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">@@ -5663,6 +5678,7 @@ _Matrix*    _Matrix::Exponentiate (hyFloat scale_to, bool check_transition, _Mat</td>

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<td class="old_line diff-line-num" data-linenumber="5663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5663

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<td class="new_line diff-line-num" data-linenumber="5678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5678

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5678" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5664

</td>

<td class="new_line diff-line-num" data-linenumber="5679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5679

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5679" class="line" lang="cpp">                <span class="n" style="color: #333;">power2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5665

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<td class="new_line diff-line-num" data-linenumber="5680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5680

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5680" class="line" lang="cpp">            <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5681

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5681" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//fprintf (stderr, "MAX %18.12g SCALE %d\n", max, power2);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5666

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<td class="new_line diff-line-num" data-linenumber="5682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5682

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5682" class="line" lang="cpp">            </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5667

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<td class="new_line diff-line-num" data-linenumber="5683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5683

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5683" class="line" lang="cpp">            </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5668

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<td class="new_line diff-line-num" data-linenumber="5684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5684

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5684" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5730" style="width: 35px; color: rgba(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="5746" style="width: 35px; color: rgba(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">@@ -5730,6 +5746,8 @@ _Matrix*    _Matrix::Exponentiate (hyFloat scale_to, bool check_transition, _Mat</td>

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<td class="old_line diff-line-num" data-linenumber="5730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5730

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<td class="new_line diff-line-num" data-linenumber="5746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5746

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5746" class="line" lang="cpp">            </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5731

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<td class="new_line diff-line-num" data-linenumber="5747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5747

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5747" class="line" lang="cpp">            <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5732

</td>

<td class="new_line diff-line-num" data-linenumber="5748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5748

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5748" class="line" lang="cpp">            </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5749

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5749" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//hyFloat const errorBound      = truncPrecision * 10.;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5750

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5750" class="line" lang="cpp">            </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5733

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<td class="new_line diff-line-num" data-linenumber="5751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5751

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5751" class="line" lang="cpp">            </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5734

</td>

<td class="new_line diff-line-num" data-linenumber="5752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5752

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5752" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_dense</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// avoid matrix allocation</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5735

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<td class="new_line diff-line-num" data-linenumber="5753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5753

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5753" class="line" lang="cpp">                <span class="n" style="color: #333;">_Matrix</span> <span class="n" style="color: #333;">temp</span> <span class="p">;</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5752" style="width: 35px; color: rgba(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="5770" style="width: 35px; color: rgba(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">@@ -5752,12 +5770,14 @@ _Matrix*    _Matrix::Exponentiate (hyFloat scale_to, bool check_transition, _Mat</td>

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<td class="old_line diff-line-num" data-linenumber="5752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5752

</td>

<td class="new_line diff-line-num" data-linenumber="5770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5770

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5770" class="line" lang="cpp">                    <span class="n" style="color: #333;">temp</span>      <span class="o" style="font-weight: 600;">*=</span> <span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5753

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<td class="new_line diff-line-num" data-linenumber="5771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5771

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5771" class="line" lang="cpp">                    <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>

</pre></td>

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5754

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<td class="new_line diff-line-num" data-linenumber="5772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5772

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5772" class="line" lang="cpp">                    <span class="n" style="color: #333;">i</span>         <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5755

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<td class="new_line diff-line-num old" data-linenumber="5773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5755" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*#ifndef _OPENMP</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5773

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5773" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5774

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5774" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">#ifndef _OPENMP</span></span>

</pre></td>

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5756

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<td class="new_line diff-line-num" data-linenumber="5775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5775

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5775" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    taylor_terms_count++;</span></span>

</pre></td>

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5757

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<td class="new_line diff-line-num" data-linenumber="5776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5776

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5776" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">#else</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5758

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<td class="new_line diff-line-num" data-linenumber="5777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5777

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5777" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            #pragma omp atomic</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5759

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<td class="new_line diff-line-num" data-linenumber="5778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5778

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5778" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                taylor_terms_count++;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5760

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<td class="new_line diff-line-num old" data-linenumber="5779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5760" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">#endif*/</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5779

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5779" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">#endif</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5780

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5780" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>

</pre></td>

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5761

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<td class="new_line diff-line-num" data-linenumber="5781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5781" class="line" lang="cpp">                <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">.</span><span class="n" style="color: #333;">IsMaxElement</span><span class="p">(</span><span class="n" style="color: #333;">tMax</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">truncPrecision</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5762

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<td class="new_line diff-line-num" data-linenumber="5782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5782

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5782" class="line" lang="cpp">                </span>

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<td class="old_line diff-line-num" data-linenumber="5763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5763

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<td class="new_line diff-line-num" data-linenumber="5783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5783

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5783" class="line" lang="cpp">                </span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5770" style="width: 35px; color: rgba(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="5790" style="width: 35px; color: rgba(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">@@ -5770,19 +5790,35 @@ _Matrix*    _Matrix::Exponentiate (hyFloat scale_to, bool check_transition, _Mat</td>

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5770

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<td class="new_line diff-line-num" data-linenumber="5790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5790" class="line" lang="cpp">                </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="5791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5791

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5791" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span>  <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5772

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<td class="new_line diff-line-num" data-linenumber="5792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5792

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5792" class="line" lang="cpp">                <span class="n" style="color: #333;">_Matrix</span> <span class="n" style="color: #333;">temp</span>    <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5793

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5793" class="line" lang="cpp">                </span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5794

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5794" class="line" lang="cpp">                <span class="cm" style="color: #998; font-style: italic;">/*hyFloat matrixNorm     =  L11Norm();</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5795

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5795" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5796

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5796" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                hyFloat errorEstimate1 = matrixNorm * matrixNorm / 2.,</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="5773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5797

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5797" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                errorEstimate  ;</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="5773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5798

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5798" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                */</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5773

</td>

<td class="new_line diff-line-num" data-linenumber="5799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5799

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5799" class="line" lang="cpp">                <span class="n" style="color: #333;">_Matrix</span> <span class="n" style="color: #333;">tempS</span> <span class="p">(</span><span class="n" style="color: #333;">hDim</span><span class="p">,</span> <span class="n" style="color: #333;">vDim</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">temp</span><span class="p">.</span><span class="n" style="color: #333;">storageType</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5774

</td>

<td class="new_line diff-line-num" data-linenumber="5800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5800

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5800" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5775

</td>

<td class="new_line diff-line-num" data-linenumber="5801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5801

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5801" class="line" lang="cpp">                    <span class="n" style="color: #333;">temp</span><span class="p">.</span><span class="n" style="color: #333;">MultbyS</span>        <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">this</span><span class="p">,</span><span class="n" style="color: #333;">theIndex</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">nil</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tempS</span><span class="p">,</span> <span class="n" style="color: #333;">stash</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5776

</td>

<td class="new_line diff-line-num" data-linenumber="5802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5802

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5802" class="line" lang="cpp">                    <span class="n" style="color: #333;">temp</span>      <span class="o" style="font-weight: 600;">*=</span> <span class="mf" style="color: #099;">1.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5777

</td>

<td class="new_line diff-line-num" data-linenumber="5803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5803

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5803" class="line" lang="cpp">                    <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">temp</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5778

</td>

<td class="new_line diff-line-num" data-linenumber="5804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5804

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5804" class="line" lang="cpp">                    <span class="n" style="color: #333;">i</span>         <span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5779

</td>

<td class="new_line diff-line-num old" data-linenumber="5805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5779" class="line" lang="cpp">    <span class="cm" style="color: #998; font-style: italic;">/*#ifndef _OPENMP</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="5780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5805

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5805" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="5780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5806

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5806" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    #ifndef _OPENMP</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5780

</td>

<td class="new_line diff-line-num" data-linenumber="5807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5807

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5807" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                        taylor_terms_count++;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5781

</td>

<td class="new_line diff-line-num" data-linenumber="5808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5808

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5808" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    #else</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5782

</td>

<td class="new_line diff-line-num" data-linenumber="5809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5809

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5809" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                #pragma omp atomic</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5783

</td>

<td class="new_line diff-line-num" data-linenumber="5810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5810

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5810" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    taylor_terms_count++;</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="5784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5784

</td>

<td class="new_line diff-line-num old" data-linenumber="5811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5784" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    #endif*/</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="5785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5811

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5811" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">    #endif</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="5785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5812

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5812" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="5785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5813

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5813" class="line" lang="cpp">                    <span class="cm" style="color: #998; font-style: italic;">/*errorEstimate1 *= matrixNorm / (i+1.);</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="5814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5814

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5814" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    errorEstimate = errorEstimate1  * (1./ ( 1. - matrixNorm/(i + 1.)));</span></span>

</pre></td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="5815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5815

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5815" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    if (errorEstimate > 0. && errorEstimate < errorBound) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5816

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5816" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                        break;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5817

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5817" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    }*/</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5818

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5818" class="line" lang="cpp">                  </span>

</pre></td>

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5785

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<td class="new_line diff-line-num" data-linenumber="5819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5819

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5819" class="line" lang="cpp">                <span class="p">}</span> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">temp</span><span class="p">.</span><span class="n" style="color: #333;">IsMaxElement</span><span class="p">(</span><span class="n" style="color: #333;">tMax</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">truncPrecision</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5820

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5820" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">//printf ("%ld %g %20.16g %ld\n",i,matrixNorm, errorEstimate,temp.IsMaxElement(tMax*truncPrecision*i));</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5821

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5821" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5786

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<td class="new_line diff-line-num" data-linenumber="5822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5822

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5822" class="line" lang="cpp">            <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5787

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<td class="new_line diff-line-num" data-linenumber="5823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5823

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5823" class="line" lang="cpp">            </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5788

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<td class="new_line diff-line-num" data-linenumber="5824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5824

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5824" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// use Pade (4,4) here</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5822" style="width: 35px; color: rgba(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="5858" style="width: 35px; color: rgba(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">@@ -5822,7 +5858,7 @@ _Matrix*    _Matrix::Exponentiate (hyFloat scale_to, bool check_transition, _Mat</td>

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5822

</td>

<td class="new_line diff-line-num" data-linenumber="5858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5858

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5858" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5823

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<td class="new_line diff-line-num" data-linenumber="5859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5859

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5859" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5824

</td>

<td class="new_line diff-line-num" data-linenumber="5860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5860

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5860" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5825

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<td class="new_line diff-line-num old" data-linenumber="5861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5825" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5861

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5861" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5826

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<td class="new_line diff-line-num" data-linenumber="5862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5862

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5862" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="p">];</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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5827

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<td class="new_line diff-line-num" data-linenumber="5863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5863

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5863" class="line" lang="cpp">                        <span class="n" style="color: #333;">theIndex</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;">compressedIndex</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">hDim</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>

</pre></td>

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5828

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<td class="new_line diff-line-num" data-linenumber="5864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5864" class="line" lang="cpp">                    <span class="p">}</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5884" style="width: 35px; color: rgba(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="5920" style="width: 35px; color: rgba(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">@@ -5884,6 +5920,18 @@ _Matrix*    _Matrix::Exponentiate (hyFloat scale_to, bool check_transition, _Mat</td>

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5884

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5920" class="line" lang="cpp">        </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5885

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<td class="new_line diff-line-num" data-linenumber="5921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5921" class="line" lang="cpp">        </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="5922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5922" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">check_transition</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5923" class="line" lang="cpp">            <span class="cm" style="color: #998; font-style: italic;">/*printf ("SCALE %lg : \n", scale_to);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5924

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5924" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            </span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5925" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            for (unsigned long r = 0L; r < hDim; r ++) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5926

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5926" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                hyFloat sum = 0.;</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5927" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                //printf ("%ld %18.16lg %18.16lg\n", r, (*result)(r,r), (*result)(r,r) - 1.);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5928" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                for (unsigned long c = 0L; c < vDim; c++) {</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5929" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    sum += (*result)(r,c);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5930

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5930" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                }</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5931

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5931" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                if (sum != 1.)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5932" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    printf ("%ld %18.16g\n", r, sum);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5933" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            }*/</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5934" class="line" lang="cpp"></span>

</pre></td>

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5887

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<td class="new_line diff-line-num" data-linenumber="5935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5935" class="line" lang="cpp">            <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5888

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<td class="new_line diff-line-num" data-linenumber="5936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5936" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_dense</span><span class="p">())</span> <span class="p">{</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="5937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5937

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5937" 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;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">vDim</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5906" style="width: 35px; color: rgba(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="5954" style="width: 35px; color: rgba(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">@@ -5906,22 +5954,22 @@ _Matrix*    _Matrix::Exponentiate (hyFloat scale_to, bool check_transition, _Mat</td>

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<td class="old_line diff-line-num" data-linenumber="5906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5906

</td>

<td class="new_line diff-line-num" data-linenumber="5954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5954

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5954" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Exponentiate</span><span class="p">(</span><span class="n" style="color: #333;">scale_to</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5907

</td>

<td class="new_line diff-line-num" data-linenumber="5955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5955

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5955" class="line" lang="cpp">                <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5908

</td>

<td class="new_line diff-line-num" data-linenumber="5956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5956

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5956" class="line" lang="cpp">                </span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5909

</td>

<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5909" class="line" lang="cpp">                <span class="cm" style="color: #998; font-style: italic;">/*printf ("SCALE %lg : \n", scale_to);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5910

</td>

<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5910" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                </span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5911

</td>

<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5911" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                for (unsigned long r = 0L; r < hDim; r ++) {</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5912

</td>

<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5912" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    hyFloat sum = 0.;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5913

</td>

<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5913" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    printf ("%ld %18.16lg %18.16lg\n", r, (*result)(r,r), (*result)(r,r) - 1.);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5914

</td>

<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5914" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    for (unsigned long c = 0L; c < vDim; c++) {</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5915

</td>

<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5915" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                        sum += (*this)(r,c);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5916

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<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5916" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    }</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5917

</td>

<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5917" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                    printf ("%ld %g\n", r, sum);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5918

</td>

<td class="new_line diff-line-num old" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5918" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                }</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5919

</td>

<td class="new_line diff-line-num" data-linenumber="5957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5957

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5957" class="line" lang="cpp"></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5920

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<td class="new_line diff-line-num" data-linenumber="5958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5958

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5958" class="line" lang="cpp">                </span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5921

</td>

<td class="new_line diff-line-num old" data-linenumber="5959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5921" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                ObjectToConsole(this);</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="5922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5922

</td>

<td class="new_line diff-line-num old" data-linenumber="5959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5922" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                ObjectToConsole(result);<span class="idiff left right deletion">*/</span></span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5959

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5959" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>ObjectToConsole(this);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5960

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5960" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>ObjectToConsole(result);</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5923

</td>

<td class="new_line diff-line-num" data-linenumber="5961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5961

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5961" class="line" lang="cpp">                </span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="5924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5924

</td>

<td class="new_line diff-line-num" data-linenumber="5962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5962

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5962" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">_String</span> <span class="p">(</span><span class="s" style="color: #d14;">"Failed to compute a valid transition matrix; this is usually caused by ill-conditioned rate matrices (e.g. very large rate values)"</span><span class="p">);</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5963

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5963" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// set diag to 1 - rest of row</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5964

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5964" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">is_dense</span><span class="p">())</span> <span class="p">{</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5965

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5965" 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;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5966

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5966" class="line" lang="cpp">                        <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.</span><span class="p">;</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5967

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5967" 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;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">r</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hDim</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hDim</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5968

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5968" class="line" lang="cpp">                            <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5969

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5969" class="line" lang="cpp">                        <span class="p">}</span></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5970

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5970" class="line" lang="cpp">                        <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">theData</span> <span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">vDim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mf" style="color: #099;">1.</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">sum</span><span class="p">;</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5971

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5971" class="line" lang="cpp">                    <span class="p">}</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="5972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5972

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5972" class="line" lang="cpp">                <span class="p">}</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="5925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5925

</td>

<td class="new_line diff-line-num" data-linenumber="5973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5973

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5973" class="line" lang="cpp">            <span class="p">}</span></span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="5926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5926

</td>

<td class="new_line diff-line-num" data-linenumber="5974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5974

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5974" class="line" lang="cpp">        <span class="p">}</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="5927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5927

</td>

<td class="new_line diff-line-num" data-linenumber="5975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5975

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5975" class="line" lang="cpp">        </span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6988" style="width: 35px; color: rgba(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="7036" style="width: 35px; color: rgba(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">@@ -6988,7 +7036,7 @@ hyFloat        _Matrix::Sqr (hyFloat* _hprestrict_ stash) {</td>

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<td class="old_line diff-line-num" data-linenumber="6988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6988

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<td class="new_line diff-line-num" data-linenumber="7036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7036

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7036" class="line" lang="cpp">                        <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="6989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6989

</td>

<td class="new_line diff-line-num" data-linenumber="7037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7037

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7037" class="line" lang="cpp">                        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="6990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6990

</td>

<td class="new_line diff-line-num" data-linenumber="7038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7038

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7038" class="line" lang="cpp">                        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="6991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6991

</td>

<td class="new_line diff-line-num old" data-linenumber="7039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC6991" class="line" lang="cpp">                        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="6992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="7039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7039

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7039" class="line" lang="cpp">                        <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="6992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6992

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<td class="new_line diff-line-num" data-linenumber="7040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7040

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7040" class="line" lang="cpp">                        <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC ivdep</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="6993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6993

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<td class="new_line diff-line-num" data-linenumber="7041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7041

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7041" class="line" lang="cpp">                        <span class="cp" style="color: #999; font-weight: 600;">#pragma ivdep</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="6994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6994

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<td class="new_line diff-line-num" data-linenumber="7042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7042

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7042" class="line" lang="cpp">                        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">loopBound</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<br>

</li>

<li id="9f127084157a2a4e11faf03320db0541dbae15dc">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#9f127084157a2a4e11faf03320db0541dbae15dc"><strong>src/core/tree_evaluator.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -127,7 +127,7 @@ inline double _sse_sum_2 (__m128d const & x) {</td>

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<td class="old_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<td class="new_line diff-line-num" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">D</span><span class="p">></span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">__ll_handle_matrix_transpose</span> <span class="p">(</span><span class="n" style="color: #333;">hyFloat</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">transitionMatrix</span><span class="p">,</span> <span class="n" style="color: #333;">hyFloat</span> <span class="o" style="font-weight: 600;">*</span> <span class="kr" style="font-weight: 600;">__restrict</span> <span class="n" style="color: #333;">tMatrixT</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp">    <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;">0L</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC130" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp">            <span class="n" style="color: #333;">tMatrixT</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">r</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transitionMatrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -154,7 +154,7 @@ template<long D> inline bool __ll_handle_conditional_array_initialization ( long</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                }</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            }*/</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp">            </span>

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<td class="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp">                <span class="n" style="color: #333;">parentConditionals</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;">tMatrix</span><span class="p">[</span><span class="n" style="color: #333;">siteState</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(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="172" style="width: 35px; color: rgba(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">@@ -172,7 +172,7 @@ template<long D> inline bool __ll_handle_conditional_array_initialization ( long</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tcc</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__builtin_expect</span><span class="p">((</span><span class="n" style="color: #333;">tcc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">currentTCCIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bitMaskArray</span><span class="p">.</span><span class="n" style="color: #333;">masks</span><span class="p">[</span><span class="n" style="color: #333;">currentTCCBit</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp">                    <span class="n" style="color: #333;">childVector</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;">lastUpdatedSite</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -200,7 +200,7 @@ inline bool __ll_handle_conditional_array_initialization_generic ( long * __rest</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__builtin_expect</span><span class="p">(</span><span class="n" style="color: #333;">siteState</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0L</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">// a single character state; sweep down the appropriate column</span></span>

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<td class="old_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp">                <span class="n" style="color: #333;">parentConditionals</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;">tMatrix</span><span class="p">[</span><span class="n" style="color: #333;">siteState</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">D</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="212" style="width: 35px; color: rgba(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">@@ -212,7 +212,7 @@ inline bool __ll_handle_conditional_array_initialization_generic ( long * __rest</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tcc</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC214" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">__builtin_expect</span><span class="p">((</span><span class="n" style="color: #333;">tcc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">currentTCCIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bitMaskArray</span><span class="p">.</span><span class="n" style="color: #333;">masks</span><span class="p">[</span><span class="n" style="color: #333;">currentTCCBit</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">siteFrom</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC215" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

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<td class="new_line diff-line-num" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp">                    <span class="n" style="color: #333;">childVector</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;">lastUpdatedSite</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="542" style="width: 35px; color: rgba(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="542" style="width: 35px; color: rgba(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">@@ -542,7 +542,7 @@ template<long D> inline void __ll_product_sum_loop (hyFloat const* _hprestrict_</td>

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542

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC542" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 8</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC545" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll(enable)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp">            <span class="n" style="color: #333;">accumulator</span> <span class="o" style="font-weight: 600;">+=</span>  <span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span>   <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="558" style="width: 35px; color: rgba(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">@@ -558,7 +558,7 @@ inline void __ll_product_sum_loop_generic (hyFloat const* _hprestrict_ tMatrix,</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC558" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 8</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC559" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC561" class="line" lang="cpp">        <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll(enable)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC562" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp">            <span class="n" style="color: #333;">accumulator</span> <span class="o" style="font-weight: 600;">+=</span>  <span class="n" style="color: #333;">tMatrix</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span>   <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">childVector</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">];</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp">        </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="595" style="width: 35px; color: rgba(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">@@ -595,7 +595,7 @@ template<long D, bool ADJUST> inline void __ll_loop_handle_scaling (hyFloat& sum</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC595" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">            fprintf (stderr, "UP %ld (%ld) %lg\n", didScale, parentCode, scaler);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC596" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">        }*/</span></span>

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<td class="old_line diff-line-num" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC597" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num old" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC598" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp">           <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span> #pragma unroll(4)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC599" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

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<td class="new_line diff-line-num" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC600" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp">                <span class="n" style="color: #333;">parentConditionals</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scaler</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="626" style="width: 35px; color: rgba(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="626" style="width: 35px; color: rgba(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">@@ -626,7 +626,7 @@ template<long D, bool ADJUST> inline void __ll_loop_handle_scaling (hyFloat& sum</td>

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<td class="new_line diff-line-num" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC626" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">                }*/</span></span>

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<td class="new_line diff-line-num" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC627" class="line" lang="cpp">                </span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC629" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC630" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC631" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC632" class="line" lang="cpp">                        <span class="n" style="color: #333;">parentConditionals</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scaler</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="657" style="width: 35px; color: rgba(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="657" style="width: 35px; color: rgba(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">@@ -657,7 +657,7 @@ template<bool ADJUST> inline void __ll_loop_handle_scaling_generic (hyFloat& sum</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC657" class="line" lang="cpp">        <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">scaler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_computeBoostScaler</span><span class="p">(</span><span class="n" style="color: #333;">scalingAdjustments</span> <span class="p">[</span><span class="n" style="color: #333;">parentCode</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">siteCount</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">siteID</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_lfScalerUpwards</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">,</span> <span class="n" style="color: #333;">didScale</span><span class="p">);</span></span>

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658

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC658" class="line" lang="cpp">        </span>

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<td class="new_line diff-line-num" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC659" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">)</span> <span class="p">{</span></span>

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660

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<td class="new_line diff-line-num old" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC660" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(8)</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC660" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(8)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC661" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 8</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC662" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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663

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC663" class="line" lang="cpp">                <span class="n" style="color: #333;">parentConditionals</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scaler</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="679" style="width: 35px; color: rgba(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="679" style="width: 35px; color: rgba(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">@@ -679,7 +679,7 @@ template<bool ADJUST> inline void __ll_loop_handle_scaling_generic (hyFloat& sum</td>

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<td class="new_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC679" class="line" lang="cpp">                <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">scaler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_computeReductionScaler</span> <span class="p">(</span><span class="n" style="color: #333;">scalingAdjustments</span> <span class="p">[</span><span class="n" style="color: #333;">parentCode</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">siteCount</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">siteID</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">_lfScalingFactorThreshold</span><span class="p">,</span> <span class="n" style="color: #333;">sum</span><span class="p">,</span> <span class="n" style="color: #333;">didScale</span><span class="p">);</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC680" class="line" lang="cpp">                </span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC681" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">didScale</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="new_line diff-line-num old" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC682" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(8)</span></span>

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(8)</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC683" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 8</span></span>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC684" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

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685

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC685" class="line" lang="cpp">                         <span class="n" style="color: #333;">parentConditionals</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">scaler</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="707" style="width: 35px; color: rgba(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="707" style="width: 35px; color: rgba(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">@@ -707,7 +707,7 @@ template<long D> inline void __ll_loop_handle_leaf_case (hyFloat* _hprestrict_ p</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC707" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">siteTo</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">pp</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC709" class="line" lang="cpp">            <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">lsf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">localScalingFactor</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC710" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC710" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC713" class="line" lang="cpp">                <span class="n" style="color: #333;">pp</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lsf</span><span class="p">;</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1585" style="width: 35px; color: rgba(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="1585" style="width: 35px; color: rgba(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">@@ -1585,7 +1585,7 @@ hyFloat      _TheTree::ComputeTreeBlockByBranch  (                   _SimpleList</td>

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<td class="new_line diff-line-num" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1585" class="line" lang="cpp">            <span class="n" style="color: #333;">accumulator</span>         <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rootConditionals</span><span class="p">[</span><span class="n" style="color: #333;">rootIndex</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rootState</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">theProbs</span><span class="p">[</span><span class="n" style="color: #333;">rootState</span><span class="p">];</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1586

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<td class="new_line diff-line-num" data-linenumber="1586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1586

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1586" class="line" lang="cpp">            <span class="n" style="color: #333;">rootIndex</span>           <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">alphabetDimension</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1587" class="line" lang="cpp">        <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1588

</td>

<td class="new_line diff-line-num old" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1588" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1588" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1589

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<td class="new_line diff-line-num" data-linenumber="1589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1589

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1589" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1590

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<td class="new_line diff-line-num" data-linenumber="1590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1590

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1590" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alphabetDimension</span><span class="p">;</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span><span class="n" style="color: #333;">rootIndex</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1591

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<td class="new_line diff-line-num" data-linenumber="1591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1591

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1591" class="line" lang="cpp">                <span class="n" style="color: #333;">accumulator</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rootConditionals</span><span class="p">[</span><span class="n" style="color: #333;">rootIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">theProbs</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">];</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1644" style="width: 35px; color: rgba(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="1644" style="width: 35px; color: rgba(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">@@ -1644,7 +1644,7 @@ template<long D> inline bool __lcache_loop_preface (bool isLeaf, long* __restric</td>

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<td class="new_line diff-line-num" data-linenumber="1644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1644" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">siteState</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">[</span><span class="n" style="color: #333;">nodeCode</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">siteCount</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">siteID</span><span class="p">]]</span> <span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1645" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">siteState</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1646" 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;">target_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteState</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1647" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1647" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

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<td class="old_line diff-line-num" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1648" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1649" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">target_index</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="old_line diff-line-num" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1650" class="line" lang="cpp">                <span class="n" style="color: #333;">parentConditionals</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;">tMatrix</span><span class="p">[</span><span class="n" style="color: #333;">target_index</span><span class="p">];</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1659" style="width: 35px; color: rgba(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="1659" style="width: 35px; color: rgba(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">@@ -1659,7 +1659,7 @@ template<long D> inline bool __lcache_loop_preface (bool isLeaf, long* __restric</td>

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<td class="old_line diff-line-num" data-linenumber="1659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1659" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">tcc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">currentTCCIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bitMaskArray</span><span class="p">.</span><span class="n" style="color: #333;">masks</span><span class="p">[</span><span class="n" style="color: #333;">currentTCCBit</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">siteFrom</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1660" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// the value of this conditional vector needs to be copied from a previously stored site</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1661" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// subtree duplication</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1662" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

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<td class="old_line diff-line-num new" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1662" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1663" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1664" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0UL</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="new_line diff-line-num" data-linenumber="1665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1665" class="line" lang="cpp">                    <span class="n" style="color: #333;">childVector</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;">lastUpdatedSite</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1688" style="width: 35px; color: rgba(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="1688" style="width: 35px; color: rgba(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">@@ -1688,7 +1688,7 @@ inline bool __lcache_loop_preface_generic (bool isLeaf, long* __restrict lNodeFl</td>

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<td class="new_line diff-line-num" data-linenumber="1688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1688

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1688" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">siteState</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lNodeFlags</span><span class="p">[</span><span class="n" style="color: #333;">nodeCode</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">siteCount</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">siteOrdering</span><span class="p">.</span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">siteID</span><span class="p">]]</span> <span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1689

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<td class="new_line diff-line-num" data-linenumber="1689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1689

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1689" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">siteState</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0L</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1690

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1690" 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;">target_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteState</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="1691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1691" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="1691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1691" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1692" class="line" lang="cpp">            <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1693" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0L</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">target_index</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">D</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1694" class="line" lang="cpp">                <span class="n" style="color: #333;">parentConditionals</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;">tMatrix</span><span class="p">[</span><span class="n" style="color: #333;">target_index</span><span class="p">];</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1704" style="width: 35px; color: rgba(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="1704" style="width: 35px; color: rgba(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">@@ -1704,7 +1704,7 @@ inline bool __lcache_loop_preface_generic (bool isLeaf, long* __restrict lNodeFl</td>

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<td class="old_line diff-line-num" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1704

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<td class="new_line diff-line-num" data-linenumber="1704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1704" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">tcc</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list_data</span><span class="p">[</span><span class="n" style="color: #333;">currentTCCIndex</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">bitMaskArray</span><span class="p">.</span><span class="n" style="color: #333;">masks</span><span class="p">[</span><span class="n" style="color: #333;">currentTCCBit</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">siteID</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">siteFrom</span><span class="p">)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="1705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1705" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// the value of this conditional vector needs to be copied from a previously stored site</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1706

</td>

<td class="new_line diff-line-num" data-linenumber="1706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1706" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// subtree duplication</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1707

</td>

<td class="new_line diff-line-num old" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1707" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1707" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1708

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<td class="new_line diff-line-num" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1708

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1708" class="line" lang="cpp">                <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1709

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<td class="new_line diff-line-num" data-linenumber="1709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1709

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1709" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0UL</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">D</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1710

</td>

<td class="new_line diff-line-num" data-linenumber="1710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1710

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1710" class="line" lang="cpp">                    <span class="n" style="color: #333;">childVector</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;">lastUpdatedSite</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1966" style="width: 35px; color: rgba(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="1966" style="width: 35px; color: rgba(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">@@ -1966,7 +1966,7 @@ void            _TheTree::ComputeBranchCache    (</td>

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<td class="old_line diff-line-num" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1966

</td>

<td class="new_line diff-line-num" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1966

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1966" 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;">k3</span>     <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0UL</span><span class="p">;</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1967

</td>

<td class="new_line diff-line-num" data-linenumber="1967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1967

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1967" 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;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">siteFrom</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">siteTo</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1968

</td>

<td class="new_line diff-line-num" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1968

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1968" class="line" lang="cpp">                    <span class="n" style="color: #333;">hyFloat</span> <span class="n" style="color: #333;">scaler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">localScalingFactor</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1969

</td>

<td class="new_line diff-line-num old" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1969" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="1969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1969

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1969" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma unroll(4)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1970

</td>

<td class="new_line diff-line-num" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1970

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1970" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 4</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1971

</td>

<td class="new_line diff-line-num" data-linenumber="1971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1971

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1971" 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;">k2</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;">k2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alphabetDimension</span><span class="p">;</span> <span class="n" style="color: #333;">k2</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">k3</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="1972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1972

</td>

<td class="new_line diff-line-num" data-linenumber="1972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1972

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1972" class="line" lang="cpp">                        <span class="n" style="color: #333;">parentConditionals</span> <span class="p">[</span><span class="n" style="color: #333;">k3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scaler</span><span class="p">;</span></span>

</pre></td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2474" style="width: 35px; color: rgba(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="2474" style="width: 35px; color: rgba(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">@@ -2474,7 +2474,7 @@ void            _TheTree::ComputeBranchCache    (</td>

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<td class="old_line diff-line-num" data-linenumber="2474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2474

</td>

<td class="new_line diff-line-num" data-linenumber="2474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2474

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2474" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma GCC unroll 8</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2475

</td>

<td class="new_line diff-line-num" data-linenumber="2475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2475

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2475" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop vectorize(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2476

</td>

<td class="new_line diff-line-num" data-linenumber="2476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2476

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2476" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop interleave(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num old" data-linenumber="2477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2477

</td>

<td class="new_line diff-line-num old" data-linenumber="2477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC2477" class="line" lang="cpp">                    <span class="cp" style="color: #999; font-weight: 600;">#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num new" data-linenumber="2478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="2477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2477

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2477" class="line" lang="cpp">                    <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right addition">//</span>#pragma clang loop unroll(enable)</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2478

</td>

<td class="new_line diff-line-num" data-linenumber="2478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2478

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2478" class="line" lang="cpp">                    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alphabetDimension</span><span class="p">;</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2479

</td>

<td class="new_line diff-line-num" data-linenumber="2479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2479

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2479" class="line" lang="cpp">                        <span class="n" style="color: #333;">sum</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">parentConditionals</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="2480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2480

</td>

<td class="new_line diff-line-num" data-linenumber="2480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2480

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2480" class="line" lang="cpp">                    <span class="p">}</span></span>

</pre></td>

</tr>

</table>

<br>

</li>

<li id="aeaccdf9a873c05871ba3cd1bca1ae0e9f8254e4">

<a href="https://salsa.debian.org/med-team/hyphy/-/compare/cdf1984eab53222846d882ea6158c759356b4b13...4f0aba6e86789e08a9608db344716433dac9383e#aeaccdf9a873c05871ba3cd1bca1ae0e9f8254e4"><strong>src/mains/unix.cpp</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="981" style="width: 35px; color: rgba(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="981" style="width: 35px; color: rgba(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">@@ -981,6 +981,8 @@ int main (int argc, char* argv[]) {</td>

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<td class="old_line diff-line-num" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

981

</td>

<td class="new_line diff-line-num" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

981

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC981" class="line" lang="cpp">    <span class="n" style="color: #333;">ex</span><span class="p">.</span><span class="n" style="color: #333;">ClearExecutionList</span><span class="p">();</span></span>

</pre></td>

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<td class="old_line diff-line-num" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

982

</td>

<td class="new_line diff-line-num" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

982

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC982" class="line" lang="cpp">    </span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

983

</td>

<td class="new_line diff-line-num" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

983

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC983" class="line" lang="cpp"></span>

</pre></td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

984

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC984" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//printf ("\nTAYLOR SERIES TERMS %ld\n", taylor_terms_count);</span></span>

</pre></td>

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

<td class="old_line diff-line-num new" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

985

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC985" class="line" lang="cpp">    </span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

984

</td>

<td class="new_line diff-line-num" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC986" class="line" lang="cpp">    <span class="n" style="color: #333;">GlobalShutdown</span>              <span class="p">();</span></span>

</pre></td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

985

</td>

<td class="new_line diff-line-num" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

987

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC987" class="line" lang="cpp">    </span>

</pre></td>

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

<td class="old_line diff-line-num" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

</td>

<td class="new_line diff-line-num" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

988

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC988" class="line" lang="cpp"></span>

</pre></td>

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